Institute of Cardiovascular Regeneration Webtool Repository

Region Summary

Source ID	Type	Tax ID	Position
NIPBL	UCNEbase	9606	5:36878759-37065607
Gene	Transcript	Position	Biotype
ENSG00000249850 (KRT18P31) keratin 18 pseudogene 31	ENST00000506277 (KRT18P31-001)	36885206-36886497	processed_pseudogene
ENSG00000274687 (AC008902.1)	ENST00000622531 (AC008902.1-201)	37021692-37022036	miRNA

CIL_0007PI_0002 (Click to Hide/Show)

Source ID	Type	Tax ID	Position
NIPBL	UCNEbase	10090	15:8290515-8442513
Gene	Transcript	Position	Biotype
ENSMUSG00000022141 (Nipbl) Nipped-B homolog (Drosophila)	ENSMUST00000052965 (Nipbl-201)	8291225-8444463	protein_coding

CIL_0007PI_0003 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007PI_0003 [APP/View/Region/show.ctp, line 46]Code Context
        <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
        <?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
	'region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000249850' => 'keratin 18 pseudogene 31',
		'ENSG00000274687' => null,
		'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
		'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
	),
	'gene_name_arr' => array(
		'ENSG00000249850' => 'KRT18P31',
		'ENSG00000274687' => 'AC008902.1',
		'ENSMUSG00000022141' => 'Nipbl',
		'ENSDARG00000061052' => 'nipblb'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Bladder',
		(int) 6 => 'Brain',
		(int) 11 => 'Breast',
		(int) 13 => 'Colon',
		(int) 16 => 'Heart',
		(int) 19 => 'Kidney',
		(int) 22 => 'Liver',
		(int) 24 => 'Lung',
		(int) 26 => 'Muscle',
		(int) 29 => 'Ovary',
		(int) 32 => 'Placenta',
		(int) 34 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000506277' => array(
			'start' => '36885206',
			'end' => '36886497',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'KRT18P31-001'
		),
		'ENST00000622531' => array(
			'start' => '37021692',
			'end' => '37022036',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC008902.1-201'
		),
		'ENSMUST00000052965' => array(
			'start' => '8291225',
			'end' => '8444463',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Nipbl-201'
		),
		'ENSDART00000086653' => array(
			'start' => '37720648',
			'end' => '37791148',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-201'
		),
		'ENSDART00000086861' => array(
			'start' => '37720330',
			'end' => '37791209',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-001'
		),
		'ENSDART00000108484' => array(
			'start' => '37719940',
			'end' => '37781210',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-202'
		),
		'ENSDART00000140556' => array(
			'start' => '37731699',
			'end' => '37746412',
			'transcript_biotype' => 'processed_transcript',
			'transcript_name' => 'nipblb-002'
		)
	),
	'accession_map' => array(
		'ENST000' => '9606',
		'ENSMUST' => '10090',
		'ENSDART' => '7955',
		'ENSG000' => '9606',
		'ENSMUSG' => '10090',
		'ENSDARG' => '7955'
	),
	'sci_name_map' => array(
		(int) 9606 => 'Homo_sapiens',
		(int) 10090 => 'Mus_musculus',
		(int) 7955 => 'Danio_rerio'
	),
	'UCSC_links' => array(
		(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
		(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
		(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
	),
	'expressed_region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000249850' => 'keratin 18 pseudogene 31',
	'ENSG00000274687' => null,
	'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
	'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
)
$gene_name_arr = array(
	'ENSG00000249850' => 'KRT18P31',
	'ENSG00000274687' => 'AC008902.1',
	'ENSMUSG00000022141' => 'Nipbl',
	'ENSDARG00000061052' => 'nipblb'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0001',
			'tax_id' => '9606',
			'chromosome' => '5',
			'seq_start' => '36878759',
			'seq_end' => '37065607',
			'region_length' => '186848',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0002',
			'tax_id' => '10090',
			'chromosome' => '15',
			'seq_start' => '8290515',
			'seq_end' => '8442513',
			'region_length' => '151998',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '37719889',
			'seq_end' => '37720465',
			'region_length' => '576',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 3 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0004',
			'tax_id' => '7955',
			'chromosome' => '5',
			'seq_start' => '8419188',
			'seq_end' => '8419363',
			'region_length' => '175',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Bladder',
	(int) 6 => 'Brain',
	(int) 11 => 'Breast',
	(int) 13 => 'Colon',
	(int) 16 => 'Heart',
	(int) 19 => 'Kidney',
	(int) 22 => 'Liver',
	(int) 24 => 'Lung',
	(int) 26 => 'Muscle',
	(int) 29 => 'Ovary',
	(int) 32 => 'Placenta',
	(int) 34 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000506277' => array(
		'start' => '36885206',
		'end' => '36886497',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'KRT18P31-001'
	),
	'ENST00000622531' => array(
		'start' => '37021692',
		'end' => '37022036',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC008902.1-201'
	),
	'ENSMUST00000052965' => array(
		'start' => '8291225',
		'end' => '8444463',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Nipbl-201'
	),
	'ENSDART00000086653' => array(
		'start' => '37720648',
		'end' => '37791148',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-201'
	),
	'ENSDART00000086861' => array(
		'start' => '37720330',
		'end' => '37791209',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-001'
	),
	'ENSDART00000108484' => array(
		'start' => '37719940',
		'end' => '37781210',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-202'
	),
	'ENSDART00000140556' => array(
		'start' => '37731699',
		'end' => '37746412',
		'transcript_biotype' => 'processed_transcript',
		'transcript_name' => 'nipblb-002'
	)
)
$accession_map = array(
	'ENST000' => '9606',
	'ENSMUST' => '10090',
	'ENSDART' => '7955',
	'ENSG000' => '9606',
	'ENSMUSG' => '10090',
	'ENSDARG' => '7955'
)
$sci_name_map = array(
	(int) 9606 => 'Homo_sapiens',
	(int) 10090 => 'Mus_musculus',
	(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
	(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
	(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
	(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007PI_0003',
		'tax_id' => '7955',
		'chromosome' => '10',
		'seq_start' => '37719889',
		'seq_end' => '37720465',
		'region_length' => '576',
		'region_type' => 'UCNEbase',
		'el_id' => 'NIPBL'
	)
)
$gene_el = array(
	'ENSMUST00000052965' => array(
		'Adipose' => array(
			'average_FPKM' => '3.941',
			'stddev_FPKM' => '2.24'
		),
		'Adrenal' => array(
			'average_FPKM' => '3.103',
			'stddev_FPKM' => '0.35'
		),
		'Bladder' => array(
			'average_FPKM' => '3.673',
			'stddev_FPKM' => '1.17'
		),
		'Brain' => array(
			'average_FPKM' => '4.982',
			'stddev_FPKM' => '4.02'
		),
		'Breast' => array(
			'average_FPKM' => '4.624',
			'stddev_FPKM' => '1.59'
		),
		'Colon' => array(
			'average_FPKM' => '3.856',
			'stddev_FPKM' => '0.74'
		),
		'Heart' => array(
			'average_FPKM' => '3.003',
			'stddev_FPKM' => '0.26'
		),
		'Kidney' => array(
			'average_FPKM' => '2.222',
			'stddev_FPKM' => '0.25'
		),
		'Liver' => array(
			'average_FPKM' => '2.797',
			'stddev_FPKM' => '1.47'
		),
		'Lung' => array(
			'average_FPKM' => '5.039',
			'stddev_FPKM' => '1.06'
		),
		'Muscle' => array(
			'average_FPKM' => '1.527',
			'stddev_FPKM' => '0.81'
		),
		'Ovary' => array(
			'average_FPKM' => '7.317',
			'stddev_FPKM' => '3.83'
		),
		'Placenta' => array(
			'average_FPKM' => '4.456',
			'stddev_FPKM' => '0.81'
		),
		'Testis' => array(
			'average_FPKM' => '12.150',
			'stddev_FPKM' => '5.80'
		)
	)
)
$gene_key = 'ENSMUSG00000022141'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '3.941',
		'stddev_FPKM' => '2.24'
	),
	'Adrenal' => array(
		'average_FPKM' => '3.103',
		'stddev_FPKM' => '0.35'
	),
	'Bladder' => array(
		'average_FPKM' => '3.673',
		'stddev_FPKM' => '1.17'
	),
	'Brain' => array(
		'average_FPKM' => '4.982',
		'stddev_FPKM' => '4.02'
	),
	'Breast' => array(
		'average_FPKM' => '4.624',
		'stddev_FPKM' => '1.59'
	),
	'Colon' => array(
		'average_FPKM' => '3.856',
		'stddev_FPKM' => '0.74'
	),
	'Heart' => array(
		'average_FPKM' => '3.003',
		'stddev_FPKM' => '0.26'
	),
	'Kidney' => array(
		'average_FPKM' => '2.222',
		'stddev_FPKM' => '0.25'
	),
	'Liver' => array(
		'average_FPKM' => '2.797',
		'stddev_FPKM' => '1.47'
	),
	'Lung' => array(
		'average_FPKM' => '5.039',
		'stddev_FPKM' => '1.06'
	),
	'Muscle' => array(
		'average_FPKM' => '1.527',
		'stddev_FPKM' => '0.81'
	),
	'Ovary' => array(
		'average_FPKM' => '7.317',
		'stddev_FPKM' => '3.83'
	),
	'Placenta' => array(
		'average_FPKM' => '4.456',
		'stddev_FPKM' => '0.81'
	),
	'Testis' => array(
		'average_FPKM' => '12.150',
		'stddev_FPKM' => '5.80'
	)
)
$tran_key = 'ENSMUST00000052965'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context
        <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
        <?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
	'region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000249850' => 'keratin 18 pseudogene 31',
		'ENSG00000274687' => null,
		'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
		'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
	),
	'gene_name_arr' => array(
		'ENSG00000249850' => 'KRT18P31',
		'ENSG00000274687' => 'AC008902.1',
		'ENSMUSG00000022141' => 'Nipbl',
		'ENSDARG00000061052' => 'nipblb'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Bladder',
		(int) 6 => 'Brain',
		(int) 11 => 'Breast',
		(int) 13 => 'Colon',
		(int) 16 => 'Heart',
		(int) 19 => 'Kidney',
		(int) 22 => 'Liver',
		(int) 24 => 'Lung',
		(int) 26 => 'Muscle',
		(int) 29 => 'Ovary',
		(int) 32 => 'Placenta',
		(int) 34 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000506277' => array(
			'start' => '36885206',
			'end' => '36886497',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'KRT18P31-001'
		),
		'ENST00000622531' => array(
			'start' => '37021692',
			'end' => '37022036',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC008902.1-201'
		),
		'ENSMUST00000052965' => array(
			'start' => '8291225',
			'end' => '8444463',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Nipbl-201'
		),
		'ENSDART00000086653' => array(
			'start' => '37720648',
			'end' => '37791148',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-201'
		),
		'ENSDART00000086861' => array(
			'start' => '37720330',
			'end' => '37791209',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-001'
		),
		'ENSDART00000108484' => array(
			'start' => '37719940',
			'end' => '37781210',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-202'
		),
		'ENSDART00000140556' => array(
			'start' => '37731699',
			'end' => '37746412',
			'transcript_biotype' => 'processed_transcript',
			'transcript_name' => 'nipblb-002'
		)
	),
	'accession_map' => array(
		'ENST000' => '9606',
		'ENSMUST' => '10090',
		'ENSDART' => '7955',
		'ENSG000' => '9606',
		'ENSMUSG' => '10090',
		'ENSDARG' => '7955'
	),
	'sci_name_map' => array(
		(int) 9606 => 'Homo_sapiens',
		(int) 10090 => 'Mus_musculus',
		(int) 7955 => 'Danio_rerio'
	),
	'UCSC_links' => array(
		(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
		(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
		(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
	),
	'expressed_region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000249850' => 'keratin 18 pseudogene 31',
	'ENSG00000274687' => null,
	'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
	'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
)
$gene_name_arr = array(
	'ENSG00000249850' => 'KRT18P31',
	'ENSG00000274687' => 'AC008902.1',
	'ENSMUSG00000022141' => 'Nipbl',
	'ENSDARG00000061052' => 'nipblb'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0001',
			'tax_id' => '9606',
			'chromosome' => '5',
			'seq_start' => '36878759',
			'seq_end' => '37065607',
			'region_length' => '186848',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0002',
			'tax_id' => '10090',
			'chromosome' => '15',
			'seq_start' => '8290515',
			'seq_end' => '8442513',
			'region_length' => '151998',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '37719889',
			'seq_end' => '37720465',
			'region_length' => '576',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 3 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0004',
			'tax_id' => '7955',
			'chromosome' => '5',
			'seq_start' => '8419188',
			'seq_end' => '8419363',
			'region_length' => '175',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Bladder',
	(int) 6 => 'Brain',
	(int) 11 => 'Breast',
	(int) 13 => 'Colon',
	(int) 16 => 'Heart',
	(int) 19 => 'Kidney',
	(int) 22 => 'Liver',
	(int) 24 => 'Lung',
	(int) 26 => 'Muscle',
	(int) 29 => 'Ovary',
	(int) 32 => 'Placenta',
	(int) 34 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000506277' => array(
		'start' => '36885206',
		'end' => '36886497',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'KRT18P31-001'
	),
	'ENST00000622531' => array(
		'start' => '37021692',
		'end' => '37022036',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC008902.1-201'
	),
	'ENSMUST00000052965' => array(
		'start' => '8291225',
		'end' => '8444463',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Nipbl-201'
	),
	'ENSDART00000086653' => array(
		'start' => '37720648',
		'end' => '37791148',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-201'
	),
	'ENSDART00000086861' => array(
		'start' => '37720330',
		'end' => '37791209',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-001'
	),
	'ENSDART00000108484' => array(
		'start' => '37719940',
		'end' => '37781210',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-202'
	),
	'ENSDART00000140556' => array(
		'start' => '37731699',
		'end' => '37746412',
		'transcript_biotype' => 'processed_transcript',
		'transcript_name' => 'nipblb-002'
	)
)
$accession_map = array(
	'ENST000' => '9606',
	'ENSMUST' => '10090',
	'ENSDART' => '7955',
	'ENSG000' => '9606',
	'ENSMUSG' => '10090',
	'ENSDARG' => '7955'
)
$sci_name_map = array(
	(int) 9606 => 'Homo_sapiens',
	(int) 10090 => 'Mus_musculus',
	(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
	(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
	(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
	(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007PI_0003',
		'tax_id' => '7955',
		'chromosome' => '10',
		'seq_start' => '37719889',
		'seq_end' => '37720465',
		'region_length' => '576',
		'region_type' => 'UCNEbase',
		'el_id' => 'NIPBL'
	)
)
$gene_el = array(
	'ENSMUST00000052965' => array(
		'Adipose' => array(
			'average_FPKM' => '3.941',
			'stddev_FPKM' => '2.24'
		),
		'Adrenal' => array(
			'average_FPKM' => '3.103',
			'stddev_FPKM' => '0.35'
		),
		'Bladder' => array(
			'average_FPKM' => '3.673',
			'stddev_FPKM' => '1.17'
		),
		'Brain' => array(
			'average_FPKM' => '4.982',
			'stddev_FPKM' => '4.02'
		),
		'Breast' => array(
			'average_FPKM' => '4.624',
			'stddev_FPKM' => '1.59'
		),
		'Colon' => array(
			'average_FPKM' => '3.856',
			'stddev_FPKM' => '0.74'
		),
		'Heart' => array(
			'average_FPKM' => '3.003',
			'stddev_FPKM' => '0.26'
		),
		'Kidney' => array(
			'average_FPKM' => '2.222',
			'stddev_FPKM' => '0.25'
		),
		'Liver' => array(
			'average_FPKM' => '2.797',
			'stddev_FPKM' => '1.47'
		),
		'Lung' => array(
			'average_FPKM' => '5.039',
			'stddev_FPKM' => '1.06'
		),
		'Muscle' => array(
			'average_FPKM' => '1.527',
			'stddev_FPKM' => '0.81'
		),
		'Ovary' => array(
			'average_FPKM' => '7.317',
			'stddev_FPKM' => '3.83'
		),
		'Placenta' => array(
			'average_FPKM' => '4.456',
			'stddev_FPKM' => '0.81'
		),
		'Testis' => array(
			'average_FPKM' => '12.150',
			'stddev_FPKM' => '5.80'
		)
	)
)
$gene_key = 'ENSMUSG00000022141'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '3.941',
		'stddev_FPKM' => '2.24'
	),
	'Adrenal' => array(
		'average_FPKM' => '3.103',
		'stddev_FPKM' => '0.35'
	),
	'Bladder' => array(
		'average_FPKM' => '3.673',
		'stddev_FPKM' => '1.17'
	),
	'Brain' => array(
		'average_FPKM' => '4.982',
		'stddev_FPKM' => '4.02'
	),
	'Breast' => array(
		'average_FPKM' => '4.624',
		'stddev_FPKM' => '1.59'
	),
	'Colon' => array(
		'average_FPKM' => '3.856',
		'stddev_FPKM' => '0.74'
	),
	'Heart' => array(
		'average_FPKM' => '3.003',
		'stddev_FPKM' => '0.26'
	),
	'Kidney' => array(
		'average_FPKM' => '2.222',
		'stddev_FPKM' => '0.25'
	),
	'Liver' => array(
		'average_FPKM' => '2.797',
		'stddev_FPKM' => '1.47'
	),
	'Lung' => array(
		'average_FPKM' => '5.039',
		'stddev_FPKM' => '1.06'
	),
	'Muscle' => array(
		'average_FPKM' => '1.527',
		'stddev_FPKM' => '0.81'
	),
	'Ovary' => array(
		'average_FPKM' => '7.317',
		'stddev_FPKM' => '3.83'
	),
	'Placenta' => array(
		'average_FPKM' => '4.456',
		'stddev_FPKM' => '0.81'
	),
	'Testis' => array(
		'average_FPKM' => '12.150',
		'stddev_FPKM' => '5.80'
	)
)
$tran_key = 'ENSMUST00000052965'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

Source ID		Type	Tax ID	Position
NIPBL		UCNEbase	7955	10:37719889-37720465
Gene		Transcript	Position	Biotype

CIL_0007PI_0004 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007PI_0004 [APP/View/Region/show.ctp, line 46]Code Context
        <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
        <?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
	'region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000249850' => 'keratin 18 pseudogene 31',
		'ENSG00000274687' => null,
		'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
		'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
	),
	'gene_name_arr' => array(
		'ENSG00000249850' => 'KRT18P31',
		'ENSG00000274687' => 'AC008902.1',
		'ENSMUSG00000022141' => 'Nipbl',
		'ENSDARG00000061052' => 'nipblb'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Bladder',
		(int) 6 => 'Brain',
		(int) 11 => 'Breast',
		(int) 13 => 'Colon',
		(int) 16 => 'Heart',
		(int) 19 => 'Kidney',
		(int) 22 => 'Liver',
		(int) 24 => 'Lung',
		(int) 26 => 'Muscle',
		(int) 29 => 'Ovary',
		(int) 32 => 'Placenta',
		(int) 34 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000506277' => array(
			'start' => '36885206',
			'end' => '36886497',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'KRT18P31-001'
		),
		'ENST00000622531' => array(
			'start' => '37021692',
			'end' => '37022036',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC008902.1-201'
		),
		'ENSMUST00000052965' => array(
			'start' => '8291225',
			'end' => '8444463',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Nipbl-201'
		),
		'ENSDART00000086653' => array(
			'start' => '37720648',
			'end' => '37791148',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-201'
		),
		'ENSDART00000086861' => array(
			'start' => '37720330',
			'end' => '37791209',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-001'
		),
		'ENSDART00000108484' => array(
			'start' => '37719940',
			'end' => '37781210',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-202'
		),
		'ENSDART00000140556' => array(
			'start' => '37731699',
			'end' => '37746412',
			'transcript_biotype' => 'processed_transcript',
			'transcript_name' => 'nipblb-002'
		)
	),
	'accession_map' => array(
		'ENST000' => '9606',
		'ENSMUST' => '10090',
		'ENSDART' => '7955',
		'ENSG000' => '9606',
		'ENSMUSG' => '10090',
		'ENSDARG' => '7955'
	),
	'sci_name_map' => array(
		(int) 9606 => 'Homo_sapiens',
		(int) 10090 => 'Mus_musculus',
		(int) 7955 => 'Danio_rerio'
	),
	'UCSC_links' => array(
		(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
		(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
		(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
	),
	'expressed_region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000249850' => 'keratin 18 pseudogene 31',
	'ENSG00000274687' => null,
	'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
	'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
)
$gene_name_arr = array(
	'ENSG00000249850' => 'KRT18P31',
	'ENSG00000274687' => 'AC008902.1',
	'ENSMUSG00000022141' => 'Nipbl',
	'ENSDARG00000061052' => 'nipblb'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0001',
			'tax_id' => '9606',
			'chromosome' => '5',
			'seq_start' => '36878759',
			'seq_end' => '37065607',
			'region_length' => '186848',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0002',
			'tax_id' => '10090',
			'chromosome' => '15',
			'seq_start' => '8290515',
			'seq_end' => '8442513',
			'region_length' => '151998',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '37719889',
			'seq_end' => '37720465',
			'region_length' => '576',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 3 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0004',
			'tax_id' => '7955',
			'chromosome' => '5',
			'seq_start' => '8419188',
			'seq_end' => '8419363',
			'region_length' => '175',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Bladder',
	(int) 6 => 'Brain',
	(int) 11 => 'Breast',
	(int) 13 => 'Colon',
	(int) 16 => 'Heart',
	(int) 19 => 'Kidney',
	(int) 22 => 'Liver',
	(int) 24 => 'Lung',
	(int) 26 => 'Muscle',
	(int) 29 => 'Ovary',
	(int) 32 => 'Placenta',
	(int) 34 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000506277' => array(
		'start' => '36885206',
		'end' => '36886497',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'KRT18P31-001'
	),
	'ENST00000622531' => array(
		'start' => '37021692',
		'end' => '37022036',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC008902.1-201'
	),
	'ENSMUST00000052965' => array(
		'start' => '8291225',
		'end' => '8444463',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Nipbl-201'
	),
	'ENSDART00000086653' => array(
		'start' => '37720648',
		'end' => '37791148',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-201'
	),
	'ENSDART00000086861' => array(
		'start' => '37720330',
		'end' => '37791209',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-001'
	),
	'ENSDART00000108484' => array(
		'start' => '37719940',
		'end' => '37781210',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-202'
	),
	'ENSDART00000140556' => array(
		'start' => '37731699',
		'end' => '37746412',
		'transcript_biotype' => 'processed_transcript',
		'transcript_name' => 'nipblb-002'
	)
)
$accession_map = array(
	'ENST000' => '9606',
	'ENSMUST' => '10090',
	'ENSDART' => '7955',
	'ENSG000' => '9606',
	'ENSMUSG' => '10090',
	'ENSDARG' => '7955'
)
$sci_name_map = array(
	(int) 9606 => 'Homo_sapiens',
	(int) 10090 => 'Mus_musculus',
	(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
	(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
	(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
	(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007PI_0004',
		'tax_id' => '7955',
		'chromosome' => '5',
		'seq_start' => '8419188',
		'seq_end' => '8419363',
		'region_length' => '175',
		'region_type' => 'UCNEbase',
		'el_id' => 'NIPBL'
	)
)
$gene_el = array(
	'ENSMUST00000052965' => array(
		'Adipose' => array(
			'average_FPKM' => '3.941',
			'stddev_FPKM' => '2.24'
		),
		'Adrenal' => array(
			'average_FPKM' => '3.103',
			'stddev_FPKM' => '0.35'
		),
		'Bladder' => array(
			'average_FPKM' => '3.673',
			'stddev_FPKM' => '1.17'
		),
		'Brain' => array(
			'average_FPKM' => '4.982',
			'stddev_FPKM' => '4.02'
		),
		'Breast' => array(
			'average_FPKM' => '4.624',
			'stddev_FPKM' => '1.59'
		),
		'Colon' => array(
			'average_FPKM' => '3.856',
			'stddev_FPKM' => '0.74'
		),
		'Heart' => array(
			'average_FPKM' => '3.003',
			'stddev_FPKM' => '0.26'
		),
		'Kidney' => array(
			'average_FPKM' => '2.222',
			'stddev_FPKM' => '0.25'
		),
		'Liver' => array(
			'average_FPKM' => '2.797',
			'stddev_FPKM' => '1.47'
		),
		'Lung' => array(
			'average_FPKM' => '5.039',
			'stddev_FPKM' => '1.06'
		),
		'Muscle' => array(
			'average_FPKM' => '1.527',
			'stddev_FPKM' => '0.81'
		),
		'Ovary' => array(
			'average_FPKM' => '7.317',
			'stddev_FPKM' => '3.83'
		),
		'Placenta' => array(
			'average_FPKM' => '4.456',
			'stddev_FPKM' => '0.81'
		),
		'Testis' => array(
			'average_FPKM' => '12.150',
			'stddev_FPKM' => '5.80'
		)
	)
)
$gene_key = 'ENSMUSG00000022141'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '3.941',
		'stddev_FPKM' => '2.24'
	),
	'Adrenal' => array(
		'average_FPKM' => '3.103',
		'stddev_FPKM' => '0.35'
	),
	'Bladder' => array(
		'average_FPKM' => '3.673',
		'stddev_FPKM' => '1.17'
	),
	'Brain' => array(
		'average_FPKM' => '4.982',
		'stddev_FPKM' => '4.02'
	),
	'Breast' => array(
		'average_FPKM' => '4.624',
		'stddev_FPKM' => '1.59'
	),
	'Colon' => array(
		'average_FPKM' => '3.856',
		'stddev_FPKM' => '0.74'
	),
	'Heart' => array(
		'average_FPKM' => '3.003',
		'stddev_FPKM' => '0.26'
	),
	'Kidney' => array(
		'average_FPKM' => '2.222',
		'stddev_FPKM' => '0.25'
	),
	'Liver' => array(
		'average_FPKM' => '2.797',
		'stddev_FPKM' => '1.47'
	),
	'Lung' => array(
		'average_FPKM' => '5.039',
		'stddev_FPKM' => '1.06'
	),
	'Muscle' => array(
		'average_FPKM' => '1.527',
		'stddev_FPKM' => '0.81'
	),
	'Ovary' => array(
		'average_FPKM' => '7.317',
		'stddev_FPKM' => '3.83'
	),
	'Placenta' => array(
		'average_FPKM' => '4.456',
		'stddev_FPKM' => '0.81'
	),
	'Testis' => array(
		'average_FPKM' => '12.150',
		'stddev_FPKM' => '5.80'
	)
)
$tran_key = 'ENSMUST00000052965'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context
        <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
        <?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
	'region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000249850' => 'keratin 18 pseudogene 31',
		'ENSG00000274687' => null,
		'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
		'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
	),
	'gene_name_arr' => array(
		'ENSG00000249850' => 'KRT18P31',
		'ENSG00000274687' => 'AC008902.1',
		'ENSMUSG00000022141' => 'Nipbl',
		'ENSDARG00000061052' => 'nipblb'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Bladder',
		(int) 6 => 'Brain',
		(int) 11 => 'Breast',
		(int) 13 => 'Colon',
		(int) 16 => 'Heart',
		(int) 19 => 'Kidney',
		(int) 22 => 'Liver',
		(int) 24 => 'Lung',
		(int) 26 => 'Muscle',
		(int) 29 => 'Ovary',
		(int) 32 => 'Placenta',
		(int) 34 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000506277' => array(
			'start' => '36885206',
			'end' => '36886497',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'KRT18P31-001'
		),
		'ENST00000622531' => array(
			'start' => '37021692',
			'end' => '37022036',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC008902.1-201'
		),
		'ENSMUST00000052965' => array(
			'start' => '8291225',
			'end' => '8444463',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Nipbl-201'
		),
		'ENSDART00000086653' => array(
			'start' => '37720648',
			'end' => '37791148',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-201'
		),
		'ENSDART00000086861' => array(
			'start' => '37720330',
			'end' => '37791209',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-001'
		),
		'ENSDART00000108484' => array(
			'start' => '37719940',
			'end' => '37781210',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'nipblb-202'
		),
		'ENSDART00000140556' => array(
			'start' => '37731699',
			'end' => '37746412',
			'transcript_biotype' => 'processed_transcript',
			'transcript_name' => 'nipblb-002'
		)
	),
	'accession_map' => array(
		'ENST000' => '9606',
		'ENSMUST' => '10090',
		'ENSDART' => '7955',
		'ENSG000' => '9606',
		'ENSMUSG' => '10090',
		'ENSDARG' => '7955'
	),
	'sci_name_map' => array(
		(int) 9606 => 'Homo_sapiens',
		(int) 10090 => 'Mus_musculus',
		(int) 7955 => 'Danio_rerio'
	),
	'UCSC_links' => array(
		(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
		(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
		(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
	),
	'expressed_region_arr' => array(
		'CIL_0007PI_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007PI_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000249850' => 'keratin 18 pseudogene 31',
	'ENSG00000274687' => null,
	'ENSMUSG00000022141' => 'Nipped-B homolog (Drosophila)',
	'ENSDARG00000061052' => 'nipped-b homolog b (Drosophila)'
)
$gene_name_arr = array(
	'ENSG00000249850' => 'KRT18P31',
	'ENSG00000274687' => 'AC008902.1',
	'ENSMUSG00000022141' => 'Nipbl',
	'ENSDARG00000061052' => 'nipblb'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0001',
			'tax_id' => '9606',
			'chromosome' => '5',
			'seq_start' => '36878759',
			'seq_end' => '37065607',
			'region_length' => '186848',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0002',
			'tax_id' => '10090',
			'chromosome' => '15',
			'seq_start' => '8290515',
			'seq_end' => '8442513',
			'region_length' => '151998',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '37719889',
			'seq_end' => '37720465',
			'region_length' => '576',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	),
	(int) 3 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007PI_0004',
			'tax_id' => '7955',
			'chromosome' => '5',
			'seq_start' => '8419188',
			'seq_end' => '8419363',
			'region_length' => '175',
			'region_type' => 'UCNEbase',
			'el_id' => 'NIPBL'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Bladder',
	(int) 6 => 'Brain',
	(int) 11 => 'Breast',
	(int) 13 => 'Colon',
	(int) 16 => 'Heart',
	(int) 19 => 'Kidney',
	(int) 22 => 'Liver',
	(int) 24 => 'Lung',
	(int) 26 => 'Muscle',
	(int) 29 => 'Ovary',
	(int) 32 => 'Placenta',
	(int) 34 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000506277' => array(
		'start' => '36885206',
		'end' => '36886497',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'KRT18P31-001'
	),
	'ENST00000622531' => array(
		'start' => '37021692',
		'end' => '37022036',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC008902.1-201'
	),
	'ENSMUST00000052965' => array(
		'start' => '8291225',
		'end' => '8444463',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Nipbl-201'
	),
	'ENSDART00000086653' => array(
		'start' => '37720648',
		'end' => '37791148',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-201'
	),
	'ENSDART00000086861' => array(
		'start' => '37720330',
		'end' => '37791209',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-001'
	),
	'ENSDART00000108484' => array(
		'start' => '37719940',
		'end' => '37781210',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'nipblb-202'
	),
	'ENSDART00000140556' => array(
		'start' => '37731699',
		'end' => '37746412',
		'transcript_biotype' => 'processed_transcript',
		'transcript_name' => 'nipblb-002'
	)
)
$accession_map = array(
	'ENST000' => '9606',
	'ENSMUST' => '10090',
	'ENSDART' => '7955',
	'ENSG000' => '9606',
	'ENSMUSG' => '10090',
	'ENSDARG' => '7955'
)
$sci_name_map = array(
	(int) 9606 => 'Homo_sapiens',
	(int) 10090 => 'Mus_musculus',
	(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
	(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
	(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
	(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
	'CIL_0007PI_0001' => array(
		'genes_in_region' => array(
			'ENSG00000249850' => array(
				[maximum depth reached]
			),
			'ENSG00000274687' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis',
			(int) 14 => 'Brain',
			(int) 15 => 'Colon',
			(int) 16 => 'Ovary'
		)
	),
	'CIL_0007PI_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000022141' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Placenta',
			(int) 13 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007PI_0004',
		'tax_id' => '7955',
		'chromosome' => '5',
		'seq_start' => '8419188',
		'seq_end' => '8419363',
		'region_length' => '175',
		'region_type' => 'UCNEbase',
		'el_id' => 'NIPBL'
	)
)
$gene_el = array(
	'ENSMUST00000052965' => array(
		'Adipose' => array(
			'average_FPKM' => '3.941',
			'stddev_FPKM' => '2.24'
		),
		'Adrenal' => array(
			'average_FPKM' => '3.103',
			'stddev_FPKM' => '0.35'
		),
		'Bladder' => array(
			'average_FPKM' => '3.673',
			'stddev_FPKM' => '1.17'
		),
		'Brain' => array(
			'average_FPKM' => '4.982',
			'stddev_FPKM' => '4.02'
		),
		'Breast' => array(
			'average_FPKM' => '4.624',
			'stddev_FPKM' => '1.59'
		),
		'Colon' => array(
			'average_FPKM' => '3.856',
			'stddev_FPKM' => '0.74'
		),
		'Heart' => array(
			'average_FPKM' => '3.003',
			'stddev_FPKM' => '0.26'
		),
		'Kidney' => array(
			'average_FPKM' => '2.222',
			'stddev_FPKM' => '0.25'
		),
		'Liver' => array(
			'average_FPKM' => '2.797',
			'stddev_FPKM' => '1.47'
		),
		'Lung' => array(
			'average_FPKM' => '5.039',
			'stddev_FPKM' => '1.06'
		),
		'Muscle' => array(
			'average_FPKM' => '1.527',
			'stddev_FPKM' => '0.81'
		),
		'Ovary' => array(
			'average_FPKM' => '7.317',
			'stddev_FPKM' => '3.83'
		),
		'Placenta' => array(
			'average_FPKM' => '4.456',
			'stddev_FPKM' => '0.81'
		),
		'Testis' => array(
			'average_FPKM' => '12.150',
			'stddev_FPKM' => '5.80'
		)
	)
)
$gene_key = 'ENSMUSG00000022141'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '3.941',
		'stddev_FPKM' => '2.24'
	),
	'Adrenal' => array(
		'average_FPKM' => '3.103',
		'stddev_FPKM' => '0.35'
	),
	'Bladder' => array(
		'average_FPKM' => '3.673',
		'stddev_FPKM' => '1.17'
	),
	'Brain' => array(
		'average_FPKM' => '4.982',
		'stddev_FPKM' => '4.02'
	),
	'Breast' => array(
		'average_FPKM' => '4.624',
		'stddev_FPKM' => '1.59'
	),
	'Colon' => array(
		'average_FPKM' => '3.856',
		'stddev_FPKM' => '0.74'
	),
	'Heart' => array(
		'average_FPKM' => '3.003',
		'stddev_FPKM' => '0.26'
	),
	'Kidney' => array(
		'average_FPKM' => '2.222',
		'stddev_FPKM' => '0.25'
	),
	'Liver' => array(
		'average_FPKM' => '2.797',
		'stddev_FPKM' => '1.47'
	),
	'Lung' => array(
		'average_FPKM' => '5.039',
		'stddev_FPKM' => '1.06'
	),
	'Muscle' => array(
		'average_FPKM' => '1.527',
		'stddev_FPKM' => '0.81'
	),
	'Ovary' => array(
		'average_FPKM' => '7.317',
		'stddev_FPKM' => '3.83'
	),
	'Placenta' => array(
		'average_FPKM' => '4.456',
		'stddev_FPKM' => '0.81'
	),
	'Testis' => array(
		'average_FPKM' => '12.150',
		'stddev_FPKM' => '5.80'
	)
)
$tran_key = 'ENSMUST00000052965'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108

Source ID		Type	Tax ID	Position
NIPBL		UCNEbase	7955	5:8419188-8419363
Gene		Transcript	Position	Biotype

Expression Patterns

Heat Map

Heat Map (Expressed Only)

Numeric Values

Gene

Transcript

Adipose

Adrenal

Bladder

Brain

Breast

Colon

Heart

Kidney

Liver

Lung

Muscle

Ovary

Placenta

Testis

ENSG00000249850

ENST00000506277

0.014±0.00

0.063±0.00

1.373±0.00

0.603±0.00

2.607±0.00

3.621±0.00

0.556±0.50

0.480±0.40

0.800±0.73

2.971±0.00

0.040±0.00

0.735±1.00

0.065±0.00

0.248±0.15

ENSG00000274687

ENST00000622531

N/A

1.911±0.00

N/A

1.091±1.07

N/A

0.265±0.00

N/A

Gene

Transcript

Adipose

Adrenal

Bladder

Brain

Breast

Colon

Heart

Kidney

Liver

Lung

Muscle

Ovary

Placenta

Testis

ENSMUSG00000022141

ENSMUST00000052965

3.941±2.24

3.103±0.35

3.673±1.17

4.982±4.02

4.624±1.59

3.856±0.74

3.003±0.26

2.222±0.25

2.797±1.47

5.039±1.06

1.527±0.81

7.317±3.83

4.456±0.81

12.150±5.80

C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Region Summary

Expression Patterns

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