Institute of Cardiovascular Regeneration Webtool Repository

CIL_0007OL_0001 (Click to Hide/Show)

Source ID	Type	Tax ID	Position
TCF12	UCNEbase	9606	15:57134123-57288405
Gene	Transcript	Position	Biotype
ENSG00000239035 (snoU13) Small nucleolar RNA U13	ENST00000459428 (snoU13.1-224)	57278570-57278673	snoRNA
ENSG00000260689 (HNRNPA3P11) heterogeneous nuclear ribonucleoprotein A3 pseudogene 11	ENST00000564298 (HNRNPA3P11-001)	57246960-57247893	processed_pseudogene

CIL_0007OL_0002 (Click to Hide/Show)

Source ID	Type	Tax ID	Position
TCF12	UCNEbase	10090	9:71844385-71975607
Gene	Transcript	Position	Biotype
ENSMUSG00000098761 (Gm18821) predicted gene, 18821	ENSMUST00000184135 (Gm18821-001)	71908843-71909551	processed_pseudogene
ENSMUSG00000099313 (Gm27152) predicted gene 27152	ENSMUST00000183828 (Gm27152-001)	71948879-71948977	processed_pseudogene

CIL_0007OL_0003 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007OL_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_0007OL_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007OL_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000239035' => 'Small nucleolar RNA U13',
		'ENSG00000260689' => 'heterogeneous nuclear ribonucleoprotein A3 pseudogene 11',
		'ENSMUSG00000098761' => 'predicted gene, 18821',
		'ENSMUSG00000099313' => 'predicted gene 27152',
		'ENSDARG00000080040' => '5S ribosomal RNA'
	),
	'gene_name_arr' => array(
		'ENSG00000239035' => 'snoU13',
		'ENSG00000260689' => 'HNRNPA3P11',
		'ENSMUSG00000098761' => 'Gm18821',
		'ENSMUSG00000099313' => 'Gm27152',
		'ENSDARG00000080040' => '5S_rRNA'
	),
	'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]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Bladder',
		(int) 5 => 'Brain',
		(int) 7 => 'Breast',
		(int) 11 => 'Colon',
		(int) 12 => 'Heart',
		(int) 14 => 'Kidney',
		(int) 17 => 'Liver',
		(int) 18 => 'Lung',
		(int) 21 => 'Ovary',
		(int) 23 => 'Placenta',
		(int) 24 => '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) 5,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000459428' => array(
			'start' => '57278570',
			'end' => '57278673',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'snoU13.1-224'
		),
		'ENST00000564298' => array(
			'start' => '57246960',
			'end' => '57247893',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'HNRNPA3P11-001'
		),
		'ENSMUST00000184135' => array(
			'start' => '71908843',
			'end' => '71909551',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'Gm18821-001'
		),
		'ENSMUST00000183828' => array(
			'start' => '71948879',
			'end' => '71948977',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'Gm27152-001'
		),
		'ENSDART00000115745' => array(
			'start' => '53981384',
			'end' => '53981510',
			'transcript_biotype' => 'rRNA',
			'transcript_name' => '5S_rRNA.4-201'
		)
	),
	'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_0007OL_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007OL_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007OL_0001' => array(
		'genes_in_region' => array(
			'ENSG00000239035' => array(
				[maximum depth reached]
			),
			'ENSG00000260689' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Breast',
			(int) 1 => 'Lung',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Brain',
			(int) 5 => 'Breast',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Lung',
			(int) 9 => 'Ovary'
		)
	),
	'CIL_0007OL_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000098761' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000099313' => 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 => 'Ovary',
			(int) 11 => 'Placenta',
			(int) 12 => 'Testis',
			(int) 13 => 'Breast',
			(int) 14 => 'Kidney'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000239035' => 'Small nucleolar RNA U13',
	'ENSG00000260689' => 'heterogeneous nuclear ribonucleoprotein A3 pseudogene 11',
	'ENSMUSG00000098761' => 'predicted gene, 18821',
	'ENSMUSG00000099313' => 'predicted gene 27152',
	'ENSDARG00000080040' => '5S ribosomal RNA'
)
$gene_name_arr = array(
	'ENSG00000239035' => 'snoU13',
	'ENSG00000260689' => 'HNRNPA3P11',
	'ENSMUSG00000098761' => 'Gm18821',
	'ENSMUSG00000099313' => 'Gm27152',
	'ENSDARG00000080040' => '5S_rRNA'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007OL_0001',
			'tax_id' => '9606',
			'chromosome' => '15',
			'seq_start' => '57134123',
			'seq_end' => '57288405',
			'region_length' => '154282',
			'region_type' => 'UCNEbase',
			'el_id' => 'TCF12'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007OL_0002',
			'tax_id' => '10090',
			'chromosome' => '9',
			'seq_start' => '71844385',
			'seq_end' => '71975607',
			'region_length' => '131222',
			'region_type' => 'UCNEbase',
			'el_id' => 'TCF12'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007OL_0003',
			'tax_id' => '7955',
			'chromosome' => '7',
			'seq_start' => '53971903',
			'seq_end' => '54059134',
			'region_length' => '87231',
			'region_type' => 'UCNEbase',
			'el_id' => 'TCF12'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Bladder',
	(int) 5 => 'Brain',
	(int) 7 => 'Breast',
	(int) 11 => 'Colon',
	(int) 12 => 'Heart',
	(int) 14 => 'Kidney',
	(int) 17 => 'Liver',
	(int) 18 => 'Lung',
	(int) 21 => 'Ovary',
	(int) 23 => 'Placenta',
	(int) 24 => '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) 5
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000459428' => array(
		'start' => '57278570',
		'end' => '57278673',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'snoU13.1-224'
	),
	'ENST00000564298' => array(
		'start' => '57246960',
		'end' => '57247893',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'HNRNPA3P11-001'
	),
	'ENSMUST00000184135' => array(
		'start' => '71908843',
		'end' => '71909551',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'Gm18821-001'
	),
	'ENSMUST00000183828' => array(
		'start' => '71948879',
		'end' => '71948977',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'Gm27152-001'
	),
	'ENSDART00000115745' => array(
		'start' => '53981384',
		'end' => '53981510',
		'transcript_biotype' => 'rRNA',
		'transcript_name' => '5S_rRNA.4-201'
	)
)
$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_0007OL_0001' => array(
		'genes_in_region' => array(
			'ENSG00000239035' => array(
				[maximum depth reached]
			),
			'ENSG00000260689' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Breast',
			(int) 1 => 'Lung',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Brain',
			(int) 5 => 'Breast',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Lung',
			(int) 9 => 'Ovary'
		)
	),
	'CIL_0007OL_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000098761' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000099313' => 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 => 'Ovary',
			(int) 11 => 'Placenta',
			(int) 12 => 'Testis',
			(int) 13 => 'Breast',
			(int) 14 => 'Kidney'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007OL_0003',
		'tax_id' => '7955',
		'chromosome' => '7',
		'seq_start' => '53971903',
		'seq_end' => '54059134',
		'region_length' => '87231',
		'region_type' => 'UCNEbase',
		'el_id' => 'TCF12'
	)
)
$gene_el = array(
	'ENSMUST00000183828' => array(
		'Breast' => array(
			'average_FPKM' => '3279.140',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '3173.535',
			'stddev_FPKM' => '228.09'
		)
	)
)
$gene_key = 'ENSMUSG00000099313'
$is_first = false
$tran_el = array(
	'Breast' => array(
		'average_FPKM' => '3279.140',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '3173.535',
		'stddev_FPKM' => '228.09'
	)
)
$tran_key = 'ENSMUST00000183828'
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_0007OL_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007OL_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000239035' => 'Small nucleolar RNA U13',
		'ENSG00000260689' => 'heterogeneous nuclear ribonucleoprotein A3 pseudogene 11',
		'ENSMUSG00000098761' => 'predicted gene, 18821',
		'ENSMUSG00000099313' => 'predicted gene 27152',
		'ENSDARG00000080040' => '5S ribosomal RNA'
	),
	'gene_name_arr' => array(
		'ENSG00000239035' => 'snoU13',
		'ENSG00000260689' => 'HNRNPA3P11',
		'ENSMUSG00000098761' => 'Gm18821',
		'ENSMUSG00000099313' => 'Gm27152',
		'ENSDARG00000080040' => '5S_rRNA'
	),
	'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]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 4 => 'Bladder',
		(int) 5 => 'Brain',
		(int) 7 => 'Breast',
		(int) 11 => 'Colon',
		(int) 12 => 'Heart',
		(int) 14 => 'Kidney',
		(int) 17 => 'Liver',
		(int) 18 => 'Lung',
		(int) 21 => 'Ovary',
		(int) 23 => 'Placenta',
		(int) 24 => '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) 5,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000459428' => array(
			'start' => '57278570',
			'end' => '57278673',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'snoU13.1-224'
		),
		'ENST00000564298' => array(
			'start' => '57246960',
			'end' => '57247893',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'HNRNPA3P11-001'
		),
		'ENSMUST00000184135' => array(
			'start' => '71908843',
			'end' => '71909551',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'Gm18821-001'
		),
		'ENSMUST00000183828' => array(
			'start' => '71948879',
			'end' => '71948977',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'Gm27152-001'
		),
		'ENSDART00000115745' => array(
			'start' => '53981384',
			'end' => '53981510',
			'transcript_biotype' => 'rRNA',
			'transcript_name' => '5S_rRNA.4-201'
		)
	),
	'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_0007OL_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		),
		'CIL_0007OL_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007OL_0001' => array(
		'genes_in_region' => array(
			'ENSG00000239035' => array(
				[maximum depth reached]
			),
			'ENSG00000260689' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Breast',
			(int) 1 => 'Lung',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Brain',
			(int) 5 => 'Breast',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Lung',
			(int) 9 => 'Ovary'
		)
	),
	'CIL_0007OL_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000098761' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000099313' => 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 => 'Ovary',
			(int) 11 => 'Placenta',
			(int) 12 => 'Testis',
			(int) 13 => 'Breast',
			(int) 14 => 'Kidney'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000239035' => 'Small nucleolar RNA U13',
	'ENSG00000260689' => 'heterogeneous nuclear ribonucleoprotein A3 pseudogene 11',
	'ENSMUSG00000098761' => 'predicted gene, 18821',
	'ENSMUSG00000099313' => 'predicted gene 27152',
	'ENSDARG00000080040' => '5S ribosomal RNA'
)
$gene_name_arr = array(
	'ENSG00000239035' => 'snoU13',
	'ENSG00000260689' => 'HNRNPA3P11',
	'ENSMUSG00000098761' => 'Gm18821',
	'ENSMUSG00000099313' => 'Gm27152',
	'ENSDARG00000080040' => '5S_rRNA'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007OL_0001',
			'tax_id' => '9606',
			'chromosome' => '15',
			'seq_start' => '57134123',
			'seq_end' => '57288405',
			'region_length' => '154282',
			'region_type' => 'UCNEbase',
			'el_id' => 'TCF12'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007OL_0002',
			'tax_id' => '10090',
			'chromosome' => '9',
			'seq_start' => '71844385',
			'seq_end' => '71975607',
			'region_length' => '131222',
			'region_type' => 'UCNEbase',
			'el_id' => 'TCF12'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007OL_0003',
			'tax_id' => '7955',
			'chromosome' => '7',
			'seq_start' => '53971903',
			'seq_end' => '54059134',
			'region_length' => '87231',
			'region_type' => 'UCNEbase',
			'el_id' => 'TCF12'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 4 => 'Bladder',
	(int) 5 => 'Brain',
	(int) 7 => 'Breast',
	(int) 11 => 'Colon',
	(int) 12 => 'Heart',
	(int) 14 => 'Kidney',
	(int) 17 => 'Liver',
	(int) 18 => 'Lung',
	(int) 21 => 'Ovary',
	(int) 23 => 'Placenta',
	(int) 24 => '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) 5
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000459428' => array(
		'start' => '57278570',
		'end' => '57278673',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'snoU13.1-224'
	),
	'ENST00000564298' => array(
		'start' => '57246960',
		'end' => '57247893',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'HNRNPA3P11-001'
	),
	'ENSMUST00000184135' => array(
		'start' => '71908843',
		'end' => '71909551',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'Gm18821-001'
	),
	'ENSMUST00000183828' => array(
		'start' => '71948879',
		'end' => '71948977',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'Gm27152-001'
	),
	'ENSDART00000115745' => array(
		'start' => '53981384',
		'end' => '53981510',
		'transcript_biotype' => 'rRNA',
		'transcript_name' => '5S_rRNA.4-201'
	)
)
$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_0007OL_0001' => array(
		'genes_in_region' => array(
			'ENSG00000239035' => array(
				[maximum depth reached]
			),
			'ENSG00000260689' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Breast',
			(int) 1 => 'Lung',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Brain',
			(int) 5 => 'Breast',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Lung',
			(int) 9 => 'Ovary'
		)
	),
	'CIL_0007OL_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000098761' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000099313' => 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 => 'Ovary',
			(int) 11 => 'Placenta',
			(int) 12 => 'Testis',
			(int) 13 => 'Breast',
			(int) 14 => 'Kidney'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007OL_0003',
		'tax_id' => '7955',
		'chromosome' => '7',
		'seq_start' => '53971903',
		'seq_end' => '54059134',
		'region_length' => '87231',
		'region_type' => 'UCNEbase',
		'el_id' => 'TCF12'
	)
)
$gene_el = array(
	'ENSMUST00000183828' => array(
		'Breast' => array(
			'average_FPKM' => '3279.140',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '3173.535',
			'stddev_FPKM' => '228.09'
		)
	)
)
$gene_key = 'ENSMUSG00000099313'
$is_first = false
$tran_el = array(
	'Breast' => array(
		'average_FPKM' => '3279.140',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '3173.535',
		'stddev_FPKM' => '228.09'
	)
)
$tran_key = 'ENSMUST00000183828'
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
TCF12		UCNEbase	7955	7:53971903-54059134
Gene		Transcript	Position	Biotype

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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