Institute of Cardiovascular Regeneration Webtool Repository

Source ID	Type	Tax ID	Position
hs601	VISTA	9606	4:28590930-29192066
Gene	Transcript	Position	Biotype
ENSG00000243548 (RN7SL101P) RNA, 7SL, cytoplasmic 101, pseudogene	ENST00000496350 (RN7SL101P-201)	28711198-28711476	misc_RNA
ENSG00000248176 (RP11-472K22.1)	ENST00000503299 (RP11-472K22.1-001)	29118308-29202770	lincRNA
ENSG00000249228 (RP11-769N22.1)	ENST00000514855 (RP11-769N22.1-001)	29046591-29048765	lincRNA
ENSG00000250064 (RP11-123O22.1)	ENST00000509416 (RP11-123O22.1-001)	28435449-28600275	lincRNA
ENSG00000250190 (RP11-292B1.2)	ENST00000514802 (RP11-292B1.2-001)	28996524-29014594	lincRNA
ENSG00000250927 (MESTP3) mesoderm specific transcript pseudogene 3	ENST00000503460 (MESTP3-001)	28823244-28824211	processed_pseudogene

Notice (8): Undefined index: CIL_00098M_0002 [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_00098M_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000243548' => 'RNA, 7SL, cytoplasmic 101, pseudogene',
		'ENSG00000248176' => null,
		'ENSG00000249228' => null,
		'ENSG00000250064' => null,
		'ENSG00000250190' => null,
		'ENSG00000250927' => 'mesoderm specific transcript pseudogene 3',
		'ENSG00000276507' => null
	),
	'gene_name_arr' => array(
		'ENSG00000243548' => 'RN7SL101P',
		'ENSG00000248176' => 'RP11-472K22.1',
		'ENSG00000249228' => 'RP11-769N22.1',
		'ENSG00000250064' => 'RP11-123O22.1',
		'ENSG00000250190' => 'RP11-292B1.2',
		'ENSG00000250927' => 'MESTP3',
		'ENSG00000276507' => 'RP11-769N22.2'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 3 => 'Brain',
		(int) 6 => 'Breast',
		(int) 7 => 'Colon',
		(int) 10 => 'Heart',
		(int) 11 => 'Kidney',
		(int) 12 => 'Liver',
		(int) 13 => 'Lung',
		(int) 14 => 'Muscle',
		(int) 16 => 'Ovary',
		(int) 21 => 'Placenta',
		(int) 23 => '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(
		'ENST00000496350' => array(
			'start' => '28711198',
			'end' => '28711476',
			'transcript_biotype' => 'misc_RNA',
			'transcript_name' => 'RN7SL101P-201'
		),
		'ENST00000503299' => array(
			'start' => '29118308',
			'end' => '29202770',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-472K22.1-001'
		),
		'ENST00000514855' => array(
			'start' => '29046591',
			'end' => '29048765',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-769N22.1-001'
		),
		'ENST00000509416' => array(
			'start' => '28435449',
			'end' => '28600275',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-123O22.1-001'
		),
		'ENST00000514802' => array(
			'start' => '28996524',
			'end' => '29014594',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-292B1.2-001'
		),
		'ENST00000503460' => array(
			'start' => '28823244',
			'end' => '28824211',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'MESTP3-001'
		),
		'ENST00000610373' => array(
			'start' => '29010619',
			'end' => '29011021',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RP11-769N22.2-001'
		)
	),
	'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_00098M_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00098M_0001' => array(
		'genes_in_region' => array(
			'ENSG00000243548' => array(
				[maximum depth reached]
			),
			'ENSG00000248176' => array(
				[maximum depth reached]
			),
			'ENSG00000249228' => array(
				[maximum depth reached]
			),
			'ENSG00000250064' => array(
				[maximum depth reached]
			),
			'ENSG00000250190' => array(
				[maximum depth reached]
			),
			'ENSG00000250927' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Brain',
			(int) 1 => 'Ovary',
			(int) 2 => 'Placenta',
			(int) 3 => 'Testis',
			(int) 4 => 'Brain',
			(int) 5 => 'Colon',
			(int) 6 => 'Muscle',
			(int) 7 => 'Ovary',
			(int) 8 => 'Testis',
			(int) 9 => 'Adipose',
			(int) 10 => 'Adrenal',
			(int) 11 => 'Brain',
			(int) 12 => 'Breast',
			(int) 13 => 'Colon',
			(int) 14 => 'Heart',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Muscle',
			(int) 19 => 'Ovary',
			(int) 20 => 'Placenta',
			(int) 21 => 'Testis',
			(int) 22 => 'Ovary',
			(int) 23 => 'Testis',
			(int) 24 => 'Adipose',
			(int) 25 => 'Testis',
			(int) 26 => 'Colon',
			(int) 27 => 'Ovary',
			(int) 28 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000243548' => 'RNA, 7SL, cytoplasmic 101, pseudogene',
	'ENSG00000248176' => null,
	'ENSG00000249228' => null,
	'ENSG00000250064' => null,
	'ENSG00000250190' => null,
	'ENSG00000250927' => 'mesoderm specific transcript pseudogene 3',
	'ENSG00000276507' => null
)
$gene_name_arr = array(
	'ENSG00000243548' => 'RN7SL101P',
	'ENSG00000248176' => 'RP11-472K22.1',
	'ENSG00000249228' => 'RP11-769N22.1',
	'ENSG00000250064' => 'RP11-123O22.1',
	'ENSG00000250190' => 'RP11-292B1.2',
	'ENSG00000250927' => 'MESTP3',
	'ENSG00000276507' => 'RP11-769N22.2'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00098M_0001',
			'tax_id' => '9606',
			'chromosome' => '4',
			'seq_start' => '28590930',
			'seq_end' => '29192066',
			'region_length' => '601136',
			'region_type' => 'VISTA',
			'el_id' => 'hs601'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00098M_0002',
			'tax_id' => '10090',
			'chromosome' => '5',
			'seq_start' => '55676101',
			'seq_end' => '56277173',
			'region_length' => '601072',
			'region_type' => 'VISTA',
			'el_id' => 'hs601'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 3 => 'Brain',
	(int) 6 => 'Breast',
	(int) 7 => 'Colon',
	(int) 10 => 'Heart',
	(int) 11 => 'Kidney',
	(int) 12 => 'Liver',
	(int) 13 => 'Lung',
	(int) 14 => 'Muscle',
	(int) 16 => 'Ovary',
	(int) 21 => 'Placenta',
	(int) 23 => '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(
	'ENST00000496350' => array(
		'start' => '28711198',
		'end' => '28711476',
		'transcript_biotype' => 'misc_RNA',
		'transcript_name' => 'RN7SL101P-201'
	),
	'ENST00000503299' => array(
		'start' => '29118308',
		'end' => '29202770',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-472K22.1-001'
	),
	'ENST00000514855' => array(
		'start' => '29046591',
		'end' => '29048765',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-769N22.1-001'
	),
	'ENST00000509416' => array(
		'start' => '28435449',
		'end' => '28600275',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-123O22.1-001'
	),
	'ENST00000514802' => array(
		'start' => '28996524',
		'end' => '29014594',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-292B1.2-001'
	),
	'ENST00000503460' => array(
		'start' => '28823244',
		'end' => '28824211',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'MESTP3-001'
	),
	'ENST00000610373' => array(
		'start' => '29010619',
		'end' => '29011021',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RP11-769N22.2-001'
	)
)
$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_00098M_0001' => array(
		'genes_in_region' => array(
			'ENSG00000243548' => array(
				[maximum depth reached]
			),
			'ENSG00000248176' => array(
				[maximum depth reached]
			),
			'ENSG00000249228' => array(
				[maximum depth reached]
			),
			'ENSG00000250064' => array(
				[maximum depth reached]
			),
			'ENSG00000250190' => array(
				[maximum depth reached]
			),
			'ENSG00000250927' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Brain',
			(int) 1 => 'Ovary',
			(int) 2 => 'Placenta',
			(int) 3 => 'Testis',
			(int) 4 => 'Brain',
			(int) 5 => 'Colon',
			(int) 6 => 'Muscle',
			(int) 7 => 'Ovary',
			(int) 8 => 'Testis',
			(int) 9 => 'Adipose',
			(int) 10 => 'Adrenal',
			(int) 11 => 'Brain',
			(int) 12 => 'Breast',
			(int) 13 => 'Colon',
			(int) 14 => 'Heart',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Muscle',
			(int) 19 => 'Ovary',
			(int) 20 => 'Placenta',
			(int) 21 => 'Testis',
			(int) 22 => 'Ovary',
			(int) 23 => 'Testis',
			(int) 24 => 'Adipose',
			(int) 25 => 'Testis',
			(int) 26 => 'Colon',
			(int) 27 => 'Ovary',
			(int) 28 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00098M_0002',
		'tax_id' => '10090',
		'chromosome' => '5',
		'seq_start' => '55676101',
		'seq_end' => '56277173',
		'region_length' => '601072',
		'region_type' => 'VISTA',
		'el_id' => 'hs601'
	)
)
$gene_el = array(
	'ENST00000503460' => array(
		'Colon' => array(
			'average_FPKM' => '0.396',
			'stddev_FPKM' => '0.00'
		),
		'Ovary' => array(
			'average_FPKM' => '0.042',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.055',
			'stddev_FPKM' => '0.01'
		)
	)
)
$gene_key = 'ENSG00000250927'
$is_first = false
$tran_el = array(
	'Colon' => array(
		'average_FPKM' => '0.396',
		'stddev_FPKM' => '0.00'
	),
	'Ovary' => array(
		'average_FPKM' => '0.042',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.055',
		'stddev_FPKM' => '0.01'
	)
)
$tran_key = 'ENST00000503460'
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_00098M_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000243548' => 'RNA, 7SL, cytoplasmic 101, pseudogene',
		'ENSG00000248176' => null,
		'ENSG00000249228' => null,
		'ENSG00000250064' => null,
		'ENSG00000250190' => null,
		'ENSG00000250927' => 'mesoderm specific transcript pseudogene 3',
		'ENSG00000276507' => null
	),
	'gene_name_arr' => array(
		'ENSG00000243548' => 'RN7SL101P',
		'ENSG00000248176' => 'RP11-472K22.1',
		'ENSG00000249228' => 'RP11-769N22.1',
		'ENSG00000250064' => 'RP11-123O22.1',
		'ENSG00000250190' => 'RP11-292B1.2',
		'ENSG00000250927' => 'MESTP3',
		'ENSG00000276507' => 'RP11-769N22.2'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 2 => 'Adrenal',
		(int) 3 => 'Brain',
		(int) 6 => 'Breast',
		(int) 7 => 'Colon',
		(int) 10 => 'Heart',
		(int) 11 => 'Kidney',
		(int) 12 => 'Liver',
		(int) 13 => 'Lung',
		(int) 14 => 'Muscle',
		(int) 16 => 'Ovary',
		(int) 21 => 'Placenta',
		(int) 23 => '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(
		'ENST00000496350' => array(
			'start' => '28711198',
			'end' => '28711476',
			'transcript_biotype' => 'misc_RNA',
			'transcript_name' => 'RN7SL101P-201'
		),
		'ENST00000503299' => array(
			'start' => '29118308',
			'end' => '29202770',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-472K22.1-001'
		),
		'ENST00000514855' => array(
			'start' => '29046591',
			'end' => '29048765',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-769N22.1-001'
		),
		'ENST00000509416' => array(
			'start' => '28435449',
			'end' => '28600275',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-123O22.1-001'
		),
		'ENST00000514802' => array(
			'start' => '28996524',
			'end' => '29014594',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-292B1.2-001'
		),
		'ENST00000503460' => array(
			'start' => '28823244',
			'end' => '28824211',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'MESTP3-001'
		),
		'ENST00000610373' => array(
			'start' => '29010619',
			'end' => '29011021',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RP11-769N22.2-001'
		)
	),
	'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_00098M_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00098M_0001' => array(
		'genes_in_region' => array(
			'ENSG00000243548' => array(
				[maximum depth reached]
			),
			'ENSG00000248176' => array(
				[maximum depth reached]
			),
			'ENSG00000249228' => array(
				[maximum depth reached]
			),
			'ENSG00000250064' => array(
				[maximum depth reached]
			),
			'ENSG00000250190' => array(
				[maximum depth reached]
			),
			'ENSG00000250927' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Brain',
			(int) 1 => 'Ovary',
			(int) 2 => 'Placenta',
			(int) 3 => 'Testis',
			(int) 4 => 'Brain',
			(int) 5 => 'Colon',
			(int) 6 => 'Muscle',
			(int) 7 => 'Ovary',
			(int) 8 => 'Testis',
			(int) 9 => 'Adipose',
			(int) 10 => 'Adrenal',
			(int) 11 => 'Brain',
			(int) 12 => 'Breast',
			(int) 13 => 'Colon',
			(int) 14 => 'Heart',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Muscle',
			(int) 19 => 'Ovary',
			(int) 20 => 'Placenta',
			(int) 21 => 'Testis',
			(int) 22 => 'Ovary',
			(int) 23 => 'Testis',
			(int) 24 => 'Adipose',
			(int) 25 => 'Testis',
			(int) 26 => 'Colon',
			(int) 27 => 'Ovary',
			(int) 28 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000243548' => 'RNA, 7SL, cytoplasmic 101, pseudogene',
	'ENSG00000248176' => null,
	'ENSG00000249228' => null,
	'ENSG00000250064' => null,
	'ENSG00000250190' => null,
	'ENSG00000250927' => 'mesoderm specific transcript pseudogene 3',
	'ENSG00000276507' => null
)
$gene_name_arr = array(
	'ENSG00000243548' => 'RN7SL101P',
	'ENSG00000248176' => 'RP11-472K22.1',
	'ENSG00000249228' => 'RP11-769N22.1',
	'ENSG00000250064' => 'RP11-123O22.1',
	'ENSG00000250190' => 'RP11-292B1.2',
	'ENSG00000250927' => 'MESTP3',
	'ENSG00000276507' => 'RP11-769N22.2'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00098M_0001',
			'tax_id' => '9606',
			'chromosome' => '4',
			'seq_start' => '28590930',
			'seq_end' => '29192066',
			'region_length' => '601136',
			'region_type' => 'VISTA',
			'el_id' => 'hs601'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00098M_0002',
			'tax_id' => '10090',
			'chromosome' => '5',
			'seq_start' => '55676101',
			'seq_end' => '56277173',
			'region_length' => '601072',
			'region_type' => 'VISTA',
			'el_id' => 'hs601'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 2 => 'Adrenal',
	(int) 3 => 'Brain',
	(int) 6 => 'Breast',
	(int) 7 => 'Colon',
	(int) 10 => 'Heart',
	(int) 11 => 'Kidney',
	(int) 12 => 'Liver',
	(int) 13 => 'Lung',
	(int) 14 => 'Muscle',
	(int) 16 => 'Ovary',
	(int) 21 => 'Placenta',
	(int) 23 => '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(
	'ENST00000496350' => array(
		'start' => '28711198',
		'end' => '28711476',
		'transcript_biotype' => 'misc_RNA',
		'transcript_name' => 'RN7SL101P-201'
	),
	'ENST00000503299' => array(
		'start' => '29118308',
		'end' => '29202770',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-472K22.1-001'
	),
	'ENST00000514855' => array(
		'start' => '29046591',
		'end' => '29048765',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-769N22.1-001'
	),
	'ENST00000509416' => array(
		'start' => '28435449',
		'end' => '28600275',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-123O22.1-001'
	),
	'ENST00000514802' => array(
		'start' => '28996524',
		'end' => '29014594',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-292B1.2-001'
	),
	'ENST00000503460' => array(
		'start' => '28823244',
		'end' => '28824211',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'MESTP3-001'
	),
	'ENST00000610373' => array(
		'start' => '29010619',
		'end' => '29011021',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RP11-769N22.2-001'
	)
)
$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_00098M_0001' => array(
		'genes_in_region' => array(
			'ENSG00000243548' => array(
				[maximum depth reached]
			),
			'ENSG00000248176' => array(
				[maximum depth reached]
			),
			'ENSG00000249228' => array(
				[maximum depth reached]
			),
			'ENSG00000250064' => array(
				[maximum depth reached]
			),
			'ENSG00000250190' => array(
				[maximum depth reached]
			),
			'ENSG00000250927' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Brain',
			(int) 1 => 'Ovary',
			(int) 2 => 'Placenta',
			(int) 3 => 'Testis',
			(int) 4 => 'Brain',
			(int) 5 => 'Colon',
			(int) 6 => 'Muscle',
			(int) 7 => 'Ovary',
			(int) 8 => 'Testis',
			(int) 9 => 'Adipose',
			(int) 10 => 'Adrenal',
			(int) 11 => 'Brain',
			(int) 12 => 'Breast',
			(int) 13 => 'Colon',
			(int) 14 => 'Heart',
			(int) 15 => 'Kidney',
			(int) 16 => 'Liver',
			(int) 17 => 'Lung',
			(int) 18 => 'Muscle',
			(int) 19 => 'Ovary',
			(int) 20 => 'Placenta',
			(int) 21 => 'Testis',
			(int) 22 => 'Ovary',
			(int) 23 => 'Testis',
			(int) 24 => 'Adipose',
			(int) 25 => 'Testis',
			(int) 26 => 'Colon',
			(int) 27 => 'Ovary',
			(int) 28 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00098M_0002',
		'tax_id' => '10090',
		'chromosome' => '5',
		'seq_start' => '55676101',
		'seq_end' => '56277173',
		'region_length' => '601072',
		'region_type' => 'VISTA',
		'el_id' => 'hs601'
	)
)
$gene_el = array(
	'ENST00000503460' => array(
		'Colon' => array(
			'average_FPKM' => '0.396',
			'stddev_FPKM' => '0.00'
		),
		'Ovary' => array(
			'average_FPKM' => '0.042',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.055',
			'stddev_FPKM' => '0.01'
		)
	)
)
$gene_key = 'ENSG00000250927'
$is_first = false
$tran_el = array(
	'Colon' => array(
		'average_FPKM' => '0.396',
		'stddev_FPKM' => '0.00'
	),
	'Ovary' => array(
		'average_FPKM' => '0.042',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.055',
		'stddev_FPKM' => '0.01'
	)
)
$tran_key = 'ENST00000503460'
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
hs601		VISTA	10090	5:55676101-56277173
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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