Institute of Cardiovascular Regeneration Webtool Repository

Source ID	Type	Tax ID	Position
hs797	VISTA	9606	18:39618696-40219610
Gene	Transcript	Position	Biotype
ENSG00000261715 (LINC01477) long intergenic non-protein coding RNA 1477	ENST00000566101 (LINC01477-001)	40066286-40099233	lincRNA
ENSG00000267374 (LINC00669) long intergenic non-protein coding RNA 669	ENST00000591469 (LINC00669-002)	39207627-39340638	lincRNA
ENST00000591629 (LINC00669-001)	39206924-39800318	lincRNA
ENSG00000267413 (RP11-636O21.1)	ENST00000585822 (RP11-636O21.1-001)	39841174-39924840	lincRNA
ENSG00000267664 (RPL17P45) ribosomal protein L17 pseudogene 45	ENST00000586289 (RPL17P45-001)	40143926-40144504	processed_pseudogene
ENSG00000279034 (RP11-5A1.1)	ENST00000624119 (RP11-5A1.1-001)	40062903-40066471	TEC

Notice (8): Undefined index: CIL_000891_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_000891_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000212354' => 'RNA, U6 small nuclear 1242, pseudogene',
		'ENSG00000261715' => 'long intergenic non-protein coding RNA 1477',
		'ENSG00000266148' => 'microRNA 5583-1',
		'ENSG00000267374' => 'long intergenic non-protein coding RNA 669',
		'ENSG00000267413' => null,
		'ENSG00000267664' => 'ribosomal protein L17 pseudogene 45',
		'ENSG00000279034' => null,
		'ENSMUSG00000087940' => 'predicted gene, 24246'
	),
	'gene_name_arr' => array(
		'ENSG00000212354' => 'RNU6-1242P',
		'ENSG00000261715' => 'LINC01477',
		'ENSG00000266148' => 'MIR5583-1',
		'ENSG00000267374' => 'LINC00669',
		'ENSG00000267413' => 'RP11-636O21.1',
		'ENSG00000267664' => 'RPL17P45',
		'ENSG00000279034' => 'RP11-5A1.1',
		'ENSMUSG00000087940' => 'Gm24246'
	),
	'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) 3 => 'Adrenal',
		(int) 5 => 'Brain',
		(int) 8 => 'Breast',
		(int) 11 => 'Colon',
		(int) 12 => 'Heart',
		(int) 13 => 'Kidney',
		(int) 14 => 'Liver',
		(int) 17 => 'Lung',
		(int) 19 => 'Ovary',
		(int) 21 => 'Placenta',
		(int) 25 => '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) 9,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000391052' => array(
			'start' => '39678520',
			'end' => '39678622',
			'transcript_biotype' => 'snRNA',
			'transcript_name' => 'RNU6-1242P-201'
		),
		'ENST00000566101' => array(
			'start' => '40066286',
			'end' => '40099233',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC01477-001'
		),
		'ENST00000580941' => array(
			'start' => '39676721',
			'end' => '39676779',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'MIR5583-1-201'
		),
		'ENST00000591469' => array(
			'start' => '39207627',
			'end' => '39340638',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC00669-002'
		),
		'ENST00000591629' => array(
			'start' => '39206924',
			'end' => '39800318',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC00669-001'
		),
		'ENST00000585822' => array(
			'start' => '39841174',
			'end' => '39924840',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-636O21.1-001'
		),
		'ENST00000586289' => array(
			'start' => '40143926',
			'end' => '40144504',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RPL17P45-001'
		),
		'ENST00000624119' => array(
			'start' => '40062903',
			'end' => '40066471',
			'transcript_biotype' => 'TEC',
			'transcript_name' => 'RP11-5A1.1-001'
		),
		'ENSMUST00000157315' => array(
			'start' => '28309760',
			'end' => '28309891',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm24246-201'
		)
	),
	'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_000891_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_000891_0001' => array(
		'genes_in_region' => array(
			'ENSG00000261715' => array(
				[maximum depth reached]
			),
			'ENSG00000267374' => array(
				[maximum depth reached]
			),
			'ENSG00000267413' => array(
				[maximum depth reached]
			),
			'ENSG00000267664' => array(
				[maximum depth reached]
			),
			'ENSG00000279034' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adipose',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Liver',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis',
			(int) 7 => 'Adipose',
			(int) 8 => 'Adrenal',
			(int) 9 => 'Breast',
			(int) 10 => 'Colon',
			(int) 11 => 'Liver',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Brain',
			(int) 18 => 'Breast',
			(int) 19 => 'Heart',
			(int) 20 => 'Kidney',
			(int) 21 => 'Liver',
			(int) 22 => 'Lung',
			(int) 23 => 'Ovary',
			(int) 24 => 'Placenta',
			(int) 25 => 'Testis',
			(int) 26 => 'Lung',
			(int) 27 => 'Brain',
			(int) 28 => 'Placenta',
			(int) 29 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000212354' => 'RNA, U6 small nuclear 1242, pseudogene',
	'ENSG00000261715' => 'long intergenic non-protein coding RNA 1477',
	'ENSG00000266148' => 'microRNA 5583-1',
	'ENSG00000267374' => 'long intergenic non-protein coding RNA 669',
	'ENSG00000267413' => null,
	'ENSG00000267664' => 'ribosomal protein L17 pseudogene 45',
	'ENSG00000279034' => null,
	'ENSMUSG00000087940' => 'predicted gene, 24246'
)
$gene_name_arr = array(
	'ENSG00000212354' => 'RNU6-1242P',
	'ENSG00000261715' => 'LINC01477',
	'ENSG00000266148' => 'MIR5583-1',
	'ENSG00000267374' => 'LINC00669',
	'ENSG00000267413' => 'RP11-636O21.1',
	'ENSG00000267664' => 'RPL17P45',
	'ENSG00000279034' => 'RP11-5A1.1',
	'ENSMUSG00000087940' => 'Gm24246'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_000891_0001',
			'tax_id' => '9606',
			'chromosome' => '18',
			'seq_start' => '39618696',
			'seq_end' => '40219610',
			'region_length' => '600914',
			'region_type' => 'VISTA',
			'el_id' => 'hs797'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_000891_0002',
			'tax_id' => '10090',
			'chromosome' => '18',
			'seq_start' => '27861558',
			'seq_end' => '28462566',
			'region_length' => '601008',
			'region_type' => 'VISTA',
			'el_id' => 'hs797'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 3 => 'Adrenal',
	(int) 5 => 'Brain',
	(int) 8 => 'Breast',
	(int) 11 => 'Colon',
	(int) 12 => 'Heart',
	(int) 13 => 'Kidney',
	(int) 14 => 'Liver',
	(int) 17 => 'Lung',
	(int) 19 => 'Ovary',
	(int) 21 => 'Placenta',
	(int) 25 => '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) 9
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000391052' => array(
		'start' => '39678520',
		'end' => '39678622',
		'transcript_biotype' => 'snRNA',
		'transcript_name' => 'RNU6-1242P-201'
	),
	'ENST00000566101' => array(
		'start' => '40066286',
		'end' => '40099233',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC01477-001'
	),
	'ENST00000580941' => array(
		'start' => '39676721',
		'end' => '39676779',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'MIR5583-1-201'
	),
	'ENST00000591469' => array(
		'start' => '39207627',
		'end' => '39340638',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC00669-002'
	),
	'ENST00000591629' => array(
		'start' => '39206924',
		'end' => '39800318',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC00669-001'
	),
	'ENST00000585822' => array(
		'start' => '39841174',
		'end' => '39924840',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-636O21.1-001'
	),
	'ENST00000586289' => array(
		'start' => '40143926',
		'end' => '40144504',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RPL17P45-001'
	),
	'ENST00000624119' => array(
		'start' => '40062903',
		'end' => '40066471',
		'transcript_biotype' => 'TEC',
		'transcript_name' => 'RP11-5A1.1-001'
	),
	'ENSMUST00000157315' => array(
		'start' => '28309760',
		'end' => '28309891',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm24246-201'
	)
)
$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_000891_0001' => array(
		'genes_in_region' => array(
			'ENSG00000261715' => array(
				[maximum depth reached]
			),
			'ENSG00000267374' => array(
				[maximum depth reached]
			),
			'ENSG00000267413' => array(
				[maximum depth reached]
			),
			'ENSG00000267664' => array(
				[maximum depth reached]
			),
			'ENSG00000279034' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adipose',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Liver',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis',
			(int) 7 => 'Adipose',
			(int) 8 => 'Adrenal',
			(int) 9 => 'Breast',
			(int) 10 => 'Colon',
			(int) 11 => 'Liver',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Brain',
			(int) 18 => 'Breast',
			(int) 19 => 'Heart',
			(int) 20 => 'Kidney',
			(int) 21 => 'Liver',
			(int) 22 => 'Lung',
			(int) 23 => 'Ovary',
			(int) 24 => 'Placenta',
			(int) 25 => 'Testis',
			(int) 26 => 'Lung',
			(int) 27 => 'Brain',
			(int) 28 => 'Placenta',
			(int) 29 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_000891_0002',
		'tax_id' => '10090',
		'chromosome' => '18',
		'seq_start' => '27861558',
		'seq_end' => '28462566',
		'region_length' => '601008',
		'region_type' => 'VISTA',
		'el_id' => 'hs797'
	)
)
$gene_el = array(
	'ENST00000624119' => array(
		'Brain' => array(
			'average_FPKM' => '0.003',
			'stddev_FPKM' => '0.00'
		),
		'Placenta' => array(
			'average_FPKM' => '0.009',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.076',
			'stddev_FPKM' => '0.07'
		)
	)
)
$gene_key = 'ENSG00000279034'
$is_first = false
$tran_el = array(
	'Brain' => array(
		'average_FPKM' => '0.003',
		'stddev_FPKM' => '0.00'
	),
	'Placenta' => array(
		'average_FPKM' => '0.009',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.076',
		'stddev_FPKM' => '0.07'
	)
)
$tran_key = 'ENST00000624119'
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_000891_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000212354' => 'RNA, U6 small nuclear 1242, pseudogene',
		'ENSG00000261715' => 'long intergenic non-protein coding RNA 1477',
		'ENSG00000266148' => 'microRNA 5583-1',
		'ENSG00000267374' => 'long intergenic non-protein coding RNA 669',
		'ENSG00000267413' => null,
		'ENSG00000267664' => 'ribosomal protein L17 pseudogene 45',
		'ENSG00000279034' => null,
		'ENSMUSG00000087940' => 'predicted gene, 24246'
	),
	'gene_name_arr' => array(
		'ENSG00000212354' => 'RNU6-1242P',
		'ENSG00000261715' => 'LINC01477',
		'ENSG00000266148' => 'MIR5583-1',
		'ENSG00000267374' => 'LINC00669',
		'ENSG00000267413' => 'RP11-636O21.1',
		'ENSG00000267664' => 'RPL17P45',
		'ENSG00000279034' => 'RP11-5A1.1',
		'ENSMUSG00000087940' => 'Gm24246'
	),
	'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) 3 => 'Adrenal',
		(int) 5 => 'Brain',
		(int) 8 => 'Breast',
		(int) 11 => 'Colon',
		(int) 12 => 'Heart',
		(int) 13 => 'Kidney',
		(int) 14 => 'Liver',
		(int) 17 => 'Lung',
		(int) 19 => 'Ovary',
		(int) 21 => 'Placenta',
		(int) 25 => '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) 9,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000391052' => array(
			'start' => '39678520',
			'end' => '39678622',
			'transcript_biotype' => 'snRNA',
			'transcript_name' => 'RNU6-1242P-201'
		),
		'ENST00000566101' => array(
			'start' => '40066286',
			'end' => '40099233',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC01477-001'
		),
		'ENST00000580941' => array(
			'start' => '39676721',
			'end' => '39676779',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'MIR5583-1-201'
		),
		'ENST00000591469' => array(
			'start' => '39207627',
			'end' => '39340638',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC00669-002'
		),
		'ENST00000591629' => array(
			'start' => '39206924',
			'end' => '39800318',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC00669-001'
		),
		'ENST00000585822' => array(
			'start' => '39841174',
			'end' => '39924840',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'RP11-636O21.1-001'
		),
		'ENST00000586289' => array(
			'start' => '40143926',
			'end' => '40144504',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RPL17P45-001'
		),
		'ENST00000624119' => array(
			'start' => '40062903',
			'end' => '40066471',
			'transcript_biotype' => 'TEC',
			'transcript_name' => 'RP11-5A1.1-001'
		),
		'ENSMUST00000157315' => array(
			'start' => '28309760',
			'end' => '28309891',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm24246-201'
		)
	),
	'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_000891_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_000891_0001' => array(
		'genes_in_region' => array(
			'ENSG00000261715' => array(
				[maximum depth reached]
			),
			'ENSG00000267374' => array(
				[maximum depth reached]
			),
			'ENSG00000267413' => array(
				[maximum depth reached]
			),
			'ENSG00000267664' => array(
				[maximum depth reached]
			),
			'ENSG00000279034' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adipose',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Liver',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis',
			(int) 7 => 'Adipose',
			(int) 8 => 'Adrenal',
			(int) 9 => 'Breast',
			(int) 10 => 'Colon',
			(int) 11 => 'Liver',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Brain',
			(int) 18 => 'Breast',
			(int) 19 => 'Heart',
			(int) 20 => 'Kidney',
			(int) 21 => 'Liver',
			(int) 22 => 'Lung',
			(int) 23 => 'Ovary',
			(int) 24 => 'Placenta',
			(int) 25 => 'Testis',
			(int) 26 => 'Lung',
			(int) 27 => 'Brain',
			(int) 28 => 'Placenta',
			(int) 29 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000212354' => 'RNA, U6 small nuclear 1242, pseudogene',
	'ENSG00000261715' => 'long intergenic non-protein coding RNA 1477',
	'ENSG00000266148' => 'microRNA 5583-1',
	'ENSG00000267374' => 'long intergenic non-protein coding RNA 669',
	'ENSG00000267413' => null,
	'ENSG00000267664' => 'ribosomal protein L17 pseudogene 45',
	'ENSG00000279034' => null,
	'ENSMUSG00000087940' => 'predicted gene, 24246'
)
$gene_name_arr = array(
	'ENSG00000212354' => 'RNU6-1242P',
	'ENSG00000261715' => 'LINC01477',
	'ENSG00000266148' => 'MIR5583-1',
	'ENSG00000267374' => 'LINC00669',
	'ENSG00000267413' => 'RP11-636O21.1',
	'ENSG00000267664' => 'RPL17P45',
	'ENSG00000279034' => 'RP11-5A1.1',
	'ENSMUSG00000087940' => 'Gm24246'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_000891_0001',
			'tax_id' => '9606',
			'chromosome' => '18',
			'seq_start' => '39618696',
			'seq_end' => '40219610',
			'region_length' => '600914',
			'region_type' => 'VISTA',
			'el_id' => 'hs797'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_000891_0002',
			'tax_id' => '10090',
			'chromosome' => '18',
			'seq_start' => '27861558',
			'seq_end' => '28462566',
			'region_length' => '601008',
			'region_type' => 'VISTA',
			'el_id' => 'hs797'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 3 => 'Adrenal',
	(int) 5 => 'Brain',
	(int) 8 => 'Breast',
	(int) 11 => 'Colon',
	(int) 12 => 'Heart',
	(int) 13 => 'Kidney',
	(int) 14 => 'Liver',
	(int) 17 => 'Lung',
	(int) 19 => 'Ovary',
	(int) 21 => 'Placenta',
	(int) 25 => '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) 9
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000391052' => array(
		'start' => '39678520',
		'end' => '39678622',
		'transcript_biotype' => 'snRNA',
		'transcript_name' => 'RNU6-1242P-201'
	),
	'ENST00000566101' => array(
		'start' => '40066286',
		'end' => '40099233',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC01477-001'
	),
	'ENST00000580941' => array(
		'start' => '39676721',
		'end' => '39676779',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'MIR5583-1-201'
	),
	'ENST00000591469' => array(
		'start' => '39207627',
		'end' => '39340638',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC00669-002'
	),
	'ENST00000591629' => array(
		'start' => '39206924',
		'end' => '39800318',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC00669-001'
	),
	'ENST00000585822' => array(
		'start' => '39841174',
		'end' => '39924840',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'RP11-636O21.1-001'
	),
	'ENST00000586289' => array(
		'start' => '40143926',
		'end' => '40144504',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RPL17P45-001'
	),
	'ENST00000624119' => array(
		'start' => '40062903',
		'end' => '40066471',
		'transcript_biotype' => 'TEC',
		'transcript_name' => 'RP11-5A1.1-001'
	),
	'ENSMUST00000157315' => array(
		'start' => '28309760',
		'end' => '28309891',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm24246-201'
	)
)
$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_000891_0001' => array(
		'genes_in_region' => array(
			'ENSG00000261715' => array(
				[maximum depth reached]
			),
			'ENSG00000267374' => array(
				[maximum depth reached]
			),
			'ENSG00000267413' => array(
				[maximum depth reached]
			),
			'ENSG00000267664' => array(
				[maximum depth reached]
			),
			'ENSG00000279034' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adipose',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Liver',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis',
			(int) 7 => 'Adipose',
			(int) 8 => 'Adrenal',
			(int) 9 => 'Breast',
			(int) 10 => 'Colon',
			(int) 11 => 'Liver',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Brain',
			(int) 18 => 'Breast',
			(int) 19 => 'Heart',
			(int) 20 => 'Kidney',
			(int) 21 => 'Liver',
			(int) 22 => 'Lung',
			(int) 23 => 'Ovary',
			(int) 24 => 'Placenta',
			(int) 25 => 'Testis',
			(int) 26 => 'Lung',
			(int) 27 => 'Brain',
			(int) 28 => 'Placenta',
			(int) 29 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_000891_0002',
		'tax_id' => '10090',
		'chromosome' => '18',
		'seq_start' => '27861558',
		'seq_end' => '28462566',
		'region_length' => '601008',
		'region_type' => 'VISTA',
		'el_id' => 'hs797'
	)
)
$gene_el = array(
	'ENST00000624119' => array(
		'Brain' => array(
			'average_FPKM' => '0.003',
			'stddev_FPKM' => '0.00'
		),
		'Placenta' => array(
			'average_FPKM' => '0.009',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.076',
			'stddev_FPKM' => '0.07'
		)
	)
)
$gene_key = 'ENSG00000279034'
$is_first = false
$tran_el = array(
	'Brain' => array(
		'average_FPKM' => '0.003',
		'stddev_FPKM' => '0.00'
	),
	'Placenta' => array(
		'average_FPKM' => '0.009',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.076',
		'stddev_FPKM' => '0.07'
	)
)
$tran_key = 'ENST00000624119'
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
hs797		VISTA	10090	18:27861558-28462566
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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