Institute of Cardiovascular Regeneration Webtool Repository

Region Summary

Notice (8): Undefined index: CIL_00057P_0001 [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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
		'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
		'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
		'ENSMUSG00000050158' => 'olfactory receptor 165',
		'ENSMUSG00000050742' => 'olfactory receptor 164',
		'ENSMUSG00000089036' => 'predicted gene, 22158',
		'ENSMUSG00000095529' => 'predicted gene, 23612'
	),
	'gene_name_arr' => array(
		'ENSG00000162727' => 'OR2M5',
		'ENSG00000198601' => 'OR2M2',
		'ENSG00000228198' => 'OR2M3',
		'ENSMUSG00000050158' => 'Olfr165',
		'ENSMUSG00000050742' => 'Olfr164',
		'ENSMUSG00000089036' => 'Gm22158',
		'ENSMUSG00000095529' => 'Gm23612'
	),
	'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 => 'Colon',
		(int) 2 => 'Liver',
		(int) 3 => 'Muscle',
		(int) 4 => 'Placenta',
		(int) 5 => '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) 8,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000366476' => array(
			'start' => '248145148',
			'end' => '248146086',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M5-001'
		),
		'ENST00000359682' => array(
			'start' => '248179986',
			'end' => '248181029',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M2-001'
		),
		'ENST00000456743' => array(
			'start' => '248203068',
			'end' => '248204006',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M3-001'
		),
		'ENSMUST00000052516' => array(
			'start' => '19407039',
			'end' => '19408078',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr165-201'
		),
		'ENSMUST00000056727' => array(
			'start' => '19285743',
			'end' => '19286837',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr164-201'
		),
		'ENSMUST00000158411' => array(
			'start' => '19307699',
			'end' => '19307824',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm22158-201'
		),
		'ENSMUST00000103823' => array(
			'start' => '19319686',
			'end' => '19319795',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'Gm23612-201'
		)
	),
	'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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
	'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
	'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
	'ENSMUSG00000050158' => 'olfactory receptor 165',
	'ENSMUSG00000050742' => 'olfactory receptor 164',
	'ENSMUSG00000089036' => 'predicted gene, 22158',
	'ENSMUSG00000095529' => 'predicted gene, 23612'
)
$gene_name_arr = array(
	'ENSG00000162727' => 'OR2M5',
	'ENSG00000198601' => 'OR2M2',
	'ENSG00000228198' => 'OR2M3',
	'ENSMUSG00000050158' => 'Olfr165',
	'ENSMUSG00000050742' => 'Olfr164',
	'ENSMUSG00000089036' => 'Gm22158',
	'ENSMUSG00000095529' => 'Gm23612'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0001',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248145148',
			'seq_end' => '248181029',
			'region_length' => '35881',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000162727-ENSG00000198601'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0002',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248179986',
			'seq_end' => '248204006',
			'region_length' => '24020',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000198601-ENSG00000228198'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0003',
			'tax_id' => '10090',
			'chromosome' => '16',
			'seq_start' => '19285743',
			'seq_end' => '19408078',
			'region_length' => '122335',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000050742-ENSMUSG00000050158'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Colon',
	(int) 2 => 'Liver',
	(int) 3 => 'Muscle',
	(int) 4 => 'Placenta',
	(int) 5 => '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) 8
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000366476' => array(
		'start' => '248145148',
		'end' => '248146086',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M5-001'
	),
	'ENST00000359682' => array(
		'start' => '248179986',
		'end' => '248181029',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M2-001'
	),
	'ENST00000456743' => array(
		'start' => '248203068',
		'end' => '248204006',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M3-001'
	),
	'ENSMUST00000052516' => array(
		'start' => '19407039',
		'end' => '19408078',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr165-201'
	),
	'ENSMUST00000056727' => array(
		'start' => '19285743',
		'end' => '19286837',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr164-201'
	),
	'ENSMUST00000158411' => array(
		'start' => '19307699',
		'end' => '19307824',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm22158-201'
	),
	'ENSMUST00000103823' => array(
		'start' => '19319686',
		'end' => '19319795',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'Gm23612-201'
	)
)
$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_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00057P_0001',
		'tax_id' => '9606',
		'chromosome' => '1',
		'seq_start' => '248145148',
		'seq_end' => '248181029',
		'region_length' => '35881',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000162727-ENSG00000198601'
	)
)
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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
		'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
		'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
		'ENSMUSG00000050158' => 'olfactory receptor 165',
		'ENSMUSG00000050742' => 'olfactory receptor 164',
		'ENSMUSG00000089036' => 'predicted gene, 22158',
		'ENSMUSG00000095529' => 'predicted gene, 23612'
	),
	'gene_name_arr' => array(
		'ENSG00000162727' => 'OR2M5',
		'ENSG00000198601' => 'OR2M2',
		'ENSG00000228198' => 'OR2M3',
		'ENSMUSG00000050158' => 'Olfr165',
		'ENSMUSG00000050742' => 'Olfr164',
		'ENSMUSG00000089036' => 'Gm22158',
		'ENSMUSG00000095529' => 'Gm23612'
	),
	'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 => 'Colon',
		(int) 2 => 'Liver',
		(int) 3 => 'Muscle',
		(int) 4 => 'Placenta',
		(int) 5 => '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) 8,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000366476' => array(
			'start' => '248145148',
			'end' => '248146086',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M5-001'
		),
		'ENST00000359682' => array(
			'start' => '248179986',
			'end' => '248181029',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M2-001'
		),
		'ENST00000456743' => array(
			'start' => '248203068',
			'end' => '248204006',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M3-001'
		),
		'ENSMUST00000052516' => array(
			'start' => '19407039',
			'end' => '19408078',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr165-201'
		),
		'ENSMUST00000056727' => array(
			'start' => '19285743',
			'end' => '19286837',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr164-201'
		),
		'ENSMUST00000158411' => array(
			'start' => '19307699',
			'end' => '19307824',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm22158-201'
		),
		'ENSMUST00000103823' => array(
			'start' => '19319686',
			'end' => '19319795',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'Gm23612-201'
		)
	),
	'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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
	'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
	'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
	'ENSMUSG00000050158' => 'olfactory receptor 165',
	'ENSMUSG00000050742' => 'olfactory receptor 164',
	'ENSMUSG00000089036' => 'predicted gene, 22158',
	'ENSMUSG00000095529' => 'predicted gene, 23612'
)
$gene_name_arr = array(
	'ENSG00000162727' => 'OR2M5',
	'ENSG00000198601' => 'OR2M2',
	'ENSG00000228198' => 'OR2M3',
	'ENSMUSG00000050158' => 'Olfr165',
	'ENSMUSG00000050742' => 'Olfr164',
	'ENSMUSG00000089036' => 'Gm22158',
	'ENSMUSG00000095529' => 'Gm23612'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0001',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248145148',
			'seq_end' => '248181029',
			'region_length' => '35881',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000162727-ENSG00000198601'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0002',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248179986',
			'seq_end' => '248204006',
			'region_length' => '24020',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000198601-ENSG00000228198'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0003',
			'tax_id' => '10090',
			'chromosome' => '16',
			'seq_start' => '19285743',
			'seq_end' => '19408078',
			'region_length' => '122335',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000050742-ENSMUSG00000050158'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Colon',
	(int) 2 => 'Liver',
	(int) 3 => 'Muscle',
	(int) 4 => 'Placenta',
	(int) 5 => '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) 8
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000366476' => array(
		'start' => '248145148',
		'end' => '248146086',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M5-001'
	),
	'ENST00000359682' => array(
		'start' => '248179986',
		'end' => '248181029',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M2-001'
	),
	'ENST00000456743' => array(
		'start' => '248203068',
		'end' => '248204006',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M3-001'
	),
	'ENSMUST00000052516' => array(
		'start' => '19407039',
		'end' => '19408078',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr165-201'
	),
	'ENSMUST00000056727' => array(
		'start' => '19285743',
		'end' => '19286837',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr164-201'
	),
	'ENSMUST00000158411' => array(
		'start' => '19307699',
		'end' => '19307824',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm22158-201'
	),
	'ENSMUST00000103823' => array(
		'start' => '19319686',
		'end' => '19319795',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'Gm23612-201'
	)
)
$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_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00057P_0001',
		'tax_id' => '9606',
		'chromosome' => '1',
		'seq_start' => '248145148',
		'seq_end' => '248181029',
		'region_length' => '35881',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000162727-ENSG00000198601'
	)
)
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
ENSG00000162727-ENSG00000198601		CGP	9606	1:248145148-248181029
Gene		Transcript	Position	Biotype

CIL_00057P_0002 (Click to Hide/Show)

Notice (8): Undefined index: CIL_00057P_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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
		'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
		'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
		'ENSMUSG00000050158' => 'olfactory receptor 165',
		'ENSMUSG00000050742' => 'olfactory receptor 164',
		'ENSMUSG00000089036' => 'predicted gene, 22158',
		'ENSMUSG00000095529' => 'predicted gene, 23612'
	),
	'gene_name_arr' => array(
		'ENSG00000162727' => 'OR2M5',
		'ENSG00000198601' => 'OR2M2',
		'ENSG00000228198' => 'OR2M3',
		'ENSMUSG00000050158' => 'Olfr165',
		'ENSMUSG00000050742' => 'Olfr164',
		'ENSMUSG00000089036' => 'Gm22158',
		'ENSMUSG00000095529' => 'Gm23612'
	),
	'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 => 'Colon',
		(int) 2 => 'Liver',
		(int) 3 => 'Muscle',
		(int) 4 => 'Placenta',
		(int) 5 => '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) 8,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000366476' => array(
			'start' => '248145148',
			'end' => '248146086',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M5-001'
		),
		'ENST00000359682' => array(
			'start' => '248179986',
			'end' => '248181029',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M2-001'
		),
		'ENST00000456743' => array(
			'start' => '248203068',
			'end' => '248204006',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M3-001'
		),
		'ENSMUST00000052516' => array(
			'start' => '19407039',
			'end' => '19408078',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr165-201'
		),
		'ENSMUST00000056727' => array(
			'start' => '19285743',
			'end' => '19286837',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr164-201'
		),
		'ENSMUST00000158411' => array(
			'start' => '19307699',
			'end' => '19307824',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm22158-201'
		),
		'ENSMUST00000103823' => array(
			'start' => '19319686',
			'end' => '19319795',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'Gm23612-201'
		)
	),
	'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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
	'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
	'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
	'ENSMUSG00000050158' => 'olfactory receptor 165',
	'ENSMUSG00000050742' => 'olfactory receptor 164',
	'ENSMUSG00000089036' => 'predicted gene, 22158',
	'ENSMUSG00000095529' => 'predicted gene, 23612'
)
$gene_name_arr = array(
	'ENSG00000162727' => 'OR2M5',
	'ENSG00000198601' => 'OR2M2',
	'ENSG00000228198' => 'OR2M3',
	'ENSMUSG00000050158' => 'Olfr165',
	'ENSMUSG00000050742' => 'Olfr164',
	'ENSMUSG00000089036' => 'Gm22158',
	'ENSMUSG00000095529' => 'Gm23612'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0001',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248145148',
			'seq_end' => '248181029',
			'region_length' => '35881',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000162727-ENSG00000198601'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0002',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248179986',
			'seq_end' => '248204006',
			'region_length' => '24020',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000198601-ENSG00000228198'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0003',
			'tax_id' => '10090',
			'chromosome' => '16',
			'seq_start' => '19285743',
			'seq_end' => '19408078',
			'region_length' => '122335',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000050742-ENSMUSG00000050158'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Colon',
	(int) 2 => 'Liver',
	(int) 3 => 'Muscle',
	(int) 4 => 'Placenta',
	(int) 5 => '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) 8
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000366476' => array(
		'start' => '248145148',
		'end' => '248146086',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M5-001'
	),
	'ENST00000359682' => array(
		'start' => '248179986',
		'end' => '248181029',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M2-001'
	),
	'ENST00000456743' => array(
		'start' => '248203068',
		'end' => '248204006',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M3-001'
	),
	'ENSMUST00000052516' => array(
		'start' => '19407039',
		'end' => '19408078',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr165-201'
	),
	'ENSMUST00000056727' => array(
		'start' => '19285743',
		'end' => '19286837',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr164-201'
	),
	'ENSMUST00000158411' => array(
		'start' => '19307699',
		'end' => '19307824',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm22158-201'
	),
	'ENSMUST00000103823' => array(
		'start' => '19319686',
		'end' => '19319795',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'Gm23612-201'
	)
)
$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_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00057P_0002',
		'tax_id' => '9606',
		'chromosome' => '1',
		'seq_start' => '248179986',
		'seq_end' => '248204006',
		'region_length' => '24020',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000198601-ENSG00000228198'
	)
)
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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
		'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
		'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
		'ENSMUSG00000050158' => 'olfactory receptor 165',
		'ENSMUSG00000050742' => 'olfactory receptor 164',
		'ENSMUSG00000089036' => 'predicted gene, 22158',
		'ENSMUSG00000095529' => 'predicted gene, 23612'
	),
	'gene_name_arr' => array(
		'ENSG00000162727' => 'OR2M5',
		'ENSG00000198601' => 'OR2M2',
		'ENSG00000228198' => 'OR2M3',
		'ENSMUSG00000050158' => 'Olfr165',
		'ENSMUSG00000050742' => 'Olfr164',
		'ENSMUSG00000089036' => 'Gm22158',
		'ENSMUSG00000095529' => 'Gm23612'
	),
	'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 => 'Colon',
		(int) 2 => 'Liver',
		(int) 3 => 'Muscle',
		(int) 4 => 'Placenta',
		(int) 5 => '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) 8,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000366476' => array(
			'start' => '248145148',
			'end' => '248146086',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M5-001'
		),
		'ENST00000359682' => array(
			'start' => '248179986',
			'end' => '248181029',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M2-001'
		),
		'ENST00000456743' => array(
			'start' => '248203068',
			'end' => '248204006',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'OR2M3-001'
		),
		'ENSMUST00000052516' => array(
			'start' => '19407039',
			'end' => '19408078',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr165-201'
		),
		'ENSMUST00000056727' => array(
			'start' => '19285743',
			'end' => '19286837',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Olfr164-201'
		),
		'ENSMUST00000158411' => array(
			'start' => '19307699',
			'end' => '19307824',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm22158-201'
		),
		'ENSMUST00000103823' => array(
			'start' => '19319686',
			'end' => '19319795',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'Gm23612-201'
		)
	),
	'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_00057P_0003' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000162727' => 'olfactory receptor, family 2, subfamily M, member 5',
	'ENSG00000198601' => 'olfactory receptor, family 2, subfamily M, member 2',
	'ENSG00000228198' => 'olfactory receptor, family 2, subfamily M, member 3',
	'ENSMUSG00000050158' => 'olfactory receptor 165',
	'ENSMUSG00000050742' => 'olfactory receptor 164',
	'ENSMUSG00000089036' => 'predicted gene, 22158',
	'ENSMUSG00000095529' => 'predicted gene, 23612'
)
$gene_name_arr = array(
	'ENSG00000162727' => 'OR2M5',
	'ENSG00000198601' => 'OR2M2',
	'ENSG00000228198' => 'OR2M3',
	'ENSMUSG00000050158' => 'Olfr165',
	'ENSMUSG00000050742' => 'Olfr164',
	'ENSMUSG00000089036' => 'Gm22158',
	'ENSMUSG00000095529' => 'Gm23612'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0001',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248145148',
			'seq_end' => '248181029',
			'region_length' => '35881',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000162727-ENSG00000198601'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0002',
			'tax_id' => '9606',
			'chromosome' => '1',
			'seq_start' => '248179986',
			'seq_end' => '248204006',
			'region_length' => '24020',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000198601-ENSG00000228198'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00057P_0003',
			'tax_id' => '10090',
			'chromosome' => '16',
			'seq_start' => '19285743',
			'seq_end' => '19408078',
			'region_length' => '122335',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000050742-ENSMUSG00000050158'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Colon',
	(int) 2 => 'Liver',
	(int) 3 => 'Muscle',
	(int) 4 => 'Placenta',
	(int) 5 => '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) 8
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000366476' => array(
		'start' => '248145148',
		'end' => '248146086',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M5-001'
	),
	'ENST00000359682' => array(
		'start' => '248179986',
		'end' => '248181029',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M2-001'
	),
	'ENST00000456743' => array(
		'start' => '248203068',
		'end' => '248204006',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'OR2M3-001'
	),
	'ENSMUST00000052516' => array(
		'start' => '19407039',
		'end' => '19408078',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr165-201'
	),
	'ENSMUST00000056727' => array(
		'start' => '19285743',
		'end' => '19286837',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Olfr164-201'
	),
	'ENSMUST00000158411' => array(
		'start' => '19307699',
		'end' => '19307824',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm22158-201'
	),
	'ENSMUST00000103823' => array(
		'start' => '19319686',
		'end' => '19319795',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'Gm23612-201'
	)
)
$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_00057P_0003' => array(
		'genes_in_region' => array(
			'ENSMUSG00000050158' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000050742' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Colon',
			(int) 1 => 'Liver',
			(int) 2 => 'Testis',
			(int) 3 => 'Colon',
			(int) 4 => 'Muscle',
			(int) 5 => 'Placenta',
			(int) 6 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00057P_0002',
		'tax_id' => '9606',
		'chromosome' => '1',
		'seq_start' => '248179986',
		'seq_end' => '248204006',
		'region_length' => '24020',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000198601-ENSG00000228198'
	)
)
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
ENSG00000198601-ENSG00000228198		CGP	9606	1:248179986-248204006
Gene		Transcript	Position	Biotype

CIL_00057P_0003 (Click to Hide/Show)

Source ID	Type	Tax ID	Position
ENSMUSG00000050742-ENSMUSG00000050158	CGP	10090	16:19285743-19408078
Gene	Transcript	Position	Biotype
ENSMUSG00000050158 (Olfr165) olfactory receptor 165	ENSMUST00000052516 (Olfr165-201)	19407039-19408078	protein_coding
ENSMUSG00000050742 (Olfr164) olfactory receptor 164	ENSMUST00000056727 (Olfr164-201)	19285743-19286837	protein_coding

Expression Patterns

Heat Map

Heat Map (Expressed Only)

Numeric Values

Gene	Transcript	Colon	Liver	Muscle	Placenta	Testis
ENSMUSG00000050158	ENSMUST00000052516	2.349±0.53	0.031±0.00	N/A	N/A	0.101±0.03
ENSMUSG00000050742	ENSMUST00000056727	0.105±0.01	N/A	0.079±0.00	0.011±0.00	0.066±0.00

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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