Notice (8): Undefined index: CIL_00083C_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_00083C_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000226554' => 'MTCL1 pseudogene 1',
		'ENSG00000226846' => 'long intergenic non-protein coding RNA 348',
		'ENSG00000275653' => null,
		'ENSG00000276841' => null,
		'ENSMUSG00000088538' => 'predicted gene, 23276',
		'ENSMUSG00000089130' => 'predicted gene, 24770',
		'ENSMUSG00000098772' => 'predicted gene, 27441'
	),
	'gene_name_arr' => array(
		'ENSG00000226554' => 'MTCL1P1',
		'ENSG00000226846' => 'LINC00348',
		'ENSG00000275653' => 'AL391123.1',
		'ENSG00000276841' => 'RP11-475F14.1',
		'ENSMUSG00000088538' => 'Gm23276',
		'ENSMUSG00000089130' => 'Gm24770',
		'ENSMUSG00000098772' => 'Gm27441'
	),
	'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 => 'Adrenal',
		(int) 1 => 'Brain',
		(int) 2 => 'Breast',
		(int) 3 => 'Heart',
		(int) 4 => 'Liver',
		(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) 7,
	'longest_tissue_len' => (int) 7,
	'transcript_data' => array(
		'ENST00000446207' => array(
			'start' => '70923664',
			'end' => '70924455',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'MTCL1P1-001'
		),
		'ENST00000428761' => array(
			'start' => '71015141',
			'end' => '71168417',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC00348-001'
		),
		'ENST00000617891' => array(
			'start' => '70901151',
			'end' => '70901241',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AL391123.1-201'
		),
		'ENST00000621719' => array(
			'start' => '70564267',
			'end' => '70564437',
			'transcript_biotype' => 'unprocessed_pseudogene',
			'transcript_name' => 'RP11-475F14.1-001'
		),
		'ENSMUST00000157913' => array(
			'start' => '97336495',
			'end' => '97336632',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm23276-201'
		),
		'ENSMUST00000158505' => array(
			'start' => '96945019',
			'end' => '96945110',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm24770-201'
		),
		'ENSMUST00000185000' => array(
			'start' => '97049481',
			'end' => '97049585',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'Gm27441-201'
		)
	),
	'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_00083C_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00083C_0001' => array(
		'genes_in_region' => array(
			'ENSG00000226554' => array(
				[maximum depth reached]
			),
			'ENSG00000226846' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Heart',
			(int) 5 => 'Liver',
			(int) 6 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000226554' => 'MTCL1 pseudogene 1',
	'ENSG00000226846' => 'long intergenic non-protein coding RNA 348',
	'ENSG00000275653' => null,
	'ENSG00000276841' => null,
	'ENSMUSG00000088538' => 'predicted gene, 23276',
	'ENSMUSG00000089130' => 'predicted gene, 24770',
	'ENSMUSG00000098772' => 'predicted gene, 27441'
)
$gene_name_arr = array(
	'ENSG00000226554' => 'MTCL1P1',
	'ENSG00000226846' => 'LINC00348',
	'ENSG00000275653' => 'AL391123.1',
	'ENSG00000276841' => 'RP11-475F14.1',
	'ENSMUSG00000088538' => 'Gm23276',
	'ENSMUSG00000089130' => 'Gm24770',
	'ENSMUSG00000098772' => 'Gm27441'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00083C_0001',
			'tax_id' => '9606',
			'chromosome' => '13',
			'seq_start' => '70483961',
			'seq_end' => '71085375',
			'region_length' => '601414',
			'region_type' => 'VISTA',
			'el_id' => 'hs540'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00083C_0002',
			'tax_id' => '10090',
			'chromosome' => '14',
			'seq_start' => '96800876',
			'seq_end' => '97402241',
			'region_length' => '601365',
			'region_type' => 'VISTA',
			'el_id' => 'hs540'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adrenal',
	(int) 1 => 'Brain',
	(int) 2 => 'Breast',
	(int) 3 => 'Heart',
	(int) 4 => 'Liver',
	(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) 7
$longest_tissue_len = (int) 7
$transcript_data = array(
	'ENST00000446207' => array(
		'start' => '70923664',
		'end' => '70924455',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'MTCL1P1-001'
	),
	'ENST00000428761' => array(
		'start' => '71015141',
		'end' => '71168417',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC00348-001'
	),
	'ENST00000617891' => array(
		'start' => '70901151',
		'end' => '70901241',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AL391123.1-201'
	),
	'ENST00000621719' => array(
		'start' => '70564267',
		'end' => '70564437',
		'transcript_biotype' => 'unprocessed_pseudogene',
		'transcript_name' => 'RP11-475F14.1-001'
	),
	'ENSMUST00000157913' => array(
		'start' => '97336495',
		'end' => '97336632',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm23276-201'
	),
	'ENSMUST00000158505' => array(
		'start' => '96945019',
		'end' => '96945110',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm24770-201'
	),
	'ENSMUST00000185000' => array(
		'start' => '97049481',
		'end' => '97049585',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'Gm27441-201'
	)
)
$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_00083C_0001' => array(
		'genes_in_region' => array(
			'ENSG00000226554' => array(
				[maximum depth reached]
			),
			'ENSG00000226846' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Heart',
			(int) 5 => 'Liver',
			(int) 6 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00083C_0002',
		'tax_id' => '10090',
		'chromosome' => '14',
		'seq_start' => '96800876',
		'seq_end' => '97402241',
		'region_length' => '601365',
		'region_type' => 'VISTA',
		'el_id' => 'hs540'
	)
)
$gene_el = array(
	'ENST00000428761' => array(
		'Adrenal' => array(
			'average_FPKM' => '0.009',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.042',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.031',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.025',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.058',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.392',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000226846'
$is_first = false
$tran_el = array(
	'Adrenal' => array(
		'average_FPKM' => '0.009',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.042',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.031',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.025',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.058',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.392',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000428761'
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_00083C_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000226554' => 'MTCL1 pseudogene 1',
		'ENSG00000226846' => 'long intergenic non-protein coding RNA 348',
		'ENSG00000275653' => null,
		'ENSG00000276841' => null,
		'ENSMUSG00000088538' => 'predicted gene, 23276',
		'ENSMUSG00000089130' => 'predicted gene, 24770',
		'ENSMUSG00000098772' => 'predicted gene, 27441'
	),
	'gene_name_arr' => array(
		'ENSG00000226554' => 'MTCL1P1',
		'ENSG00000226846' => 'LINC00348',
		'ENSG00000275653' => 'AL391123.1',
		'ENSG00000276841' => 'RP11-475F14.1',
		'ENSMUSG00000088538' => 'Gm23276',
		'ENSMUSG00000089130' => 'Gm24770',
		'ENSMUSG00000098772' => 'Gm27441'
	),
	'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 => 'Adrenal',
		(int) 1 => 'Brain',
		(int) 2 => 'Breast',
		(int) 3 => 'Heart',
		(int) 4 => 'Liver',
		(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) 7,
	'longest_tissue_len' => (int) 7,
	'transcript_data' => array(
		'ENST00000446207' => array(
			'start' => '70923664',
			'end' => '70924455',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'MTCL1P1-001'
		),
		'ENST00000428761' => array(
			'start' => '71015141',
			'end' => '71168417',
			'transcript_biotype' => 'lincRNA',
			'transcript_name' => 'LINC00348-001'
		),
		'ENST00000617891' => array(
			'start' => '70901151',
			'end' => '70901241',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AL391123.1-201'
		),
		'ENST00000621719' => array(
			'start' => '70564267',
			'end' => '70564437',
			'transcript_biotype' => 'unprocessed_pseudogene',
			'transcript_name' => 'RP11-475F14.1-001'
		),
		'ENSMUST00000157913' => array(
			'start' => '97336495',
			'end' => '97336632',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm23276-201'
		),
		'ENSMUST00000158505' => array(
			'start' => '96945019',
			'end' => '96945110',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'Gm24770-201'
		),
		'ENSMUST00000185000' => array(
			'start' => '97049481',
			'end' => '97049585',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'Gm27441-201'
		)
	),
	'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_00083C_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00083C_0001' => array(
		'genes_in_region' => array(
			'ENSG00000226554' => array(
				[maximum depth reached]
			),
			'ENSG00000226846' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Heart',
			(int) 5 => 'Liver',
			(int) 6 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000226554' => 'MTCL1 pseudogene 1',
	'ENSG00000226846' => 'long intergenic non-protein coding RNA 348',
	'ENSG00000275653' => null,
	'ENSG00000276841' => null,
	'ENSMUSG00000088538' => 'predicted gene, 23276',
	'ENSMUSG00000089130' => 'predicted gene, 24770',
	'ENSMUSG00000098772' => 'predicted gene, 27441'
)
$gene_name_arr = array(
	'ENSG00000226554' => 'MTCL1P1',
	'ENSG00000226846' => 'LINC00348',
	'ENSG00000275653' => 'AL391123.1',
	'ENSG00000276841' => 'RP11-475F14.1',
	'ENSMUSG00000088538' => 'Gm23276',
	'ENSMUSG00000089130' => 'Gm24770',
	'ENSMUSG00000098772' => 'Gm27441'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00083C_0001',
			'tax_id' => '9606',
			'chromosome' => '13',
			'seq_start' => '70483961',
			'seq_end' => '71085375',
			'region_length' => '601414',
			'region_type' => 'VISTA',
			'el_id' => 'hs540'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00083C_0002',
			'tax_id' => '10090',
			'chromosome' => '14',
			'seq_start' => '96800876',
			'seq_end' => '97402241',
			'region_length' => '601365',
			'region_type' => 'VISTA',
			'el_id' => 'hs540'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adrenal',
	(int) 1 => 'Brain',
	(int) 2 => 'Breast',
	(int) 3 => 'Heart',
	(int) 4 => 'Liver',
	(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) 7
$longest_tissue_len = (int) 7
$transcript_data = array(
	'ENST00000446207' => array(
		'start' => '70923664',
		'end' => '70924455',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'MTCL1P1-001'
	),
	'ENST00000428761' => array(
		'start' => '71015141',
		'end' => '71168417',
		'transcript_biotype' => 'lincRNA',
		'transcript_name' => 'LINC00348-001'
	),
	'ENST00000617891' => array(
		'start' => '70901151',
		'end' => '70901241',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AL391123.1-201'
	),
	'ENST00000621719' => array(
		'start' => '70564267',
		'end' => '70564437',
		'transcript_biotype' => 'unprocessed_pseudogene',
		'transcript_name' => 'RP11-475F14.1-001'
	),
	'ENSMUST00000157913' => array(
		'start' => '97336495',
		'end' => '97336632',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm23276-201'
	),
	'ENSMUST00000158505' => array(
		'start' => '96945019',
		'end' => '96945110',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'Gm24770-201'
	),
	'ENSMUST00000185000' => array(
		'start' => '97049481',
		'end' => '97049585',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'Gm27441-201'
	)
)
$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_00083C_0001' => array(
		'genes_in_region' => array(
			'ENSG00000226554' => array(
				[maximum depth reached]
			),
			'ENSG00000226846' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Testis',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Heart',
			(int) 5 => 'Liver',
			(int) 6 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00083C_0002',
		'tax_id' => '10090',
		'chromosome' => '14',
		'seq_start' => '96800876',
		'seq_end' => '97402241',
		'region_length' => '601365',
		'region_type' => 'VISTA',
		'el_id' => 'hs540'
	)
)
$gene_el = array(
	'ENST00000428761' => array(
		'Adrenal' => array(
			'average_FPKM' => '0.009',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.042',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.031',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.025',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.058',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.392',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000226846'
$is_first = false
$tran_el = array(
	'Adrenal' => array(
		'average_FPKM' => '0.009',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.042',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.031',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.025',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.058',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.392',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000428761'
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
hs540		VISTA	10090	14:96800876-97402241
Gene		Transcript	Position	Biotype