Institute of Cardiovascular Regeneration Webtool Repository

Region Summary

Source ID	Type	Tax ID	Position
NRXN1	UCNEbase	9606	2:49921042-50621486
Gene	Transcript	Position	Biotype
ENSG00000230327 (AC009234.1)	ENST00000457379 (AC009234.1-001)	50588690-50589415	processed_pseudogene

CIL_0007KN_0002 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007KN_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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000230327' => null,
		'ENSG00000276506' => null
	),
	'gene_name_arr' => array(
		'ENSG00000230327' => 'AC009234.1',
		'ENSG00000276506' => 'AC068715.1'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 1 => 'Adrenal',
		(int) 2 => 'Brain',
		(int) 3 => 'Breast',
		(int) 4 => 'Colon',
		(int) 5 => 'Heart',
		(int) 6 => 'Kidney',
		(int) 7 => 'Liver',
		(int) 8 => 'Lung',
		(int) 9 => 'Muscle',
		(int) 10 => '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) 2,
	'longest_tissue_len' => (int) 7,
	'transcript_data' => array(
		'ENST00000457379' => array(
			'start' => '50588690',
			'end' => '50589415',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'AC009234.1-001'
		),
		'ENST00000611858' => array(
			'start' => '50381657',
			'end' => '50381751',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC068715.1-201'
		)
	),
	'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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000230327' => null,
	'ENSG00000276506' => null
)
$gene_name_arr = array(
	'ENSG00000230327' => 'AC009234.1',
	'ENSG00000276506' => 'AC068715.1'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0001',
			'tax_id' => '9606',
			'chromosome' => '2',
			'seq_start' => '49921042',
			'seq_end' => '50621486',
			'region_length' => '700444',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0002',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90036076',
			'seq_end' => '90164100',
			'region_length' => '128024',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0003',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90701821',
			'seq_end' => '90702250',
			'region_length' => '429',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Brain',
	(int) 3 => 'Breast',
	(int) 4 => 'Colon',
	(int) 5 => 'Heart',
	(int) 6 => 'Kidney',
	(int) 7 => 'Liver',
	(int) 8 => 'Lung',
	(int) 9 => 'Muscle',
	(int) 10 => '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) 2
$longest_tissue_len = (int) 7
$transcript_data = array(
	'ENST00000457379' => array(
		'start' => '50588690',
		'end' => '50589415',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'AC009234.1-001'
	),
	'ENST00000611858' => array(
		'start' => '50381657',
		'end' => '50381751',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC068715.1-201'
	)
)
$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_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007KN_0002',
		'tax_id' => '10090',
		'chromosome' => '17',
		'seq_start' => '90036076',
		'seq_end' => '90164100',
		'region_length' => '128024',
		'region_type' => 'UCNEbase',
		'el_id' => 'NRXN1'
	)
)
$gene_el = array(
	'ENST00000457379' => array(
		'Adipose' => array(
			'average_FPKM' => '0.041',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.060',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.01'
		),
		'Breast' => array(
			'average_FPKM' => '0.040',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.038',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.115',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.322',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.017',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.049',
			'stddev_FPKM' => '0.00'
		),
		'Muscle' => array(
			'average_FPKM' => '0.138',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.019',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000230327'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.041',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.060',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.01'
	),
	'Breast' => array(
		'average_FPKM' => '0.040',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.038',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.115',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.322',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.017',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.049',
		'stddev_FPKM' => '0.00'
	),
	'Muscle' => array(
		'average_FPKM' => '0.138',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.019',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000457379'
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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000230327' => null,
		'ENSG00000276506' => null
	),
	'gene_name_arr' => array(
		'ENSG00000230327' => 'AC009234.1',
		'ENSG00000276506' => 'AC068715.1'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 1 => 'Adrenal',
		(int) 2 => 'Brain',
		(int) 3 => 'Breast',
		(int) 4 => 'Colon',
		(int) 5 => 'Heart',
		(int) 6 => 'Kidney',
		(int) 7 => 'Liver',
		(int) 8 => 'Lung',
		(int) 9 => 'Muscle',
		(int) 10 => '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) 2,
	'longest_tissue_len' => (int) 7,
	'transcript_data' => array(
		'ENST00000457379' => array(
			'start' => '50588690',
			'end' => '50589415',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'AC009234.1-001'
		),
		'ENST00000611858' => array(
			'start' => '50381657',
			'end' => '50381751',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC068715.1-201'
		)
	),
	'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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000230327' => null,
	'ENSG00000276506' => null
)
$gene_name_arr = array(
	'ENSG00000230327' => 'AC009234.1',
	'ENSG00000276506' => 'AC068715.1'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0001',
			'tax_id' => '9606',
			'chromosome' => '2',
			'seq_start' => '49921042',
			'seq_end' => '50621486',
			'region_length' => '700444',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0002',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90036076',
			'seq_end' => '90164100',
			'region_length' => '128024',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0003',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90701821',
			'seq_end' => '90702250',
			'region_length' => '429',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Brain',
	(int) 3 => 'Breast',
	(int) 4 => 'Colon',
	(int) 5 => 'Heart',
	(int) 6 => 'Kidney',
	(int) 7 => 'Liver',
	(int) 8 => 'Lung',
	(int) 9 => 'Muscle',
	(int) 10 => '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) 2
$longest_tissue_len = (int) 7
$transcript_data = array(
	'ENST00000457379' => array(
		'start' => '50588690',
		'end' => '50589415',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'AC009234.1-001'
	),
	'ENST00000611858' => array(
		'start' => '50381657',
		'end' => '50381751',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC068715.1-201'
	)
)
$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_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007KN_0002',
		'tax_id' => '10090',
		'chromosome' => '17',
		'seq_start' => '90036076',
		'seq_end' => '90164100',
		'region_length' => '128024',
		'region_type' => 'UCNEbase',
		'el_id' => 'NRXN1'
	)
)
$gene_el = array(
	'ENST00000457379' => array(
		'Adipose' => array(
			'average_FPKM' => '0.041',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.060',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.01'
		),
		'Breast' => array(
			'average_FPKM' => '0.040',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.038',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.115',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.322',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.017',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.049',
			'stddev_FPKM' => '0.00'
		),
		'Muscle' => array(
			'average_FPKM' => '0.138',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.019',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000230327'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.041',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.060',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.01'
	),
	'Breast' => array(
		'average_FPKM' => '0.040',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.038',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.115',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.322',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.017',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.049',
		'stddev_FPKM' => '0.00'
	),
	'Muscle' => array(
		'average_FPKM' => '0.138',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.019',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000457379'
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
NRXN1		UCNEbase	10090	17:90036076-90164100
Gene		Transcript	Position	Biotype

CIL_0007KN_0003 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007KN_0003 [APP/View/Region/show.ctp, line 46]Code Context
        <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
        <?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
	'region_arr' => array(
		'CIL_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000230327' => null,
		'ENSG00000276506' => null
	),
	'gene_name_arr' => array(
		'ENSG00000230327' => 'AC009234.1',
		'ENSG00000276506' => 'AC068715.1'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 1 => 'Adrenal',
		(int) 2 => 'Brain',
		(int) 3 => 'Breast',
		(int) 4 => 'Colon',
		(int) 5 => 'Heart',
		(int) 6 => 'Kidney',
		(int) 7 => 'Liver',
		(int) 8 => 'Lung',
		(int) 9 => 'Muscle',
		(int) 10 => '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) 2,
	'longest_tissue_len' => (int) 7,
	'transcript_data' => array(
		'ENST00000457379' => array(
			'start' => '50588690',
			'end' => '50589415',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'AC009234.1-001'
		),
		'ENST00000611858' => array(
			'start' => '50381657',
			'end' => '50381751',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC068715.1-201'
		)
	),
	'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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000230327' => null,
	'ENSG00000276506' => null
)
$gene_name_arr = array(
	'ENSG00000230327' => 'AC009234.1',
	'ENSG00000276506' => 'AC068715.1'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0001',
			'tax_id' => '9606',
			'chromosome' => '2',
			'seq_start' => '49921042',
			'seq_end' => '50621486',
			'region_length' => '700444',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0002',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90036076',
			'seq_end' => '90164100',
			'region_length' => '128024',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0003',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90701821',
			'seq_end' => '90702250',
			'region_length' => '429',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Brain',
	(int) 3 => 'Breast',
	(int) 4 => 'Colon',
	(int) 5 => 'Heart',
	(int) 6 => 'Kidney',
	(int) 7 => 'Liver',
	(int) 8 => 'Lung',
	(int) 9 => 'Muscle',
	(int) 10 => '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) 2
$longest_tissue_len = (int) 7
$transcript_data = array(
	'ENST00000457379' => array(
		'start' => '50588690',
		'end' => '50589415',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'AC009234.1-001'
	),
	'ENST00000611858' => array(
		'start' => '50381657',
		'end' => '50381751',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC068715.1-201'
	)
)
$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_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007KN_0003',
		'tax_id' => '10090',
		'chromosome' => '17',
		'seq_start' => '90701821',
		'seq_end' => '90702250',
		'region_length' => '429',
		'region_type' => 'UCNEbase',
		'el_id' => 'NRXN1'
	)
)
$gene_el = array(
	'ENST00000457379' => array(
		'Adipose' => array(
			'average_FPKM' => '0.041',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.060',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.01'
		),
		'Breast' => array(
			'average_FPKM' => '0.040',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.038',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.115',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.322',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.017',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.049',
			'stddev_FPKM' => '0.00'
		),
		'Muscle' => array(
			'average_FPKM' => '0.138',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.019',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000230327'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.041',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.060',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.01'
	),
	'Breast' => array(
		'average_FPKM' => '0.040',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.038',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.115',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.322',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.017',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.049',
		'stddev_FPKM' => '0.00'
	),
	'Muscle' => array(
		'average_FPKM' => '0.138',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.019',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000457379'
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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000230327' => null,
		'ENSG00000276506' => null
	),
	'gene_name_arr' => array(
		'ENSG00000230327' => 'AC009234.1',
		'ENSG00000276506' => 'AC068715.1'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 1 => 'Adrenal',
		(int) 2 => 'Brain',
		(int) 3 => 'Breast',
		(int) 4 => 'Colon',
		(int) 5 => 'Heart',
		(int) 6 => 'Kidney',
		(int) 7 => 'Liver',
		(int) 8 => 'Lung',
		(int) 9 => 'Muscle',
		(int) 10 => '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) 2,
	'longest_tissue_len' => (int) 7,
	'transcript_data' => array(
		'ENST00000457379' => array(
			'start' => '50588690',
			'end' => '50589415',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'AC009234.1-001'
		),
		'ENST00000611858' => array(
			'start' => '50381657',
			'end' => '50381751',
			'transcript_biotype' => 'miRNA',
			'transcript_name' => 'AC068715.1-201'
		)
	),
	'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_0007KN_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000230327' => null,
	'ENSG00000276506' => null
)
$gene_name_arr = array(
	'ENSG00000230327' => 'AC009234.1',
	'ENSG00000276506' => 'AC068715.1'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0001',
			'tax_id' => '9606',
			'chromosome' => '2',
			'seq_start' => '49921042',
			'seq_end' => '50621486',
			'region_length' => '700444',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0002',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90036076',
			'seq_end' => '90164100',
			'region_length' => '128024',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007KN_0003',
			'tax_id' => '10090',
			'chromosome' => '17',
			'seq_start' => '90701821',
			'seq_end' => '90702250',
			'region_length' => '429',
			'region_type' => 'UCNEbase',
			'el_id' => 'NRXN1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Brain',
	(int) 3 => 'Breast',
	(int) 4 => 'Colon',
	(int) 5 => 'Heart',
	(int) 6 => 'Kidney',
	(int) 7 => 'Liver',
	(int) 8 => 'Lung',
	(int) 9 => 'Muscle',
	(int) 10 => '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) 2
$longest_tissue_len = (int) 7
$transcript_data = array(
	'ENST00000457379' => array(
		'start' => '50588690',
		'end' => '50589415',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'AC009234.1-001'
	),
	'ENST00000611858' => array(
		'start' => '50381657',
		'end' => '50381751',
		'transcript_biotype' => 'miRNA',
		'transcript_name' => 'AC068715.1-201'
	)
)
$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_0007KN_0001' => array(
		'genes_in_region' => array(
			'ENSG00000230327' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Brain',
			(int) 3 => 'Breast',
			(int) 4 => 'Colon',
			(int) 5 => 'Heart',
			(int) 6 => 'Kidney',
			(int) 7 => 'Liver',
			(int) 8 => 'Lung',
			(int) 9 => 'Muscle',
			(int) 10 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007KN_0003',
		'tax_id' => '10090',
		'chromosome' => '17',
		'seq_start' => '90701821',
		'seq_end' => '90702250',
		'region_length' => '429',
		'region_type' => 'UCNEbase',
		'el_id' => 'NRXN1'
	)
)
$gene_el = array(
	'ENST00000457379' => array(
		'Adipose' => array(
			'average_FPKM' => '0.041',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.060',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.01'
		),
		'Breast' => array(
			'average_FPKM' => '0.040',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.038',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.115',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.322',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.017',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.049',
			'stddev_FPKM' => '0.00'
		),
		'Muscle' => array(
			'average_FPKM' => '0.138',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.019',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000230327'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.041',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.060',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.01'
	),
	'Breast' => array(
		'average_FPKM' => '0.040',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.038',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.115',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.322',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.017',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.049',
		'stddev_FPKM' => '0.00'
	),
	'Muscle' => array(
		'average_FPKM' => '0.138',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.019',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000457379'
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
NRXN1		UCNEbase	10090	17:90701821-90702250
Gene		Transcript	Position	Biotype

Expression Patterns

Heat Map

Heat Map (Expressed Only)

Numeric Values

Gene

Transcript

Adipose

Adrenal

Brain

Breast

Colon

Heart

Kidney

Liver

Lung

Muscle

Testis

ENSG00000230327

ENST00000457379

0.041±0.00

0.060±0.00

0.279±0.01

0.040±0.00

0.038±0.00

0.115±0.00

0.322±0.00

0.017±0.00

0.049±0.00

0.138±0.00

0.019±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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