Institute of Cardiovascular Regeneration Webtool Repository

Region Summary

Source ID	Type	Tax ID	Position
NFIB	UCNEbase	9606	9:14082259-14308187
Gene	Transcript	Position	Biotype
ENSG00000234982 (RP11-280O24.3)	ENST00000435137 (RP11-280O24.3-001)	14204248-14205039	processed_pseudogene

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CIL_0007O1_0002 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007O1_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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000234982' => null,
		'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
	),
	'gene_name_arr' => array(
		'ENSG00000234982' => 'RP11-280O24.3',
		'ENSMUSG00000084595' => 'n-R5s188'
	),
	'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 => 'Bladder',
		(int) 3 => 'Brain',
		(int) 4 => 'Breast',
		(int) 5 => 'Colon',
		(int) 6 => 'Heart',
		(int) 7 => 'Kidney',
		(int) 8 => 'Liver',
		(int) 9 => 'Lung',
		(int) 10 => 'Muscle',
		(int) 11 => 'Ovary',
		(int) 12 => '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(
		'ENST00000435137' => array(
			'start' => '14204248',
			'end' => '14205039',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RP11-280O24.3-001'
		),
		'ENSMUST00000122646' => array(
			'start' => '82439410',
			'end' => '82439514',
			'transcript_biotype' => 'rRNA',
			'transcript_name' => 'n-R5s188-201'
		)
	),
	'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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000234982' => null,
	'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
)
$gene_name_arr = array(
	'ENSG00000234982' => 'RP11-280O24.3',
	'ENSMUSG00000084595' => 'n-R5s188'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0001',
			'tax_id' => '9606',
			'chromosome' => '9',
			'seq_start' => '14082259',
			'seq_end' => '14308187',
			'region_length' => '225928',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0002',
			'tax_id' => '10090',
			'chromosome' => '4',
			'seq_start' => '82290606',
			'seq_end' => '82499472',
			'region_length' => '208866',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0003',
			'tax_id' => '7955',
			'chromosome' => '3',
			'seq_start' => '14647963',
			'seq_end' => '14648139',
			'region_length' => '176',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Bladder',
	(int) 3 => 'Brain',
	(int) 4 => 'Breast',
	(int) 5 => 'Colon',
	(int) 6 => 'Heart',
	(int) 7 => 'Kidney',
	(int) 8 => 'Liver',
	(int) 9 => 'Lung',
	(int) 10 => 'Muscle',
	(int) 11 => 'Ovary',
	(int) 12 => '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(
	'ENST00000435137' => array(
		'start' => '14204248',
		'end' => '14205039',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RP11-280O24.3-001'
	),
	'ENSMUST00000122646' => array(
		'start' => '82439410',
		'end' => '82439514',
		'transcript_biotype' => 'rRNA',
		'transcript_name' => 'n-R5s188-201'
	)
)
$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_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007O1_0002',
		'tax_id' => '10090',
		'chromosome' => '4',
		'seq_start' => '82290606',
		'seq_end' => '82499472',
		'region_length' => '208866',
		'region_type' => 'UCNEbase',
		'el_id' => 'NFIB'
	)
)
$gene_el = array(
	'ENST00000435137' => array(
		'Adipose' => array(
			'average_FPKM' => '0.088',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.468',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '0.163',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.129',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.167',
			'stddev_FPKM' => '0.02'
		),
		'Colon' => array(
			'average_FPKM' => '0.181',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.123',
			'stddev_FPKM' => '0.10'
		),
		'Kidney' => array(
			'average_FPKM' => '0.097',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.105',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.339',
			'stddev_FPKM' => '0.06'
		),
		'Muscle' => array(
			'average_FPKM' => '0.184',
			'stddev_FPKM' => '0.00'
		),
		'Ovary' => array(
			'average_FPKM' => '0.178',
			'stddev_FPKM' => '0.14'
		),
		'Testis' => array(
			'average_FPKM' => '0.208',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000234982'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.088',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.468',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '0.163',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.129',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.167',
		'stddev_FPKM' => '0.02'
	),
	'Colon' => array(
		'average_FPKM' => '0.181',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.123',
		'stddev_FPKM' => '0.10'
	),
	'Kidney' => array(
		'average_FPKM' => '0.097',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.105',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.339',
		'stddev_FPKM' => '0.06'
	),
	'Muscle' => array(
		'average_FPKM' => '0.184',
		'stddev_FPKM' => '0.00'
	),
	'Ovary' => array(
		'average_FPKM' => '0.178',
		'stddev_FPKM' => '0.14'
	),
	'Testis' => array(
		'average_FPKM' => '0.208',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000435137'
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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000234982' => null,
		'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
	),
	'gene_name_arr' => array(
		'ENSG00000234982' => 'RP11-280O24.3',
		'ENSMUSG00000084595' => 'n-R5s188'
	),
	'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 => 'Bladder',
		(int) 3 => 'Brain',
		(int) 4 => 'Breast',
		(int) 5 => 'Colon',
		(int) 6 => 'Heart',
		(int) 7 => 'Kidney',
		(int) 8 => 'Liver',
		(int) 9 => 'Lung',
		(int) 10 => 'Muscle',
		(int) 11 => 'Ovary',
		(int) 12 => '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(
		'ENST00000435137' => array(
			'start' => '14204248',
			'end' => '14205039',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RP11-280O24.3-001'
		),
		'ENSMUST00000122646' => array(
			'start' => '82439410',
			'end' => '82439514',
			'transcript_biotype' => 'rRNA',
			'transcript_name' => 'n-R5s188-201'
		)
	),
	'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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000234982' => null,
	'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
)
$gene_name_arr = array(
	'ENSG00000234982' => 'RP11-280O24.3',
	'ENSMUSG00000084595' => 'n-R5s188'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0001',
			'tax_id' => '9606',
			'chromosome' => '9',
			'seq_start' => '14082259',
			'seq_end' => '14308187',
			'region_length' => '225928',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0002',
			'tax_id' => '10090',
			'chromosome' => '4',
			'seq_start' => '82290606',
			'seq_end' => '82499472',
			'region_length' => '208866',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0003',
			'tax_id' => '7955',
			'chromosome' => '3',
			'seq_start' => '14647963',
			'seq_end' => '14648139',
			'region_length' => '176',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Bladder',
	(int) 3 => 'Brain',
	(int) 4 => 'Breast',
	(int) 5 => 'Colon',
	(int) 6 => 'Heart',
	(int) 7 => 'Kidney',
	(int) 8 => 'Liver',
	(int) 9 => 'Lung',
	(int) 10 => 'Muscle',
	(int) 11 => 'Ovary',
	(int) 12 => '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(
	'ENST00000435137' => array(
		'start' => '14204248',
		'end' => '14205039',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RP11-280O24.3-001'
	),
	'ENSMUST00000122646' => array(
		'start' => '82439410',
		'end' => '82439514',
		'transcript_biotype' => 'rRNA',
		'transcript_name' => 'n-R5s188-201'
	)
)
$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_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007O1_0002',
		'tax_id' => '10090',
		'chromosome' => '4',
		'seq_start' => '82290606',
		'seq_end' => '82499472',
		'region_length' => '208866',
		'region_type' => 'UCNEbase',
		'el_id' => 'NFIB'
	)
)
$gene_el = array(
	'ENST00000435137' => array(
		'Adipose' => array(
			'average_FPKM' => '0.088',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.468',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '0.163',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.129',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.167',
			'stddev_FPKM' => '0.02'
		),
		'Colon' => array(
			'average_FPKM' => '0.181',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.123',
			'stddev_FPKM' => '0.10'
		),
		'Kidney' => array(
			'average_FPKM' => '0.097',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.105',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.339',
			'stddev_FPKM' => '0.06'
		),
		'Muscle' => array(
			'average_FPKM' => '0.184',
			'stddev_FPKM' => '0.00'
		),
		'Ovary' => array(
			'average_FPKM' => '0.178',
			'stddev_FPKM' => '0.14'
		),
		'Testis' => array(
			'average_FPKM' => '0.208',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000234982'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.088',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.468',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '0.163',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.129',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.167',
		'stddev_FPKM' => '0.02'
	),
	'Colon' => array(
		'average_FPKM' => '0.181',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.123',
		'stddev_FPKM' => '0.10'
	),
	'Kidney' => array(
		'average_FPKM' => '0.097',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.105',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.339',
		'stddev_FPKM' => '0.06'
	),
	'Muscle' => array(
		'average_FPKM' => '0.184',
		'stddev_FPKM' => '0.00'
	),
	'Ovary' => array(
		'average_FPKM' => '0.178',
		'stddev_FPKM' => '0.14'
	),
	'Testis' => array(
		'average_FPKM' => '0.208',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000435137'
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
NFIB		UCNEbase	10090	4:82290606-82499472
Gene		Transcript	Position	Biotype

Genome

Exciting message

Genes

Connecting

Transcripts

Connecting

CIL_0007O1_0003 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007O1_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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000234982' => null,
		'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
	),
	'gene_name_arr' => array(
		'ENSG00000234982' => 'RP11-280O24.3',
		'ENSMUSG00000084595' => 'n-R5s188'
	),
	'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 => 'Bladder',
		(int) 3 => 'Brain',
		(int) 4 => 'Breast',
		(int) 5 => 'Colon',
		(int) 6 => 'Heart',
		(int) 7 => 'Kidney',
		(int) 8 => 'Liver',
		(int) 9 => 'Lung',
		(int) 10 => 'Muscle',
		(int) 11 => 'Ovary',
		(int) 12 => '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(
		'ENST00000435137' => array(
			'start' => '14204248',
			'end' => '14205039',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RP11-280O24.3-001'
		),
		'ENSMUST00000122646' => array(
			'start' => '82439410',
			'end' => '82439514',
			'transcript_biotype' => 'rRNA',
			'transcript_name' => 'n-R5s188-201'
		)
	),
	'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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000234982' => null,
	'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
)
$gene_name_arr = array(
	'ENSG00000234982' => 'RP11-280O24.3',
	'ENSMUSG00000084595' => 'n-R5s188'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0001',
			'tax_id' => '9606',
			'chromosome' => '9',
			'seq_start' => '14082259',
			'seq_end' => '14308187',
			'region_length' => '225928',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0002',
			'tax_id' => '10090',
			'chromosome' => '4',
			'seq_start' => '82290606',
			'seq_end' => '82499472',
			'region_length' => '208866',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0003',
			'tax_id' => '7955',
			'chromosome' => '3',
			'seq_start' => '14647963',
			'seq_end' => '14648139',
			'region_length' => '176',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Bladder',
	(int) 3 => 'Brain',
	(int) 4 => 'Breast',
	(int) 5 => 'Colon',
	(int) 6 => 'Heart',
	(int) 7 => 'Kidney',
	(int) 8 => 'Liver',
	(int) 9 => 'Lung',
	(int) 10 => 'Muscle',
	(int) 11 => 'Ovary',
	(int) 12 => '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(
	'ENST00000435137' => array(
		'start' => '14204248',
		'end' => '14205039',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RP11-280O24.3-001'
	),
	'ENSMUST00000122646' => array(
		'start' => '82439410',
		'end' => '82439514',
		'transcript_biotype' => 'rRNA',
		'transcript_name' => 'n-R5s188-201'
	)
)
$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_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007O1_0003',
		'tax_id' => '7955',
		'chromosome' => '3',
		'seq_start' => '14647963',
		'seq_end' => '14648139',
		'region_length' => '176',
		'region_type' => 'UCNEbase',
		'el_id' => 'NFIB'
	)
)
$gene_el = array(
	'ENST00000435137' => array(
		'Adipose' => array(
			'average_FPKM' => '0.088',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.468',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '0.163',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.129',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.167',
			'stddev_FPKM' => '0.02'
		),
		'Colon' => array(
			'average_FPKM' => '0.181',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.123',
			'stddev_FPKM' => '0.10'
		),
		'Kidney' => array(
			'average_FPKM' => '0.097',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.105',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.339',
			'stddev_FPKM' => '0.06'
		),
		'Muscle' => array(
			'average_FPKM' => '0.184',
			'stddev_FPKM' => '0.00'
		),
		'Ovary' => array(
			'average_FPKM' => '0.178',
			'stddev_FPKM' => '0.14'
		),
		'Testis' => array(
			'average_FPKM' => '0.208',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000234982'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.088',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.468',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '0.163',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.129',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.167',
		'stddev_FPKM' => '0.02'
	),
	'Colon' => array(
		'average_FPKM' => '0.181',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.123',
		'stddev_FPKM' => '0.10'
	),
	'Kidney' => array(
		'average_FPKM' => '0.097',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.105',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.339',
		'stddev_FPKM' => '0.06'
	),
	'Muscle' => array(
		'average_FPKM' => '0.184',
		'stddev_FPKM' => '0.00'
	),
	'Ovary' => array(
		'average_FPKM' => '0.178',
		'stddev_FPKM' => '0.14'
	),
	'Testis' => array(
		'average_FPKM' => '0.208',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000435137'
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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000234982' => null,
		'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
	),
	'gene_name_arr' => array(
		'ENSG00000234982' => 'RP11-280O24.3',
		'ENSMUSG00000084595' => 'n-R5s188'
	),
	'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 => 'Bladder',
		(int) 3 => 'Brain',
		(int) 4 => 'Breast',
		(int) 5 => 'Colon',
		(int) 6 => 'Heart',
		(int) 7 => 'Kidney',
		(int) 8 => 'Liver',
		(int) 9 => 'Lung',
		(int) 10 => 'Muscle',
		(int) 11 => 'Ovary',
		(int) 12 => '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(
		'ENST00000435137' => array(
			'start' => '14204248',
			'end' => '14205039',
			'transcript_biotype' => 'processed_pseudogene',
			'transcript_name' => 'RP11-280O24.3-001'
		),
		'ENSMUST00000122646' => array(
			'start' => '82439410',
			'end' => '82439514',
			'transcript_biotype' => 'rRNA',
			'transcript_name' => 'n-R5s188-201'
		)
	),
	'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_0007O1_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000234982' => null,
	'ENSMUSG00000084595' => 'nuclear encoded rRNA 5S 188'
)
$gene_name_arr = array(
	'ENSG00000234982' => 'RP11-280O24.3',
	'ENSMUSG00000084595' => 'n-R5s188'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0001',
			'tax_id' => '9606',
			'chromosome' => '9',
			'seq_start' => '14082259',
			'seq_end' => '14308187',
			'region_length' => '225928',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0002',
			'tax_id' => '10090',
			'chromosome' => '4',
			'seq_start' => '82290606',
			'seq_end' => '82499472',
			'region_length' => '208866',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007O1_0003',
			'tax_id' => '7955',
			'chromosome' => '3',
			'seq_start' => '14647963',
			'seq_end' => '14648139',
			'region_length' => '176',
			'region_type' => 'UCNEbase',
			'el_id' => 'NFIB'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 1 => 'Adrenal',
	(int) 2 => 'Bladder',
	(int) 3 => 'Brain',
	(int) 4 => 'Breast',
	(int) 5 => 'Colon',
	(int) 6 => 'Heart',
	(int) 7 => 'Kidney',
	(int) 8 => 'Liver',
	(int) 9 => 'Lung',
	(int) 10 => 'Muscle',
	(int) 11 => 'Ovary',
	(int) 12 => '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(
	'ENST00000435137' => array(
		'start' => '14204248',
		'end' => '14205039',
		'transcript_biotype' => 'processed_pseudogene',
		'transcript_name' => 'RP11-280O24.3-001'
	),
	'ENSMUST00000122646' => array(
		'start' => '82439410',
		'end' => '82439514',
		'transcript_biotype' => 'rRNA',
		'transcript_name' => 'n-R5s188-201'
	)
)
$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_0007O1_0001' => array(
		'genes_in_region' => array(
			'ENSG00000234982' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Adipose',
			(int) 1 => 'Adrenal',
			(int) 2 => 'Bladder',
			(int) 3 => 'Brain',
			(int) 4 => 'Breast',
			(int) 5 => 'Colon',
			(int) 6 => 'Heart',
			(int) 7 => 'Kidney',
			(int) 8 => 'Liver',
			(int) 9 => 'Lung',
			(int) 10 => 'Muscle',
			(int) 11 => 'Ovary',
			(int) 12 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007O1_0003',
		'tax_id' => '7955',
		'chromosome' => '3',
		'seq_start' => '14647963',
		'seq_end' => '14648139',
		'region_length' => '176',
		'region_type' => 'UCNEbase',
		'el_id' => 'NFIB'
	)
)
$gene_el = array(
	'ENST00000435137' => array(
		'Adipose' => array(
			'average_FPKM' => '0.088',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.468',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '0.163',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.129',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.167',
			'stddev_FPKM' => '0.02'
		),
		'Colon' => array(
			'average_FPKM' => '0.181',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.123',
			'stddev_FPKM' => '0.10'
		),
		'Kidney' => array(
			'average_FPKM' => '0.097',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.105',
			'stddev_FPKM' => '0.00'
		),
		'Lung' => array(
			'average_FPKM' => '0.339',
			'stddev_FPKM' => '0.06'
		),
		'Muscle' => array(
			'average_FPKM' => '0.184',
			'stddev_FPKM' => '0.00'
		),
		'Ovary' => array(
			'average_FPKM' => '0.178',
			'stddev_FPKM' => '0.14'
		),
		'Testis' => array(
			'average_FPKM' => '0.208',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000234982'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.088',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.468',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '0.163',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.129',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.167',
		'stddev_FPKM' => '0.02'
	),
	'Colon' => array(
		'average_FPKM' => '0.181',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.123',
		'stddev_FPKM' => '0.10'
	),
	'Kidney' => array(
		'average_FPKM' => '0.097',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.105',
		'stddev_FPKM' => '0.00'
	),
	'Lung' => array(
		'average_FPKM' => '0.339',
		'stddev_FPKM' => '0.06'
	),
	'Muscle' => array(
		'average_FPKM' => '0.184',
		'stddev_FPKM' => '0.00'
	),
	'Ovary' => array(
		'average_FPKM' => '0.178',
		'stddev_FPKM' => '0.14'
	),
	'Testis' => array(
		'average_FPKM' => '0.208',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000435137'
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
NFIB		UCNEbase	7955	3:14647963-14648139
Gene		Transcript	Position	Biotype

Genome

Exciting message

Genes

Connecting

Transcripts

Connecting

Expression Patterns

Heat Map

Heat Map (Expressed Only)

Numeric Values

Gene

Transcript

Adipose

Adrenal

Bladder

Brain

Breast

Colon

Heart

Kidney

Liver

Lung

Muscle

Ovary

Testis

ENSG00000234982

ENST00000435137

0.088±0.00

0.468±0.00

0.163±0.00

0.129±0.00

0.167±0.02

0.181±0.00

0.123±0.10

0.097±0.00

0.105±0.00

0.339±0.06

0.184±0.00

0.178±0.14

0.208±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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C-It-Loci: A knowledge database for tissue-enriched loci.

Institute of Cardiovascular Regeneration, Goethe-University Frankfurt am Main

Region Summary

Homo sapiens Ensembl (GRCh38)

Mus musculus Ensembl (GRCm38)

Danio rerio Ensembl (Zv9)

Expression Patterns

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