Institute of Cardiovascular Regeneration Webtool Repository

Region Summary

Source ID	Type	Tax ID	Position
CUX1	UCNEbase	9606	7:101893730-102215645
Gene	Transcript	Position	Biotype
ENSG00000252824 (SNORA48) Small nucleolar RNA SNORA48	ENST00000517015 (SNORA48.1-212)	102194076-102194164	snoRNA
ENSG00000261535 (CTA-305I2.1)	ENST00000566572 (CTA-305I2.1-001)	102153355-102154463	antisense
ENSG00000272219 (CTB-181H17.1)	ENST00000606640 (CTB-181H17.1-001)	101960116-101961894	sense_intronic
ENSG00000279724 (AC005086.1)	ENST00000624939 (AC005086.1-201)	102188599-102188828	pseudogene
ENSG00000280004 (AC005086.2)	ENST00000624984 (AC005086.2-201)	102186819-102187039	pseudogene
ENSG00000280404 (AC005086.3)	ENST00000623065 (AC005086.3-201)	102161120-102161337	pseudogene

CIL_0007NW_0002 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007NW_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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
		'ENSG00000261535' => null,
		'ENSG00000272219' => null,
		'ENSG00000279724' => null,
		'ENSG00000280004' => null,
		'ENSG00000280404' => null,
		'ENSMUSG00000086220' => 'predicted gene, 16599'
	),
	'gene_name_arr' => array(
		'ENSG00000252824' => 'SNORA48',
		'ENSG00000261535' => 'CTA-305I2.1',
		'ENSG00000272219' => 'CTB-181H17.1',
		'ENSG00000279724' => 'AC005086.1',
		'ENSG00000280004' => 'AC005086.2',
		'ENSG00000280404' => 'AC005086.3',
		'ENSMUSG00000086220' => 'Gm16599'
	),
	'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) 5 => 'Adrenal',
		(int) 9 => 'Bladder',
		(int) 12 => 'Brain',
		(int) 16 => 'Breast',
		(int) 20 => 'Colon',
		(int) 25 => 'Heart',
		(int) 29 => 'Kidney',
		(int) 33 => 'Liver',
		(int) 36 => 'Lung',
		(int) 38 => 'Muscle',
		(int) 41 => 'Ovary',
		(int) 45 => 'Placenta',
		(int) 49 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000517015' => array(
			'start' => '102194076',
			'end' => '102194164',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'SNORA48.1-212'
		),
		'ENST00000566572' => array(
			'start' => '102153355',
			'end' => '102154463',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'CTA-305I2.1-001'
		),
		'ENST00000606640' => array(
			'start' => '101960116',
			'end' => '101961894',
			'transcript_biotype' => 'sense_intronic',
			'transcript_name' => 'CTB-181H17.1-001'
		),
		'ENST00000624939' => array(
			'start' => '102188599',
			'end' => '102188828',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.1-201'
		),
		'ENST00000624984' => array(
			'start' => '102186819',
			'end' => '102187039',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.2-201'
		),
		'ENST00000623065' => array(
			'start' => '102161120',
			'end' => '102161337',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.3-201'
		),
		'ENSMUST00000148082' => array(
			'start' => '136274996',
			'end' => '136417894',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'Gm16599-001'
		)
	),
	'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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
	'ENSG00000261535' => null,
	'ENSG00000272219' => null,
	'ENSG00000279724' => null,
	'ENSG00000280004' => null,
	'ENSG00000280404' => null,
	'ENSMUSG00000086220' => 'predicted gene, 16599'
)
$gene_name_arr = array(
	'ENSG00000252824' => 'SNORA48',
	'ENSG00000261535' => 'CTA-305I2.1',
	'ENSG00000272219' => 'CTB-181H17.1',
	'ENSG00000279724' => 'AC005086.1',
	'ENSG00000280004' => 'AC005086.2',
	'ENSG00000280404' => 'AC005086.3',
	'ENSMUSG00000086220' => 'Gm16599'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0001',
			'tax_id' => '9606',
			'chromosome' => '7',
			'seq_start' => '101893730',
			'seq_end' => '102215645',
			'region_length' => '321915',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0002',
			'tax_id' => '10090',
			'chromosome' => '5',
			'seq_start' => '136296848',
			'seq_end' => '136505086',
			'region_length' => '208238',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '33885331',
			'seq_end' => '33885613',
			'region_length' => '282',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 5 => 'Adrenal',
	(int) 9 => 'Bladder',
	(int) 12 => 'Brain',
	(int) 16 => 'Breast',
	(int) 20 => 'Colon',
	(int) 25 => 'Heart',
	(int) 29 => 'Kidney',
	(int) 33 => 'Liver',
	(int) 36 => 'Lung',
	(int) 38 => 'Muscle',
	(int) 41 => 'Ovary',
	(int) 45 => 'Placenta',
	(int) 49 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000517015' => array(
		'start' => '102194076',
		'end' => '102194164',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'SNORA48.1-212'
	),
	'ENST00000566572' => array(
		'start' => '102153355',
		'end' => '102154463',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'CTA-305I2.1-001'
	),
	'ENST00000606640' => array(
		'start' => '101960116',
		'end' => '101961894',
		'transcript_biotype' => 'sense_intronic',
		'transcript_name' => 'CTB-181H17.1-001'
	),
	'ENST00000624939' => array(
		'start' => '102188599',
		'end' => '102188828',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.1-201'
	),
	'ENST00000624984' => array(
		'start' => '102186819',
		'end' => '102187039',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.2-201'
	),
	'ENST00000623065' => array(
		'start' => '102161120',
		'end' => '102161337',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.3-201'
	),
	'ENSMUST00000148082' => array(
		'start' => '136274996',
		'end' => '136417894',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'Gm16599-001'
	)
)
$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_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007NW_0002',
		'tax_id' => '10090',
		'chromosome' => '5',
		'seq_start' => '136296848',
		'seq_end' => '136505086',
		'region_length' => '208238',
		'region_type' => 'UCNEbase',
		'el_id' => 'CUX1'
	)
)
$gene_el = array(
	'ENST00000623065' => array(
		'Adipose' => array(
			'average_FPKM' => '0.390',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.788',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '1.557',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.343',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.307',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.186',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.096',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.100',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.528',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000280404'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.390',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.788',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '1.557',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.343',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.307',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.186',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.096',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.100',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.528',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000623065'
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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
		'ENSG00000261535' => null,
		'ENSG00000272219' => null,
		'ENSG00000279724' => null,
		'ENSG00000280004' => null,
		'ENSG00000280404' => null,
		'ENSMUSG00000086220' => 'predicted gene, 16599'
	),
	'gene_name_arr' => array(
		'ENSG00000252824' => 'SNORA48',
		'ENSG00000261535' => 'CTA-305I2.1',
		'ENSG00000272219' => 'CTB-181H17.1',
		'ENSG00000279724' => 'AC005086.1',
		'ENSG00000280004' => 'AC005086.2',
		'ENSG00000280404' => 'AC005086.3',
		'ENSMUSG00000086220' => 'Gm16599'
	),
	'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) 5 => 'Adrenal',
		(int) 9 => 'Bladder',
		(int) 12 => 'Brain',
		(int) 16 => 'Breast',
		(int) 20 => 'Colon',
		(int) 25 => 'Heart',
		(int) 29 => 'Kidney',
		(int) 33 => 'Liver',
		(int) 36 => 'Lung',
		(int) 38 => 'Muscle',
		(int) 41 => 'Ovary',
		(int) 45 => 'Placenta',
		(int) 49 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000517015' => array(
			'start' => '102194076',
			'end' => '102194164',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'SNORA48.1-212'
		),
		'ENST00000566572' => array(
			'start' => '102153355',
			'end' => '102154463',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'CTA-305I2.1-001'
		),
		'ENST00000606640' => array(
			'start' => '101960116',
			'end' => '101961894',
			'transcript_biotype' => 'sense_intronic',
			'transcript_name' => 'CTB-181H17.1-001'
		),
		'ENST00000624939' => array(
			'start' => '102188599',
			'end' => '102188828',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.1-201'
		),
		'ENST00000624984' => array(
			'start' => '102186819',
			'end' => '102187039',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.2-201'
		),
		'ENST00000623065' => array(
			'start' => '102161120',
			'end' => '102161337',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.3-201'
		),
		'ENSMUST00000148082' => array(
			'start' => '136274996',
			'end' => '136417894',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'Gm16599-001'
		)
	),
	'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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
	'ENSG00000261535' => null,
	'ENSG00000272219' => null,
	'ENSG00000279724' => null,
	'ENSG00000280004' => null,
	'ENSG00000280404' => null,
	'ENSMUSG00000086220' => 'predicted gene, 16599'
)
$gene_name_arr = array(
	'ENSG00000252824' => 'SNORA48',
	'ENSG00000261535' => 'CTA-305I2.1',
	'ENSG00000272219' => 'CTB-181H17.1',
	'ENSG00000279724' => 'AC005086.1',
	'ENSG00000280004' => 'AC005086.2',
	'ENSG00000280404' => 'AC005086.3',
	'ENSMUSG00000086220' => 'Gm16599'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0001',
			'tax_id' => '9606',
			'chromosome' => '7',
			'seq_start' => '101893730',
			'seq_end' => '102215645',
			'region_length' => '321915',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0002',
			'tax_id' => '10090',
			'chromosome' => '5',
			'seq_start' => '136296848',
			'seq_end' => '136505086',
			'region_length' => '208238',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '33885331',
			'seq_end' => '33885613',
			'region_length' => '282',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 5 => 'Adrenal',
	(int) 9 => 'Bladder',
	(int) 12 => 'Brain',
	(int) 16 => 'Breast',
	(int) 20 => 'Colon',
	(int) 25 => 'Heart',
	(int) 29 => 'Kidney',
	(int) 33 => 'Liver',
	(int) 36 => 'Lung',
	(int) 38 => 'Muscle',
	(int) 41 => 'Ovary',
	(int) 45 => 'Placenta',
	(int) 49 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000517015' => array(
		'start' => '102194076',
		'end' => '102194164',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'SNORA48.1-212'
	),
	'ENST00000566572' => array(
		'start' => '102153355',
		'end' => '102154463',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'CTA-305I2.1-001'
	),
	'ENST00000606640' => array(
		'start' => '101960116',
		'end' => '101961894',
		'transcript_biotype' => 'sense_intronic',
		'transcript_name' => 'CTB-181H17.1-001'
	),
	'ENST00000624939' => array(
		'start' => '102188599',
		'end' => '102188828',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.1-201'
	),
	'ENST00000624984' => array(
		'start' => '102186819',
		'end' => '102187039',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.2-201'
	),
	'ENST00000623065' => array(
		'start' => '102161120',
		'end' => '102161337',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.3-201'
	),
	'ENSMUST00000148082' => array(
		'start' => '136274996',
		'end' => '136417894',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'Gm16599-001'
	)
)
$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_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007NW_0002',
		'tax_id' => '10090',
		'chromosome' => '5',
		'seq_start' => '136296848',
		'seq_end' => '136505086',
		'region_length' => '208238',
		'region_type' => 'UCNEbase',
		'el_id' => 'CUX1'
	)
)
$gene_el = array(
	'ENST00000623065' => array(
		'Adipose' => array(
			'average_FPKM' => '0.390',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.788',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '1.557',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.343',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.307',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.186',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.096',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.100',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.528',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000280404'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.390',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.788',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '1.557',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.343',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.307',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.186',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.096',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.100',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.528',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000623065'
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
CUX1		UCNEbase	10090	5:136296848-136505086
Gene		Transcript	Position	Biotype

CIL_0007NW_0003 (Click to Hide/Show)

Notice (8): Undefined index: CIL_0007NW_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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
		'ENSG00000261535' => null,
		'ENSG00000272219' => null,
		'ENSG00000279724' => null,
		'ENSG00000280004' => null,
		'ENSG00000280404' => null,
		'ENSMUSG00000086220' => 'predicted gene, 16599'
	),
	'gene_name_arr' => array(
		'ENSG00000252824' => 'SNORA48',
		'ENSG00000261535' => 'CTA-305I2.1',
		'ENSG00000272219' => 'CTB-181H17.1',
		'ENSG00000279724' => 'AC005086.1',
		'ENSG00000280004' => 'AC005086.2',
		'ENSG00000280404' => 'AC005086.3',
		'ENSMUSG00000086220' => 'Gm16599'
	),
	'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) 5 => 'Adrenal',
		(int) 9 => 'Bladder',
		(int) 12 => 'Brain',
		(int) 16 => 'Breast',
		(int) 20 => 'Colon',
		(int) 25 => 'Heart',
		(int) 29 => 'Kidney',
		(int) 33 => 'Liver',
		(int) 36 => 'Lung',
		(int) 38 => 'Muscle',
		(int) 41 => 'Ovary',
		(int) 45 => 'Placenta',
		(int) 49 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000517015' => array(
			'start' => '102194076',
			'end' => '102194164',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'SNORA48.1-212'
		),
		'ENST00000566572' => array(
			'start' => '102153355',
			'end' => '102154463',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'CTA-305I2.1-001'
		),
		'ENST00000606640' => array(
			'start' => '101960116',
			'end' => '101961894',
			'transcript_biotype' => 'sense_intronic',
			'transcript_name' => 'CTB-181H17.1-001'
		),
		'ENST00000624939' => array(
			'start' => '102188599',
			'end' => '102188828',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.1-201'
		),
		'ENST00000624984' => array(
			'start' => '102186819',
			'end' => '102187039',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.2-201'
		),
		'ENST00000623065' => array(
			'start' => '102161120',
			'end' => '102161337',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.3-201'
		),
		'ENSMUST00000148082' => array(
			'start' => '136274996',
			'end' => '136417894',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'Gm16599-001'
		)
	),
	'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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
	'ENSG00000261535' => null,
	'ENSG00000272219' => null,
	'ENSG00000279724' => null,
	'ENSG00000280004' => null,
	'ENSG00000280404' => null,
	'ENSMUSG00000086220' => 'predicted gene, 16599'
)
$gene_name_arr = array(
	'ENSG00000252824' => 'SNORA48',
	'ENSG00000261535' => 'CTA-305I2.1',
	'ENSG00000272219' => 'CTB-181H17.1',
	'ENSG00000279724' => 'AC005086.1',
	'ENSG00000280004' => 'AC005086.2',
	'ENSG00000280404' => 'AC005086.3',
	'ENSMUSG00000086220' => 'Gm16599'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0001',
			'tax_id' => '9606',
			'chromosome' => '7',
			'seq_start' => '101893730',
			'seq_end' => '102215645',
			'region_length' => '321915',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0002',
			'tax_id' => '10090',
			'chromosome' => '5',
			'seq_start' => '136296848',
			'seq_end' => '136505086',
			'region_length' => '208238',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '33885331',
			'seq_end' => '33885613',
			'region_length' => '282',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 5 => 'Adrenal',
	(int) 9 => 'Bladder',
	(int) 12 => 'Brain',
	(int) 16 => 'Breast',
	(int) 20 => 'Colon',
	(int) 25 => 'Heart',
	(int) 29 => 'Kidney',
	(int) 33 => 'Liver',
	(int) 36 => 'Lung',
	(int) 38 => 'Muscle',
	(int) 41 => 'Ovary',
	(int) 45 => 'Placenta',
	(int) 49 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000517015' => array(
		'start' => '102194076',
		'end' => '102194164',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'SNORA48.1-212'
	),
	'ENST00000566572' => array(
		'start' => '102153355',
		'end' => '102154463',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'CTA-305I2.1-001'
	),
	'ENST00000606640' => array(
		'start' => '101960116',
		'end' => '101961894',
		'transcript_biotype' => 'sense_intronic',
		'transcript_name' => 'CTB-181H17.1-001'
	),
	'ENST00000624939' => array(
		'start' => '102188599',
		'end' => '102188828',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.1-201'
	),
	'ENST00000624984' => array(
		'start' => '102186819',
		'end' => '102187039',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.2-201'
	),
	'ENST00000623065' => array(
		'start' => '102161120',
		'end' => '102161337',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.3-201'
	),
	'ENSMUST00000148082' => array(
		'start' => '136274996',
		'end' => '136417894',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'Gm16599-001'
	)
)
$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_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007NW_0003',
		'tax_id' => '7955',
		'chromosome' => '10',
		'seq_start' => '33885331',
		'seq_end' => '33885613',
		'region_length' => '282',
		'region_type' => 'UCNEbase',
		'el_id' => 'CUX1'
	)
)
$gene_el = array(
	'ENST00000623065' => array(
		'Adipose' => array(
			'average_FPKM' => '0.390',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.788',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '1.557',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.343',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.307',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.186',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.096',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.100',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.528',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000280404'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.390',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.788',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '1.557',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.343',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.307',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.186',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.096',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.100',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.528',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000623065'
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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
		'ENSG00000261535' => null,
		'ENSG00000272219' => null,
		'ENSG00000279724' => null,
		'ENSG00000280004' => null,
		'ENSG00000280404' => null,
		'ENSMUSG00000086220' => 'predicted gene, 16599'
	),
	'gene_name_arr' => array(
		'ENSG00000252824' => 'SNORA48',
		'ENSG00000261535' => 'CTA-305I2.1',
		'ENSG00000272219' => 'CTB-181H17.1',
		'ENSG00000279724' => 'AC005086.1',
		'ENSG00000280004' => 'AC005086.2',
		'ENSG00000280404' => 'AC005086.3',
		'ENSMUSG00000086220' => 'Gm16599'
	),
	'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) 5 => 'Adrenal',
		(int) 9 => 'Bladder',
		(int) 12 => 'Brain',
		(int) 16 => 'Breast',
		(int) 20 => 'Colon',
		(int) 25 => 'Heart',
		(int) 29 => 'Kidney',
		(int) 33 => 'Liver',
		(int) 36 => 'Lung',
		(int) 38 => 'Muscle',
		(int) 41 => 'Ovary',
		(int) 45 => 'Placenta',
		(int) 49 => 'Testis'
	),
	'column_titles' => array(
		(int) 0 => 'Region Sub-Accession',
		(int) 1 => 'Tax ID',
		(int) 2 => 'Position',
		(int) 3 => 'Region Length'
	),
	'geneviewer' => array(
		(int) 9606 => array(
			'version' => 'GRCh38',
			'coord_key' => 'Homo sapiens',
			'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCh38.2bit',
			'bwgURI' => '/static/files/GRCh38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 10090 => array(
			'version' => 'GRCm38',
			'coord_key' => 'Mus musculus',
			'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
			'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
			'desc' => 'Gene structures from GENCODE 19',
			'twoBitURI' => '/static/files/GRCm38.2bit',
			'bwgURI' => '/static/files/GRCm38.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		),
		(int) 7955 => array(
			'version' => 'Zv9',
			'coord_key' => 'Danio rerio',
			'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
			'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
			'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
			'twoBitURI' => '/static/files/Zv9.2bit',
			'bwgURI' => '/static/files/Zv9.77.bb',
			'stylesheet_uri' => '/static/files/gencode.xml',
			'collapseSuperGroups' => 'true',
			'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
		)
	),
	'transcript_count' => (int) 7,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000517015' => array(
			'start' => '102194076',
			'end' => '102194164',
			'transcript_biotype' => 'snoRNA',
			'transcript_name' => 'SNORA48.1-212'
		),
		'ENST00000566572' => array(
			'start' => '102153355',
			'end' => '102154463',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'CTA-305I2.1-001'
		),
		'ENST00000606640' => array(
			'start' => '101960116',
			'end' => '101961894',
			'transcript_biotype' => 'sense_intronic',
			'transcript_name' => 'CTB-181H17.1-001'
		),
		'ENST00000624939' => array(
			'start' => '102188599',
			'end' => '102188828',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.1-201'
		),
		'ENST00000624984' => array(
			'start' => '102186819',
			'end' => '102187039',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.2-201'
		),
		'ENST00000623065' => array(
			'start' => '102161120',
			'end' => '102161337',
			'transcript_biotype' => 'pseudogene',
			'transcript_name' => 'AC005086.3-201'
		),
		'ENSMUST00000148082' => array(
			'start' => '136274996',
			'end' => '136417894',
			'transcript_biotype' => 'antisense',
			'transcript_name' => 'Gm16599-001'
		)
	),
	'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_0007NW_0001' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000252824' => 'Small nucleolar RNA SNORA48',
	'ENSG00000261535' => null,
	'ENSG00000272219' => null,
	'ENSG00000279724' => null,
	'ENSG00000280004' => null,
	'ENSG00000280404' => null,
	'ENSMUSG00000086220' => 'predicted gene, 16599'
)
$gene_name_arr = array(
	'ENSG00000252824' => 'SNORA48',
	'ENSG00000261535' => 'CTA-305I2.1',
	'ENSG00000272219' => 'CTB-181H17.1',
	'ENSG00000279724' => 'AC005086.1',
	'ENSG00000280004' => 'AC005086.2',
	'ENSG00000280404' => 'AC005086.3',
	'ENSMUSG00000086220' => 'Gm16599'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0001',
			'tax_id' => '9606',
			'chromosome' => '7',
			'seq_start' => '101893730',
			'seq_end' => '102215645',
			'region_length' => '321915',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0002',
			'tax_id' => '10090',
			'chromosome' => '5',
			'seq_start' => '136296848',
			'seq_end' => '136505086',
			'region_length' => '208238',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	),
	(int) 2 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_0007NW_0003',
			'tax_id' => '7955',
			'chromosome' => '10',
			'seq_start' => '33885331',
			'seq_end' => '33885613',
			'region_length' => '282',
			'region_type' => 'UCNEbase',
			'el_id' => 'CUX1'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 5 => 'Adrenal',
	(int) 9 => 'Bladder',
	(int) 12 => 'Brain',
	(int) 16 => 'Breast',
	(int) 20 => 'Colon',
	(int) 25 => 'Heart',
	(int) 29 => 'Kidney',
	(int) 33 => 'Liver',
	(int) 36 => 'Lung',
	(int) 38 => 'Muscle',
	(int) 41 => 'Ovary',
	(int) 45 => 'Placenta',
	(int) 49 => 'Testis'
)
$column_titles = array(
	(int) 0 => 'Region Sub-Accession',
	(int) 1 => 'Tax ID',
	(int) 2 => 'Position',
	(int) 3 => 'Region Length'
)
$geneviewer = array(
	(int) 9606 => array(
		'version' => 'GRCh38',
		'coord_key' => 'Homo sapiens',
		'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCh38.2bit',
		'bwgURI' => '/static/files/GRCh38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 10090 => array(
		'version' => 'GRCm38',
		'coord_key' => 'Mus musculus',
		'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
		'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
		'desc' => 'Gene structures from GENCODE 19',
		'twoBitURI' => '/static/files/GRCm38.2bit',
		'bwgURI' => '/static/files/GRCm38.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	),
	(int) 7955 => array(
		'version' => 'Zv9',
		'coord_key' => 'Danio rerio',
		'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
		'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
		'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
		'twoBitURI' => '/static/files/Zv9.2bit',
		'bwgURI' => '/static/files/Zv9.77.bb',
		'stylesheet_uri' => '/static/files/gencode.xml',
		'collapseSuperGroups' => 'true',
		'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
	)
)
$transcript_count = (int) 7
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000517015' => array(
		'start' => '102194076',
		'end' => '102194164',
		'transcript_biotype' => 'snoRNA',
		'transcript_name' => 'SNORA48.1-212'
	),
	'ENST00000566572' => array(
		'start' => '102153355',
		'end' => '102154463',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'CTA-305I2.1-001'
	),
	'ENST00000606640' => array(
		'start' => '101960116',
		'end' => '101961894',
		'transcript_biotype' => 'sense_intronic',
		'transcript_name' => 'CTB-181H17.1-001'
	),
	'ENST00000624939' => array(
		'start' => '102188599',
		'end' => '102188828',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.1-201'
	),
	'ENST00000624984' => array(
		'start' => '102186819',
		'end' => '102187039',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.2-201'
	),
	'ENST00000623065' => array(
		'start' => '102161120',
		'end' => '102161337',
		'transcript_biotype' => 'pseudogene',
		'transcript_name' => 'AC005086.3-201'
	),
	'ENSMUST00000148082' => array(
		'start' => '136274996',
		'end' => '136417894',
		'transcript_biotype' => 'antisense',
		'transcript_name' => 'Gm16599-001'
	)
)
$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_0007NW_0001' => array(
		'genes_in_region' => array(
			'ENSG00000252824' => array(
				[maximum depth reached]
			),
			'ENSG00000261535' => array(
				[maximum depth reached]
			),
			'ENSG00000272219' => array(
				[maximum depth reached]
			),
			'ENSG00000279724' => array(
				[maximum depth reached]
			),
			'ENSG00000280004' => array(
				[maximum depth reached]
			),
			'ENSG00000280404' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Muscle',
			(int) 1 => 'Testis',
			(int) 2 => 'Adipose',
			(int) 3 => 'Adrenal',
			(int) 4 => 'Bladder',
			(int) 5 => 'Brain',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Placenta',
			(int) 14 => 'Testis',
			(int) 15 => 'Adipose',
			(int) 16 => 'Adrenal',
			(int) 17 => 'Bladder',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Colon',
			(int) 21 => 'Heart',
			(int) 22 => 'Kidney',
			(int) 23 => 'Liver',
			(int) 24 => 'Lung',
			(int) 25 => 'Muscle',
			(int) 26 => 'Ovary',
			(int) 27 => 'Placenta',
			(int) 28 => 'Testis',
			(int) 29 => 'Adipose',
			(int) 30 => 'Adrenal',
			(int) 31 => 'Brain',
			(int) 32 => 'Breast',
			(int) 33 => 'Colon',
			(int) 34 => 'Heart',
			(int) 35 => 'Kidney',
			(int) 36 => 'Lung',
			(int) 37 => 'Ovary',
			(int) 38 => 'Placenta',
			(int) 39 => 'Testis',
			(int) 40 => 'Adipose',
			(int) 41 => 'Colon',
			(int) 42 => 'Ovary',
			(int) 43 => 'Placenta',
			(int) 44 => 'Testis',
			(int) 45 => 'Adipose',
			(int) 46 => 'Adrenal',
			(int) 47 => 'Bladder',
			(int) 48 => 'Brain',
			(int) 49 => 'Breast',
			(int) 50 => 'Colon',
			(int) 51 => 'Heart',
			(int) 52 => 'Kidney',
			(int) 53 => 'Liver',
			(int) 54 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_0007NW_0003',
		'tax_id' => '7955',
		'chromosome' => '10',
		'seq_start' => '33885331',
		'seq_end' => '33885613',
		'region_length' => '282',
		'region_type' => 'UCNEbase',
		'el_id' => 'CUX1'
	)
)
$gene_el = array(
	'ENST00000623065' => array(
		'Adipose' => array(
			'average_FPKM' => '0.390',
			'stddev_FPKM' => '0.00'
		),
		'Adrenal' => array(
			'average_FPKM' => '0.788',
			'stddev_FPKM' => '0.00'
		),
		'Bladder' => array(
			'average_FPKM' => '1.557',
			'stddev_FPKM' => '0.00'
		),
		'Brain' => array(
			'average_FPKM' => '0.343',
			'stddev_FPKM' => '0.00'
		),
		'Breast' => array(
			'average_FPKM' => '0.307',
			'stddev_FPKM' => '0.00'
		),
		'Colon' => array(
			'average_FPKM' => '0.186',
			'stddev_FPKM' => '0.00'
		),
		'Heart' => array(
			'average_FPKM' => '0.096',
			'stddev_FPKM' => '0.00'
		),
		'Kidney' => array(
			'average_FPKM' => '0.100',
			'stddev_FPKM' => '0.00'
		),
		'Liver' => array(
			'average_FPKM' => '0.528',
			'stddev_FPKM' => '0.00'
		),
		'Testis' => array(
			'average_FPKM' => '0.279',
			'stddev_FPKM' => '0.00'
		)
	)
)
$gene_key = 'ENSG00000280404'
$is_first = false
$tran_el = array(
	'Adipose' => array(
		'average_FPKM' => '0.390',
		'stddev_FPKM' => '0.00'
	),
	'Adrenal' => array(
		'average_FPKM' => '0.788',
		'stddev_FPKM' => '0.00'
	),
	'Bladder' => array(
		'average_FPKM' => '1.557',
		'stddev_FPKM' => '0.00'
	),
	'Brain' => array(
		'average_FPKM' => '0.343',
		'stddev_FPKM' => '0.00'
	),
	'Breast' => array(
		'average_FPKM' => '0.307',
		'stddev_FPKM' => '0.00'
	),
	'Colon' => array(
		'average_FPKM' => '0.186',
		'stddev_FPKM' => '0.00'
	),
	'Heart' => array(
		'average_FPKM' => '0.096',
		'stddev_FPKM' => '0.00'
	),
	'Kidney' => array(
		'average_FPKM' => '0.100',
		'stddev_FPKM' => '0.00'
	),
	'Liver' => array(
		'average_FPKM' => '0.528',
		'stddev_FPKM' => '0.00'
	),
	'Testis' => array(
		'average_FPKM' => '0.279',
		'stddev_FPKM' => '0.00'
	)
)
$tran_key = 'ENST00000623065'
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
CUX1		UCNEbase	7955	10:33885331-33885613
Gene		Transcript	Position	Biotype

Expression Patterns

Heat Map

Heat Map (Expressed Only)

Numeric Values

Gene

Transcript

Adipose

Adrenal

Bladder

Brain

Breast

Colon

Heart

Kidney

Liver

Lung

Muscle

Ovary

Placenta

Testis

ENSG00000252824

ENST00000517015

N/A

2.622±0.00

N/A

0.277±0.00

ENSG00000261535

ENST00000566572

0.072±0.00

0.098±0.00

0.211±0.00

0.260±0.00

0.052±0.00

0.412±0.00

0.068±0.05

0.025±0.00

0.530±0.46

N/A

0.360±0.34

1.414±1.10

1.300±0.00

0.459±0.41

ENSG00000272219

ENST00000606640

0.015±0.00

0.183±0.00

0.833±0.00

0.125±0.03

0.392±0.31

0.563±0.53

0.069±0.04

0.084±0.00

0.345±0.30

0.324±0.26

0.048±0.00

0.235±0.22

0.113±0.00

0.119±0.03

ENSG00000279724

ENST00000624939

0.176±0.00

0.970±0.00

N/A

0.302±0.00

0.618±0.00

3.016±2.77

0.244±0.00

0.087±0.00

N/A

0.758±0.00

N/A

1.134±0.64

0.926±0.00

0.494±0.00

ENSG00000280004

ENST00000624984

0.235±0.00

N/A

0.142±0.00

N/A

1.467±0.63

0.819±0.00

2.987±0.00

ENSG00000280404

ENST00000623065

0.390±0.00

0.788±0.00

1.557±0.00

0.343±0.00

0.307±0.00

0.186±0.00

0.096±0.00

0.100±0.00

0.528±0.00

N/A

0.279±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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