Institute of Cardiovascular Regeneration Webtool Repository

Notice (8): Undefined index: CIL_00066U_0001 [APP/View/Region/show.ctp, line 46]Code Context
        <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
        <?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
	'region_arr' => array(
		'CIL_00066U_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
		'ENSG00000279493' => null,
		'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
		'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
		'ENSMUSG00000000732' => 'icos ligand'
	),
	'gene_name_arr' => array(
		'ENSG00000277117' => 'ICOSLG',
		'ENSG00000279493' => 'CH507-9B2.2',
		'ENSMUSG00000000730' => 'Dnmt3l',
		'ENSMUSG00000000731' => 'Aire',
		'ENSMUSG00000000732' => 'Icosl'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 3 => 'Adrenal',
		(int) 6 => 'Bladder',
		(int) 9 => 'Brain',
		(int) 16 => 'Breast',
		(int) 26 => 'Colon',
		(int) 34 => 'Heart',
		(int) 42 => 'Kidney',
		(int) 53 => 'Liver',
		(int) 59 => 'Lung',
		(int) 68 => 'Muscle',
		(int) 75 => 'Ovary',
		(int) 85 => 'Placenta',
		(int) 90 => '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) 31,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000612610' => array(
			'start' => '5022493',
			'end' => '5040661',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-003'
		),
		'ENST00000620481' => array(
			'start' => '5022493',
			'end' => '5040666',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-201'
		),
		'ENST00000623795' => array(
			'start' => '5022533',
			'end' => '5036125',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-004'
		),
		'ENST00000623903' => array(
			'start' => '5022531',
			'end' => '5034684',
			'transcript_biotype' => 'nonsense_mediated_decay',
			'transcript_name' => 'ICOSLG-002'
		),
		'ENST00000623960' => array(
			'start' => '5022494',
			'end' => '5036771',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-001'
		),
		'ENST00000624081' => array(
			'start' => '5011799',
			'end' => '5017145',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'CH507-9B2.2-001'
		),
		'ENSMUST00000000746' => array(
			'start' => '78049842',
			'end' => '78063622',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-003'
		),
		'ENSMUST00000123940' => array(
			'start' => '78055335',
			'end' => '78063615',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-006'
		),
		'ENSMUST00000131825' => array(
			'start' => '78055335',
			'end' => '78063615',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-004'
		),
		'ENSMUST00000135316' => array(
			'start' => '78041947',
			'end' => '78045903',
			'transcript_biotype' => 'processed_transcript',
			'transcript_name' => 'Dnmt3l-007'
		),
		'ENSMUST00000138785' => array(
			'start' => '78042287',
			'end' => '78063622',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-001'
		),
		'ENSMUST00000139539' => array(
			'start' => '78055335',
			'end' => '78063615',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-005'
		),
		'ENSMUST00000144446' => array(
			'start' => '78054835',
			'end' => '78057368',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Dnmt3l-008'
		),
		'ENSMUST00000151242' => array(
			'start' => '78049959',
			'end' => '78063616',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-002'
		),
		'ENSMUST00000019257' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-008'
		),
		'ENSMUST00000105395' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-010'
		),
		'ENSMUST00000105396' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-012'
		),
		'ENSMUST00000128241' => array(
			'start' => '78030022',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-007'
		),
		'ENSMUST00000130972' => array(
			'start' => '78030022',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-002'
		),
		'ENSMUST00000131028' => array(
			'start' => '78030023',
			'end' => '78043610',
			'transcript_biotype' => 'nonsense_mediated_decay',
			'transcript_name' => 'Aire-013'
		),
		'ENSMUST00000140636' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-004'
		),
		'ENSMUST00000141255' => array(
			'start' => '78036264',
			'end' => '78041717',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Aire-014'
		),
		'ENSMUST00000143452' => array(
			'start' => '78031855',
			'end' => '78038260',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Aire-016'
		),
		'ENSMUST00000143548' => array(
			'start' => '78030023',
			'end' => '78038258',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Aire-015'
		),
		'ENSMUST00000143735' => array(
			'start' => '78030071',
			'end' => '78043572',
			'transcript_biotype' => 'nonsense_mediated_decay',
			'transcript_name' => 'Aire-009'
		),
		'ENSMUST00000145975' => array(
			'start' => '78030022',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-001'
		),
		'ENSMUST00000148469' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-005'
		),
		'ENSMUST00000154374' => array(
			'start' => '78030071',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-006'
		),
		'ENSMUST00000155021' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-003'
		),
		'ENSMUST00000156417' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-011'
		),
		'ENSMUST00000105393' => array(
			'start' => '78069360',
			'end' => '78079525',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Icosl-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_00066U_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00066U_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000000730' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000000732' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Ovary',
			(int) 1 => 'Placenta',
			(int) 2 => 'Testis',
			(int) 3 => 'Adipose',
			(int) 4 => 'Adrenal',
			(int) 5 => 'Bladder',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Ovary',
			(int) 14 => 'Breast',
			(int) 15 => 'Colon',
			(int) 16 => 'Lung',
			(int) 17 => 'Testis',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Heart',
			(int) 21 => 'Kidney',
			(int) 22 => 'Liver',
			(int) 23 => 'Lung',
			(int) 24 => 'Muscle',
			(int) 25 => 'Heart',
			(int) 26 => 'Kidney',
			(int) 27 => 'Lung',
			(int) 28 => 'Muscle',
			(int) 29 => 'Ovary',
			(int) 30 => 'Placenta',
			(int) 31 => 'Testis',
			(int) 32 => 'Breast',
			(int) 33 => 'Breast',
			(int) 34 => 'Brain',
			(int) 35 => 'Breast',
			(int) 36 => 'Colon',
			(int) 37 => 'Kidney',
			(int) 38 => 'Liver',
			(int) 39 => 'Lung',
			(int) 40 => 'Ovary',
			(int) 41 => 'Heart',
			(int) 42 => 'Muscle',
			(int) 43 => 'Brain',
			(int) 44 => 'Breast',
			(int) 45 => 'Brain',
			(int) 46 => 'Heart',
			(int) 47 => 'Liver',
			(int) 48 => 'Breast',
			(int) 49 => 'Kidney',
			(int) 50 => 'Lung',
			(int) 51 => 'Muscle',
			(int) 52 => 'Ovary',
			(int) 53 => 'Kidney',
			(int) 54 => 'Colon',
			(int) 55 => 'Colon',
			(int) 56 => 'Lung',
			(int) 57 => 'Muscle',
			(int) 58 => 'Kidney',
			(int) 59 => 'Lung',
			(int) 60 => 'Ovary',
			(int) 61 => 'Kidney',
			(int) 62 => 'Ovary',
			(int) 63 => 'Adipose',
			(int) 64 => 'Adrenal',
			(int) 65 => 'Bladder',
			(int) 66 => 'Brain',
			(int) 67 => 'Breast',
			(int) 68 => 'Colon',
			(int) 69 => 'Heart',
			(int) 70 => 'Kidney',
			(int) 71 => 'Liver',
			(int) 72 => 'Lung',
			(int) 73 => 'Muscle',
			(int) 74 => 'Ovary',
			(int) 75 => 'Placenta',
			(int) 76 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
	'ENSG00000279493' => null,
	'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
	'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
	'ENSMUSG00000000732' => 'icos ligand'
)
$gene_name_arr = array(
	'ENSG00000277117' => 'ICOSLG',
	'ENSG00000279493' => 'CH507-9B2.2',
	'ENSMUSG00000000730' => 'Dnmt3l',
	'ENSMUSG00000000731' => 'Aire',
	'ENSMUSG00000000732' => 'Icosl'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00066U_0001',
			'tax_id' => '9606',
			'chromosome' => '21',
			'seq_start' => '5011799',
			'seq_end' => '5040666',
			'region_length' => '28867',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000279493-ENSG00000277117'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00066U_0002',
			'tax_id' => '10090',
			'chromosome' => '10',
			'seq_start' => '78041947',
			'seq_end' => '78079525',
			'region_length' => '37578',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000000730-ENSMUSG00000000732'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 3 => 'Adrenal',
	(int) 6 => 'Bladder',
	(int) 9 => 'Brain',
	(int) 16 => 'Breast',
	(int) 26 => 'Colon',
	(int) 34 => 'Heart',
	(int) 42 => 'Kidney',
	(int) 53 => 'Liver',
	(int) 59 => 'Lung',
	(int) 68 => 'Muscle',
	(int) 75 => 'Ovary',
	(int) 85 => 'Placenta',
	(int) 90 => '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) 31
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000612610' => array(
		'start' => '5022493',
		'end' => '5040661',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-003'
	),
	'ENST00000620481' => array(
		'start' => '5022493',
		'end' => '5040666',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-201'
	),
	'ENST00000623795' => array(
		'start' => '5022533',
		'end' => '5036125',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-004'
	),
	'ENST00000623903' => array(
		'start' => '5022531',
		'end' => '5034684',
		'transcript_biotype' => 'nonsense_mediated_decay',
		'transcript_name' => 'ICOSLG-002'
	),
	'ENST00000623960' => array(
		'start' => '5022494',
		'end' => '5036771',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-001'
	),
	'ENST00000624081' => array(
		'start' => '5011799',
		'end' => '5017145',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'CH507-9B2.2-001'
	),
	'ENSMUST00000000746' => array(
		'start' => '78049842',
		'end' => '78063622',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-003'
	),
	'ENSMUST00000123940' => array(
		'start' => '78055335',
		'end' => '78063615',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-006'
	),
	'ENSMUST00000131825' => array(
		'start' => '78055335',
		'end' => '78063615',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-004'
	),
	'ENSMUST00000135316' => array(
		'start' => '78041947',
		'end' => '78045903',
		'transcript_biotype' => 'processed_transcript',
		'transcript_name' => 'Dnmt3l-007'
	),
	'ENSMUST00000138785' => array(
		'start' => '78042287',
		'end' => '78063622',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-001'
	),
	'ENSMUST00000139539' => array(
		'start' => '78055335',
		'end' => '78063615',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-005'
	),
	'ENSMUST00000144446' => array(
		'start' => '78054835',
		'end' => '78057368',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Dnmt3l-008'
	),
	'ENSMUST00000151242' => array(
		'start' => '78049959',
		'end' => '78063616',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-002'
	),
	'ENSMUST00000019257' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-008'
	),
	'ENSMUST00000105395' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-010'
	),
	'ENSMUST00000105396' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-012'
	),
	'ENSMUST00000128241' => array(
		'start' => '78030022',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-007'
	),
	'ENSMUST00000130972' => array(
		'start' => '78030022',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-002'
	),
	'ENSMUST00000131028' => array(
		'start' => '78030023',
		'end' => '78043610',
		'transcript_biotype' => 'nonsense_mediated_decay',
		'transcript_name' => 'Aire-013'
	),
	'ENSMUST00000140636' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-004'
	),
	'ENSMUST00000141255' => array(
		'start' => '78036264',
		'end' => '78041717',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Aire-014'
	),
	'ENSMUST00000143452' => array(
		'start' => '78031855',
		'end' => '78038260',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Aire-016'
	),
	'ENSMUST00000143548' => array(
		'start' => '78030023',
		'end' => '78038258',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Aire-015'
	),
	'ENSMUST00000143735' => array(
		'start' => '78030071',
		'end' => '78043572',
		'transcript_biotype' => 'nonsense_mediated_decay',
		'transcript_name' => 'Aire-009'
	),
	'ENSMUST00000145975' => array(
		'start' => '78030022',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-001'
	),
	'ENSMUST00000148469' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-005'
	),
	'ENSMUST00000154374' => array(
		'start' => '78030071',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-006'
	),
	'ENSMUST00000155021' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-003'
	),
	'ENSMUST00000156417' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-011'
	),
	'ENSMUST00000105393' => array(
		'start' => '78069360',
		'end' => '78079525',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Icosl-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_00066U_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000000730' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000000732' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Ovary',
			(int) 1 => 'Placenta',
			(int) 2 => 'Testis',
			(int) 3 => 'Adipose',
			(int) 4 => 'Adrenal',
			(int) 5 => 'Bladder',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Ovary',
			(int) 14 => 'Breast',
			(int) 15 => 'Colon',
			(int) 16 => 'Lung',
			(int) 17 => 'Testis',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Heart',
			(int) 21 => 'Kidney',
			(int) 22 => 'Liver',
			(int) 23 => 'Lung',
			(int) 24 => 'Muscle',
			(int) 25 => 'Heart',
			(int) 26 => 'Kidney',
			(int) 27 => 'Lung',
			(int) 28 => 'Muscle',
			(int) 29 => 'Ovary',
			(int) 30 => 'Placenta',
			(int) 31 => 'Testis',
			(int) 32 => 'Breast',
			(int) 33 => 'Breast',
			(int) 34 => 'Brain',
			(int) 35 => 'Breast',
			(int) 36 => 'Colon',
			(int) 37 => 'Kidney',
			(int) 38 => 'Liver',
			(int) 39 => 'Lung',
			(int) 40 => 'Ovary',
			(int) 41 => 'Heart',
			(int) 42 => 'Muscle',
			(int) 43 => 'Brain',
			(int) 44 => 'Breast',
			(int) 45 => 'Brain',
			(int) 46 => 'Heart',
			(int) 47 => 'Liver',
			(int) 48 => 'Breast',
			(int) 49 => 'Kidney',
			(int) 50 => 'Lung',
			(int) 51 => 'Muscle',
			(int) 52 => 'Ovary',
			(int) 53 => 'Kidney',
			(int) 54 => 'Colon',
			(int) 55 => 'Colon',
			(int) 56 => 'Lung',
			(int) 57 => 'Muscle',
			(int) 58 => 'Kidney',
			(int) 59 => 'Lung',
			(int) 60 => 'Ovary',
			(int) 61 => 'Kidney',
			(int) 62 => 'Ovary',
			(int) 63 => 'Adipose',
			(int) 64 => 'Adrenal',
			(int) 65 => 'Bladder',
			(int) 66 => 'Brain',
			(int) 67 => 'Breast',
			(int) 68 => 'Colon',
			(int) 69 => 'Heart',
			(int) 70 => 'Kidney',
			(int) 71 => 'Liver',
			(int) 72 => 'Lung',
			(int) 73 => 'Muscle',
			(int) 74 => 'Ovary',
			(int) 75 => 'Placenta',
			(int) 76 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00066U_0001',
		'tax_id' => '9606',
		'chromosome' => '21',
		'seq_start' => '5011799',
		'seq_end' => '5040666',
		'region_length' => '28867',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000279493-ENSG00000277117'
	)
)
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_00066U_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	),
	'gene_desc_arr' => array(
		'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
		'ENSG00000279493' => null,
		'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
		'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
		'ENSMUSG00000000732' => 'icos ligand'
	),
	'gene_name_arr' => array(
		'ENSG00000277117' => 'ICOSLG',
		'ENSG00000279493' => 'CH507-9B2.2',
		'ENSMUSG00000000730' => 'Dnmt3l',
		'ENSMUSG00000000731' => 'Aire',
		'ENSMUSG00000000732' => 'Icosl'
	),
	'accession_table' => array(
		(int) 0 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'region_elements' => array(
				[maximum depth reached]
			)
		)
	),
	'all_tissues' => array(
		(int) 0 => 'Adipose',
		(int) 3 => 'Adrenal',
		(int) 6 => 'Bladder',
		(int) 9 => 'Brain',
		(int) 16 => 'Breast',
		(int) 26 => 'Colon',
		(int) 34 => 'Heart',
		(int) 42 => 'Kidney',
		(int) 53 => 'Liver',
		(int) 59 => 'Lung',
		(int) 68 => 'Muscle',
		(int) 75 => 'Ovary',
		(int) 85 => 'Placenta',
		(int) 90 => '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) 31,
	'longest_tissue_len' => (int) 8,
	'transcript_data' => array(
		'ENST00000612610' => array(
			'start' => '5022493',
			'end' => '5040661',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-003'
		),
		'ENST00000620481' => array(
			'start' => '5022493',
			'end' => '5040666',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-201'
		),
		'ENST00000623795' => array(
			'start' => '5022533',
			'end' => '5036125',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-004'
		),
		'ENST00000623903' => array(
			'start' => '5022531',
			'end' => '5034684',
			'transcript_biotype' => 'nonsense_mediated_decay',
			'transcript_name' => 'ICOSLG-002'
		),
		'ENST00000623960' => array(
			'start' => '5022494',
			'end' => '5036771',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'ICOSLG-001'
		),
		'ENST00000624081' => array(
			'start' => '5011799',
			'end' => '5017145',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'CH507-9B2.2-001'
		),
		'ENSMUST00000000746' => array(
			'start' => '78049842',
			'end' => '78063622',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-003'
		),
		'ENSMUST00000123940' => array(
			'start' => '78055335',
			'end' => '78063615',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-006'
		),
		'ENSMUST00000131825' => array(
			'start' => '78055335',
			'end' => '78063615',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-004'
		),
		'ENSMUST00000135316' => array(
			'start' => '78041947',
			'end' => '78045903',
			'transcript_biotype' => 'processed_transcript',
			'transcript_name' => 'Dnmt3l-007'
		),
		'ENSMUST00000138785' => array(
			'start' => '78042287',
			'end' => '78063622',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-001'
		),
		'ENSMUST00000139539' => array(
			'start' => '78055335',
			'end' => '78063615',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-005'
		),
		'ENSMUST00000144446' => array(
			'start' => '78054835',
			'end' => '78057368',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Dnmt3l-008'
		),
		'ENSMUST00000151242' => array(
			'start' => '78049959',
			'end' => '78063616',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Dnmt3l-002'
		),
		'ENSMUST00000019257' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-008'
		),
		'ENSMUST00000105395' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-010'
		),
		'ENSMUST00000105396' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-012'
		),
		'ENSMUST00000128241' => array(
			'start' => '78030022',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-007'
		),
		'ENSMUST00000130972' => array(
			'start' => '78030022',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-002'
		),
		'ENSMUST00000131028' => array(
			'start' => '78030023',
			'end' => '78043610',
			'transcript_biotype' => 'nonsense_mediated_decay',
			'transcript_name' => 'Aire-013'
		),
		'ENSMUST00000140636' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-004'
		),
		'ENSMUST00000141255' => array(
			'start' => '78036264',
			'end' => '78041717',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Aire-014'
		),
		'ENSMUST00000143452' => array(
			'start' => '78031855',
			'end' => '78038260',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Aire-016'
		),
		'ENSMUST00000143548' => array(
			'start' => '78030023',
			'end' => '78038258',
			'transcript_biotype' => 'retained_intron',
			'transcript_name' => 'Aire-015'
		),
		'ENSMUST00000143735' => array(
			'start' => '78030071',
			'end' => '78043572',
			'transcript_biotype' => 'nonsense_mediated_decay',
			'transcript_name' => 'Aire-009'
		),
		'ENSMUST00000145975' => array(
			'start' => '78030022',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-001'
		),
		'ENSMUST00000148469' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-005'
		),
		'ENSMUST00000154374' => array(
			'start' => '78030071',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-006'
		),
		'ENSMUST00000155021' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-003'
		),
		'ENSMUST00000156417' => array(
			'start' => '78030031',
			'end' => '78043580',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Aire-011'
		),
		'ENSMUST00000105393' => array(
			'start' => '78069360',
			'end' => '78079525',
			'transcript_biotype' => 'protein_coding',
			'transcript_name' => 'Icosl-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_00066U_0002' => array(
			'genes_in_region' => array(
				[maximum depth reached]
			),
			'tissues_title' => array(
				[maximum depth reached]
			)
		)
	)
)
$region_arr = array(
	'CIL_00066U_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000000730' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000000732' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Ovary',
			(int) 1 => 'Placenta',
			(int) 2 => 'Testis',
			(int) 3 => 'Adipose',
			(int) 4 => 'Adrenal',
			(int) 5 => 'Bladder',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Ovary',
			(int) 14 => 'Breast',
			(int) 15 => 'Colon',
			(int) 16 => 'Lung',
			(int) 17 => 'Testis',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Heart',
			(int) 21 => 'Kidney',
			(int) 22 => 'Liver',
			(int) 23 => 'Lung',
			(int) 24 => 'Muscle',
			(int) 25 => 'Heart',
			(int) 26 => 'Kidney',
			(int) 27 => 'Lung',
			(int) 28 => 'Muscle',
			(int) 29 => 'Ovary',
			(int) 30 => 'Placenta',
			(int) 31 => 'Testis',
			(int) 32 => 'Breast',
			(int) 33 => 'Breast',
			(int) 34 => 'Brain',
			(int) 35 => 'Breast',
			(int) 36 => 'Colon',
			(int) 37 => 'Kidney',
			(int) 38 => 'Liver',
			(int) 39 => 'Lung',
			(int) 40 => 'Ovary',
			(int) 41 => 'Heart',
			(int) 42 => 'Muscle',
			(int) 43 => 'Brain',
			(int) 44 => 'Breast',
			(int) 45 => 'Brain',
			(int) 46 => 'Heart',
			(int) 47 => 'Liver',
			(int) 48 => 'Breast',
			(int) 49 => 'Kidney',
			(int) 50 => 'Lung',
			(int) 51 => 'Muscle',
			(int) 52 => 'Ovary',
			(int) 53 => 'Kidney',
			(int) 54 => 'Colon',
			(int) 55 => 'Colon',
			(int) 56 => 'Lung',
			(int) 57 => 'Muscle',
			(int) 58 => 'Kidney',
			(int) 59 => 'Lung',
			(int) 60 => 'Ovary',
			(int) 61 => 'Kidney',
			(int) 62 => 'Ovary',
			(int) 63 => 'Adipose',
			(int) 64 => 'Adrenal',
			(int) 65 => 'Bladder',
			(int) 66 => 'Brain',
			(int) 67 => 'Breast',
			(int) 68 => 'Colon',
			(int) 69 => 'Heart',
			(int) 70 => 'Kidney',
			(int) 71 => 'Liver',
			(int) 72 => 'Lung',
			(int) 73 => 'Muscle',
			(int) 74 => 'Ovary',
			(int) 75 => 'Placenta',
			(int) 76 => 'Testis'
		)
	)
)
$gene_desc_arr = array(
	'ENSG00000277117' => 'inducible T-cell co-stimulator ligand',
	'ENSG00000279493' => null,
	'ENSMUSG00000000730' => 'DNA (cytosine-5-)-methyltransferase 3-like',
	'ENSMUSG00000000731' => 'autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)',
	'ENSMUSG00000000732' => 'icos ligand'
)
$gene_name_arr = array(
	'ENSG00000277117' => 'ICOSLG',
	'ENSG00000279493' => 'CH507-9B2.2',
	'ENSMUSG00000000730' => 'Dnmt3l',
	'ENSMUSG00000000731' => 'Aire',
	'ENSMUSG00000000732' => 'Icosl'
)
$accession_table = array(
	(int) 0 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00066U_0001',
			'tax_id' => '9606',
			'chromosome' => '21',
			'seq_start' => '5011799',
			'seq_end' => '5040666',
			'region_length' => '28867',
			'region_type' => 'CGP',
			'el_id' => 'ENSG00000279493-ENSG00000277117'
		)
	),
	(int) 1 => array(
		'region_elements' => array(
			'region_element_id' => 'CIL_00066U_0002',
			'tax_id' => '10090',
			'chromosome' => '10',
			'seq_start' => '78041947',
			'seq_end' => '78079525',
			'region_length' => '37578',
			'region_type' => 'CGP',
			'el_id' => 'ENSMUSG00000000730-ENSMUSG00000000732'
		)
	)
)
$all_tissues = array(
	(int) 0 => 'Adipose',
	(int) 3 => 'Adrenal',
	(int) 6 => 'Bladder',
	(int) 9 => 'Brain',
	(int) 16 => 'Breast',
	(int) 26 => 'Colon',
	(int) 34 => 'Heart',
	(int) 42 => 'Kidney',
	(int) 53 => 'Liver',
	(int) 59 => 'Lung',
	(int) 68 => 'Muscle',
	(int) 75 => 'Ovary',
	(int) 85 => 'Placenta',
	(int) 90 => '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) 31
$longest_tissue_len = (int) 8
$transcript_data = array(
	'ENST00000612610' => array(
		'start' => '5022493',
		'end' => '5040661',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-003'
	),
	'ENST00000620481' => array(
		'start' => '5022493',
		'end' => '5040666',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-201'
	),
	'ENST00000623795' => array(
		'start' => '5022533',
		'end' => '5036125',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-004'
	),
	'ENST00000623903' => array(
		'start' => '5022531',
		'end' => '5034684',
		'transcript_biotype' => 'nonsense_mediated_decay',
		'transcript_name' => 'ICOSLG-002'
	),
	'ENST00000623960' => array(
		'start' => '5022494',
		'end' => '5036771',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'ICOSLG-001'
	),
	'ENST00000624081' => array(
		'start' => '5011799',
		'end' => '5017145',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'CH507-9B2.2-001'
	),
	'ENSMUST00000000746' => array(
		'start' => '78049842',
		'end' => '78063622',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-003'
	),
	'ENSMUST00000123940' => array(
		'start' => '78055335',
		'end' => '78063615',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-006'
	),
	'ENSMUST00000131825' => array(
		'start' => '78055335',
		'end' => '78063615',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-004'
	),
	'ENSMUST00000135316' => array(
		'start' => '78041947',
		'end' => '78045903',
		'transcript_biotype' => 'processed_transcript',
		'transcript_name' => 'Dnmt3l-007'
	),
	'ENSMUST00000138785' => array(
		'start' => '78042287',
		'end' => '78063622',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-001'
	),
	'ENSMUST00000139539' => array(
		'start' => '78055335',
		'end' => '78063615',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-005'
	),
	'ENSMUST00000144446' => array(
		'start' => '78054835',
		'end' => '78057368',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Dnmt3l-008'
	),
	'ENSMUST00000151242' => array(
		'start' => '78049959',
		'end' => '78063616',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Dnmt3l-002'
	),
	'ENSMUST00000019257' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-008'
	),
	'ENSMUST00000105395' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-010'
	),
	'ENSMUST00000105396' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-012'
	),
	'ENSMUST00000128241' => array(
		'start' => '78030022',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-007'
	),
	'ENSMUST00000130972' => array(
		'start' => '78030022',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-002'
	),
	'ENSMUST00000131028' => array(
		'start' => '78030023',
		'end' => '78043610',
		'transcript_biotype' => 'nonsense_mediated_decay',
		'transcript_name' => 'Aire-013'
	),
	'ENSMUST00000140636' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-004'
	),
	'ENSMUST00000141255' => array(
		'start' => '78036264',
		'end' => '78041717',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Aire-014'
	),
	'ENSMUST00000143452' => array(
		'start' => '78031855',
		'end' => '78038260',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Aire-016'
	),
	'ENSMUST00000143548' => array(
		'start' => '78030023',
		'end' => '78038258',
		'transcript_biotype' => 'retained_intron',
		'transcript_name' => 'Aire-015'
	),
	'ENSMUST00000143735' => array(
		'start' => '78030071',
		'end' => '78043572',
		'transcript_biotype' => 'nonsense_mediated_decay',
		'transcript_name' => 'Aire-009'
	),
	'ENSMUST00000145975' => array(
		'start' => '78030022',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-001'
	),
	'ENSMUST00000148469' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-005'
	),
	'ENSMUST00000154374' => array(
		'start' => '78030071',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-006'
	),
	'ENSMUST00000155021' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-003'
	),
	'ENSMUST00000156417' => array(
		'start' => '78030031',
		'end' => '78043580',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Aire-011'
	),
	'ENSMUST00000105393' => array(
		'start' => '78069360',
		'end' => '78079525',
		'transcript_biotype' => 'protein_coding',
		'transcript_name' => 'Icosl-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_00066U_0002' => array(
		'genes_in_region' => array(
			'ENSMUSG00000000730' => array(
				[maximum depth reached]
			),
			'ENSMUSG00000000732' => array(
				[maximum depth reached]
			)
		),
		'tissues_title' => array(
			(int) 0 => 'Ovary',
			(int) 1 => 'Placenta',
			(int) 2 => 'Testis',
			(int) 3 => 'Adipose',
			(int) 4 => 'Adrenal',
			(int) 5 => 'Bladder',
			(int) 6 => 'Breast',
			(int) 7 => 'Colon',
			(int) 8 => 'Heart',
			(int) 9 => 'Kidney',
			(int) 10 => 'Liver',
			(int) 11 => 'Muscle',
			(int) 12 => 'Ovary',
			(int) 13 => 'Ovary',
			(int) 14 => 'Breast',
			(int) 15 => 'Colon',
			(int) 16 => 'Lung',
			(int) 17 => 'Testis',
			(int) 18 => 'Brain',
			(int) 19 => 'Breast',
			(int) 20 => 'Heart',
			(int) 21 => 'Kidney',
			(int) 22 => 'Liver',
			(int) 23 => 'Lung',
			(int) 24 => 'Muscle',
			(int) 25 => 'Heart',
			(int) 26 => 'Kidney',
			(int) 27 => 'Lung',
			(int) 28 => 'Muscle',
			(int) 29 => 'Ovary',
			(int) 30 => 'Placenta',
			(int) 31 => 'Testis',
			(int) 32 => 'Breast',
			(int) 33 => 'Breast',
			(int) 34 => 'Brain',
			(int) 35 => 'Breast',
			(int) 36 => 'Colon',
			(int) 37 => 'Kidney',
			(int) 38 => 'Liver',
			(int) 39 => 'Lung',
			(int) 40 => 'Ovary',
			(int) 41 => 'Heart',
			(int) 42 => 'Muscle',
			(int) 43 => 'Brain',
			(int) 44 => 'Breast',
			(int) 45 => 'Brain',
			(int) 46 => 'Heart',
			(int) 47 => 'Liver',
			(int) 48 => 'Breast',
			(int) 49 => 'Kidney',
			(int) 50 => 'Lung',
			(int) 51 => 'Muscle',
			(int) 52 => 'Ovary',
			(int) 53 => 'Kidney',
			(int) 54 => 'Colon',
			(int) 55 => 'Colon',
			(int) 56 => 'Lung',
			(int) 57 => 'Muscle',
			(int) 58 => 'Kidney',
			(int) 59 => 'Lung',
			(int) 60 => 'Ovary',
			(int) 61 => 'Kidney',
			(int) 62 => 'Ovary',
			(int) 63 => 'Adipose',
			(int) 64 => 'Adrenal',
			(int) 65 => 'Bladder',
			(int) 66 => 'Brain',
			(int) 67 => 'Breast',
			(int) 68 => 'Colon',
			(int) 69 => 'Heart',
			(int) 70 => 'Kidney',
			(int) 71 => 'Liver',
			(int) 72 => 'Lung',
			(int) 73 => 'Muscle',
			(int) 74 => 'Ovary',
			(int) 75 => 'Placenta',
			(int) 76 => 'Testis'
		)
	)
)
$accession = array(
	'region_elements' => array(
		'region_element_id' => 'CIL_00066U_0001',
		'tax_id' => '9606',
		'chromosome' => '21',
		'seq_start' => '5011799',
		'seq_end' => '5040666',
		'region_length' => '28867',
		'region_type' => 'CGP',
		'el_id' => 'ENSG00000279493-ENSG00000277117'
	)
)
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
ENSG00000279493-ENSG00000277117		CGP	9606	21:5011799-5040666
Gene		Transcript	Position	Biotype

Source ID	Type	Tax ID	Position
ENSMUSG00000000730-ENSMUSG00000000732	CGP	10090	10:78041947-78079525
Gene	Transcript	Position	Biotype
ENSMUSG00000000730 (Dnmt3l) DNA (cytosine-5-)-methyltransferase 3-like	ENSMUST00000000746 (Dnmt3l-003)	78049842-78063622	protein_coding
	ENSMUST00000123940 (Dnmt3l-006)	78055335-78063615	protein_coding
	ENSMUST00000131825 (Dnmt3l-004)	78055335-78063615	protein_coding
	ENSMUST00000135316 (Dnmt3l-007)	78041947-78045903	processed_transcript
	ENSMUST00000138785 (Dnmt3l-001)	78042287-78063622	protein_coding
	ENSMUST00000139539 (Dnmt3l-005)	78055335-78063615	protein_coding
	ENSMUST00000144446 (Dnmt3l-008)	78054835-78057368	retained_intron
	ENSMUST00000151242 (Dnmt3l-002)	78049959-78063616	protein_coding
ENSMUSG00000000732 (Icosl) icos ligand	ENSMUST00000105393 (Icosl-201)	78069360-78079525	protein_coding

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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