Notice (8): Undefined index: CIL_0008VY_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_0008VY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000232190' => null,
'ENSG00000260026' => null,
'ENSG00000260387' => null,
'ENSG00000260456' => 'chromosome 16 open reading frame 95',
'ENSG00000260795' => null,
'ENSG00000261095' => null,
'ENSG00000261161' => null,
'ENSG00000261175' => null,
'ENSG00000261363' => null,
'ENSG00000274478' => null,
'ENSG00000275934' => null,
'ENSMUSG00000031809' => 'RIKEN cDNA 1700018B08 gene',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000042812' => 'forkhead box F1',
'ENSMUSG00000046714' => 'forkhead box C2',
'ENSMUSG00000052934' => 'F-box protein 31',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000096952' => 'predicted gene, 26572',
'ENSMUSG00000097084' => 'forkhead box L1',
'ENSMUSG00000097097' => 'RIKEN cDNA 5033426O07 gene',
'ENSMUSG00000097336' => 'Foxf1 adjacent non-coding developmental regulatory RNA',
'ENSMUSG00000097384' => 'predicted gene, 26815',
'ENSMUSG00000097424' => 'RIKEN cDNA 1700030M09 gene',
'ENSMUSG00000097438' => 'predicted gene, 26784',
'ENSMUSG00000097783' => 'predicted gene, 26747',
'ENSMUSG00000097987' => 'predicted gene, 17786',
'ENSMUSG00000098211' => 'predicted gene, 27045',
'ENSMUSG00000098560' => 'predicted gene, 27530',
'ENSMUSG00000101886' => 'predicted gene 28324'
),
'gene_name_arr' => array(
'ENSG00000232190' => 'RP11-134D3.1',
'ENSG00000260026' => 'CTD-2015G9.1',
'ENSG00000260387' => 'RP11-463O9.6',
'ENSG00000260456' => 'C16orf95',
'ENSG00000260795' => 'RP11-107C10.1',
'ENSG00000261095' => 'RP11-899L11.1',
'ENSG00000261161' => 'RP11-58A18.1',
'ENSG00000261175' => 'CTD-2015G9.2',
'ENSG00000261363' => 'RP11-134D3.2',
'ENSG00000274478' => 'RP11-58A18.2',
'ENSG00000275934' => 'AC009108.1',
'ENSMUSG00000031809' => '1700018B08Rik',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000042812' => 'Foxf1',
'ENSMUSG00000046714' => 'Foxc2',
'ENSMUSG00000052934' => 'Fbxo31',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000096952' => 'Gm26572',
'ENSMUSG00000097084' => 'Foxl1',
'ENSMUSG00000097097' => '5033426O07Rik',
'ENSMUSG00000097336' => 'Fendrr',
'ENSMUSG00000097384' => 'Gm26815',
'ENSMUSG00000097424' => '1700030M09Rik',
'ENSMUSG00000097438' => 'Gm26784',
'ENSMUSG00000097783' => 'Gm26747',
'ENSMUSG00000097987' => 'Gm17786',
'ENSMUSG00000098211' => 'Gm27045',
'ENSMUSG00000098560' => 'Gm27530',
'ENSMUSG00000101886' => 'RP23-80D9.2'
),
'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) 4 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 12 => 'Brain',
(int) 15 => 'Breast',
(int) 18 => 'Colon',
(int) 21 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 42 => 'Placenta',
(int) 44 => '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) 67,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000430050' => array(
'start' => '87057784',
'end' => '87063991',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.1-001'
),
'ENST00000563331' => array(
'start' => '86720688',
'end' => '86721954',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.1-001'
),
'ENST00000566485' => array(
'start' => '86636328',
'end' => '86637145',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-463O9.6-001'
),
'ENST00000253461' => array(
'start' => '87302814',
'end' => '87317416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-002'
),
'ENST00000562840' => array(
'start' => '87083562',
'end' => '87302762',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-006'
),
'ENST00000564821' => array(
'start' => '87293011',
'end' => '87303073',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-005'
),
'ENST00000565212' => array(
'start' => '87302814',
'end' => '87306125',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-004'
),
'ENST00000567970' => array(
'start' => '87302884',
'end' => '87317380',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-003'
),
'ENST00000618367' => array(
'start' => '87302801',
'end' => '87317420',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-201'
),
'ENST00000618912' => array(
'start' => '87302814',
'end' => '87303655',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'C16orf95-001'
),
'ENST00000566109' => array(
'start' => '86906175',
'end' => '86906472',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-107C10.1-001'
),
'ENST00000566092' => array(
'start' => '87212122',
'end' => '87226430',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-899L11.1-001'
),
'ENST00000565822' => array(
'start' => '86646301',
'end' => '86668923',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.1-001'
),
'ENST00000562064' => array(
'start' => '86722092',
'end' => '86737719',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-001'
),
'ENST00000569740' => array(
'start' => '86722091',
'end' => '86741059',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-002'
),
'ENST00000566798' => array(
'start' => '87066705',
'end' => '87069752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.2-001'
),
'ENST00000621177' => array(
'start' => '86698118',
'end' => '86698841',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.2-001'
),
'ENST00000613364' => array(
'start' => '86613416',
'end' => '86613498',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC009108.1-201'
),
'ENSMUST00000034265' => array(
'start' => '121530780',
'end' => '121541954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-001'
),
'ENSMUST00000182460' => array(
'start' => '121531814',
'end' => '121544320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-004'
),
'ENSMUST00000182739' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-002'
),
'ENSMUST00000183280' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-003'
),
'ENSMUST00000034270' => array(
'start' => '121590361',
'end' => '121598760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-001'
),
'ENSMUST00000180548' => array(
'start' => '121590481',
'end' => '121598046',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-002'
),
'ENSMUST00000181521' => array(
'start' => '121590712',
'end' => '121596995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-005'
),
'ENSMUST00000181826' => array(
'start' => '121590477',
'end' => '121593109',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-004'
),
'ENSMUST00000181948' => array(
'start' => '121590484',
'end' => '121597012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-003'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000181504' => array(
'start' => '121084386',
'end' => '121088144',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxf1-001'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
),
'ENSMUST00000059018' => array(
'start' => '121549440',
'end' => '121578806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-001'
),
'ENSMUST00000180539' => array(
'start' => '121555623',
'end' => '121559963',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fbxo31-003'
),
'ENSMUST00000180979' => array(
'start' => '121553999',
'end' => '121559099',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fbxo31-004'
),
'ENSMUST00000181663' => array(
'start' => '121564331',
'end' => '121578790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-002'
),
'ENSMUST00000046386' => array(
'start' => '121598703',
'end' => '121652901',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-001'
),
'ENSMUST00000134212' => array(
'start' => '121608585',
'end' => '121628610',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-003'
),
'ENSMUST00000139379' => array(
'start' => '121606214',
'end' => '121607218',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-004'
),
'ENSMUST00000154725' => array(
'start' => '121600350',
'end' => '121604514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-002'
),
'ENSMUST00000181096' => array(
'start' => '121091628',
'end' => '121094858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26572-001'
),
'ENSMUST00000181609' => array(
'start' => '121127940',
'end' => '121130644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxl1-001'
),
'ENSMUST00000180796' => array(
'start' => '121198714',
'end' => '121201835',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '5033426O07Rik-001'
),
'ENSMUST00000181231' => array(
'start' => '121058803',
'end' => '121060413',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-002'
),
'ENSMUST00000181530' => array(
'start' => '121054882',
'end' => '121083032',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-001'
),
'ENSMUST00000182264' => array(
'start' => '121059119',
'end' => '121083110',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-003'
),
'ENSMUST00000181200' => array(
'start' => '121256747',
'end' => '121356836',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26815-001'
),
'ENSMUST00000181133' => array(
'start' => '121544382',
'end' => '121548342',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-002'
),
'ENSMUST00000181679' => array(
'start' => '121544388',
'end' => '121547652',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-001'
),
'ENSMUST00000181666' => array(
'start' => '121434980',
'end' => '121435389',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26784-001'
),
'ENSMUST00000180597' => array(
'start' => '121421345',
'end' => '121427188',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26747-001'
),
'ENSMUST00000182000' => array(
'start' => '121581765',
'end' => '121582191',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17786-001'
),
'ENSMUST00000182145' => array(
'start' => '121542122',
'end' => '121543481',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27045-001'
),
'ENSMUST00000184096' => array(
'start' => '121084609',
'end' => '121084706',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm27530-201'
),
'ENSMUST00000187913' => array(
'start' => '121002927',
'end' => '121003190',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-80D9.2-001'
)
),
'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_0008VY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008VY_0001' => array(
'genes_in_region' => array(
'ENSG00000232190' => array(
[maximum depth reached]
),
'ENSG00000260026' => array(
[maximum depth reached]
),
'ENSG00000260795' => array(
[maximum depth reached]
),
'ENSG00000261095' => array(
[maximum depth reached]
),
'ENSG00000261161' => array(
[maximum depth reached]
),
'ENSG00000261175' => array(
[maximum depth reached]
),
'ENSG00000261363' => array(
[maximum depth reached]
),
'ENSG00000274478' => array(
[maximum depth reached]
),
'ENSG00000275934' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Heart',
(int) 14 => 'Ovary',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Ovary',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Testis',
(int) 37 => 'Adrenal',
(int) 38 => 'Kidney',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Kidney',
(int) 45 => 'Lung',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Adipose',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Lung',
(int) 54 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000232190' => null,
'ENSG00000260026' => null,
'ENSG00000260387' => null,
'ENSG00000260456' => 'chromosome 16 open reading frame 95',
'ENSG00000260795' => null,
'ENSG00000261095' => null,
'ENSG00000261161' => null,
'ENSG00000261175' => null,
'ENSG00000261363' => null,
'ENSG00000274478' => null,
'ENSG00000275934' => null,
'ENSMUSG00000031809' => 'RIKEN cDNA 1700018B08 gene',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000042812' => 'forkhead box F1',
'ENSMUSG00000046714' => 'forkhead box C2',
'ENSMUSG00000052934' => 'F-box protein 31',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000096952' => 'predicted gene, 26572',
'ENSMUSG00000097084' => 'forkhead box L1',
'ENSMUSG00000097097' => 'RIKEN cDNA 5033426O07 gene',
'ENSMUSG00000097336' => 'Foxf1 adjacent non-coding developmental regulatory RNA',
'ENSMUSG00000097384' => 'predicted gene, 26815',
'ENSMUSG00000097424' => 'RIKEN cDNA 1700030M09 gene',
'ENSMUSG00000097438' => 'predicted gene, 26784',
'ENSMUSG00000097783' => 'predicted gene, 26747',
'ENSMUSG00000097987' => 'predicted gene, 17786',
'ENSMUSG00000098211' => 'predicted gene, 27045',
'ENSMUSG00000098560' => 'predicted gene, 27530',
'ENSMUSG00000101886' => 'predicted gene 28324'
)
$gene_name_arr = array(
'ENSG00000232190' => 'RP11-134D3.1',
'ENSG00000260026' => 'CTD-2015G9.1',
'ENSG00000260387' => 'RP11-463O9.6',
'ENSG00000260456' => 'C16orf95',
'ENSG00000260795' => 'RP11-107C10.1',
'ENSG00000261095' => 'RP11-899L11.1',
'ENSG00000261161' => 'RP11-58A18.1',
'ENSG00000261175' => 'CTD-2015G9.2',
'ENSG00000261363' => 'RP11-134D3.2',
'ENSG00000274478' => 'RP11-58A18.2',
'ENSG00000275934' => 'AC009108.1',
'ENSMUSG00000031809' => '1700018B08Rik',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000042812' => 'Foxf1',
'ENSMUSG00000046714' => 'Foxc2',
'ENSMUSG00000052934' => 'Fbxo31',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000096952' => 'Gm26572',
'ENSMUSG00000097084' => 'Foxl1',
'ENSMUSG00000097097' => '5033426O07Rik',
'ENSMUSG00000097336' => 'Fendrr',
'ENSMUSG00000097384' => 'Gm26815',
'ENSMUSG00000097424' => '1700030M09Rik',
'ENSMUSG00000097438' => 'Gm26784',
'ENSMUSG00000097783' => 'Gm26747',
'ENSMUSG00000097987' => 'Gm17786',
'ENSMUSG00000098211' => 'Gm27045',
'ENSMUSG00000098560' => 'Gm27530',
'ENSMUSG00000101886' => 'RP23-80D9.2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008VY_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '86609761',
'seq_end' => '87212569',
'region_length' => '602808',
'region_type' => 'VISTA',
'el_id' => 'hs1613'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008VY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121000361',
'seq_end' => '121603557',
'region_length' => '603196',
'region_type' => 'VISTA',
'el_id' => 'hs1613'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 12 => 'Brain',
(int) 15 => 'Breast',
(int) 18 => 'Colon',
(int) 21 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 42 => 'Placenta',
(int) 44 => '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) 67
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000430050' => array(
'start' => '87057784',
'end' => '87063991',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.1-001'
),
'ENST00000563331' => array(
'start' => '86720688',
'end' => '86721954',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.1-001'
),
'ENST00000566485' => array(
'start' => '86636328',
'end' => '86637145',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-463O9.6-001'
),
'ENST00000253461' => array(
'start' => '87302814',
'end' => '87317416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-002'
),
'ENST00000562840' => array(
'start' => '87083562',
'end' => '87302762',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-006'
),
'ENST00000564821' => array(
'start' => '87293011',
'end' => '87303073',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-005'
),
'ENST00000565212' => array(
'start' => '87302814',
'end' => '87306125',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-004'
),
'ENST00000567970' => array(
'start' => '87302884',
'end' => '87317380',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-003'
),
'ENST00000618367' => array(
'start' => '87302801',
'end' => '87317420',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-201'
),
'ENST00000618912' => array(
'start' => '87302814',
'end' => '87303655',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'C16orf95-001'
),
'ENST00000566109' => array(
'start' => '86906175',
'end' => '86906472',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-107C10.1-001'
),
'ENST00000566092' => array(
'start' => '87212122',
'end' => '87226430',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-899L11.1-001'
),
'ENST00000565822' => array(
'start' => '86646301',
'end' => '86668923',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.1-001'
),
'ENST00000562064' => array(
'start' => '86722092',
'end' => '86737719',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-001'
),
'ENST00000569740' => array(
'start' => '86722091',
'end' => '86741059',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-002'
),
'ENST00000566798' => array(
'start' => '87066705',
'end' => '87069752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.2-001'
),
'ENST00000621177' => array(
'start' => '86698118',
'end' => '86698841',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.2-001'
),
'ENST00000613364' => array(
'start' => '86613416',
'end' => '86613498',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC009108.1-201'
),
'ENSMUST00000034265' => array(
'start' => '121530780',
'end' => '121541954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-001'
),
'ENSMUST00000182460' => array(
'start' => '121531814',
'end' => '121544320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-004'
),
'ENSMUST00000182739' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-002'
),
'ENSMUST00000183280' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-003'
),
'ENSMUST00000034270' => array(
'start' => '121590361',
'end' => '121598760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-001'
),
'ENSMUST00000180548' => array(
'start' => '121590481',
'end' => '121598046',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-002'
),
'ENSMUST00000181521' => array(
'start' => '121590712',
'end' => '121596995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-005'
),
'ENSMUST00000181826' => array(
'start' => '121590477',
'end' => '121593109',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-004'
),
'ENSMUST00000181948' => array(
'start' => '121590484',
'end' => '121597012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-003'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000181504' => array(
'start' => '121084386',
'end' => '121088144',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxf1-001'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
),
'ENSMUST00000059018' => array(
'start' => '121549440',
'end' => '121578806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-001'
),
'ENSMUST00000180539' => array(
'start' => '121555623',
'end' => '121559963',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fbxo31-003'
),
'ENSMUST00000180979' => array(
'start' => '121553999',
'end' => '121559099',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fbxo31-004'
),
'ENSMUST00000181663' => array(
'start' => '121564331',
'end' => '121578790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-002'
),
'ENSMUST00000046386' => array(
'start' => '121598703',
'end' => '121652901',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-001'
),
'ENSMUST00000134212' => array(
'start' => '121608585',
'end' => '121628610',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-003'
),
'ENSMUST00000139379' => array(
'start' => '121606214',
'end' => '121607218',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-004'
),
'ENSMUST00000154725' => array(
'start' => '121600350',
'end' => '121604514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-002'
),
'ENSMUST00000181096' => array(
'start' => '121091628',
'end' => '121094858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26572-001'
),
'ENSMUST00000181609' => array(
'start' => '121127940',
'end' => '121130644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxl1-001'
),
'ENSMUST00000180796' => array(
'start' => '121198714',
'end' => '121201835',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '5033426O07Rik-001'
),
'ENSMUST00000181231' => array(
'start' => '121058803',
'end' => '121060413',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-002'
),
'ENSMUST00000181530' => array(
'start' => '121054882',
'end' => '121083032',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-001'
),
'ENSMUST00000182264' => array(
'start' => '121059119',
'end' => '121083110',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-003'
),
'ENSMUST00000181200' => array(
'start' => '121256747',
'end' => '121356836',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26815-001'
),
'ENSMUST00000181133' => array(
'start' => '121544382',
'end' => '121548342',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-002'
),
'ENSMUST00000181679' => array(
'start' => '121544388',
'end' => '121547652',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-001'
),
'ENSMUST00000181666' => array(
'start' => '121434980',
'end' => '121435389',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26784-001'
),
'ENSMUST00000180597' => array(
'start' => '121421345',
'end' => '121427188',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26747-001'
),
'ENSMUST00000182000' => array(
'start' => '121581765',
'end' => '121582191',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17786-001'
),
'ENSMUST00000182145' => array(
'start' => '121542122',
'end' => '121543481',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27045-001'
),
'ENSMUST00000184096' => array(
'start' => '121084609',
'end' => '121084706',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm27530-201'
),
'ENSMUST00000187913' => array(
'start' => '121002927',
'end' => '121003190',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-80D9.2-001'
)
)
$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_0008VY_0001' => array(
'genes_in_region' => array(
'ENSG00000232190' => array(
[maximum depth reached]
),
'ENSG00000260026' => array(
[maximum depth reached]
),
'ENSG00000260795' => array(
[maximum depth reached]
),
'ENSG00000261095' => array(
[maximum depth reached]
),
'ENSG00000261161' => array(
[maximum depth reached]
),
'ENSG00000261175' => array(
[maximum depth reached]
),
'ENSG00000261363' => array(
[maximum depth reached]
),
'ENSG00000274478' => array(
[maximum depth reached]
),
'ENSG00000275934' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Heart',
(int) 14 => 'Ovary',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Ovary',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Testis',
(int) 37 => 'Adrenal',
(int) 38 => 'Kidney',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Kidney',
(int) 45 => 'Lung',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Adipose',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Lung',
(int) 54 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008VY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121000361',
'seq_end' => '121603557',
'region_length' => '603196',
'region_type' => 'VISTA',
'el_id' => 'hs1613'
)
)
$gene_el = array(
'ENST00000613364' => array(
'Adipose' => array(
'average_FPKM' => '0.431',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.332',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.849',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.403',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.408',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000275934'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.431',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.332',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.849',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.403',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.408',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000613364'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0008VY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000232190' => null,
'ENSG00000260026' => null,
'ENSG00000260387' => null,
'ENSG00000260456' => 'chromosome 16 open reading frame 95',
'ENSG00000260795' => null,
'ENSG00000261095' => null,
'ENSG00000261161' => null,
'ENSG00000261175' => null,
'ENSG00000261363' => null,
'ENSG00000274478' => null,
'ENSG00000275934' => null,
'ENSMUSG00000031809' => 'RIKEN cDNA 1700018B08 gene',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000042812' => 'forkhead box F1',
'ENSMUSG00000046714' => 'forkhead box C2',
'ENSMUSG00000052934' => 'F-box protein 31',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000096952' => 'predicted gene, 26572',
'ENSMUSG00000097084' => 'forkhead box L1',
'ENSMUSG00000097097' => 'RIKEN cDNA 5033426O07 gene',
'ENSMUSG00000097336' => 'Foxf1 adjacent non-coding developmental regulatory RNA',
'ENSMUSG00000097384' => 'predicted gene, 26815',
'ENSMUSG00000097424' => 'RIKEN cDNA 1700030M09 gene',
'ENSMUSG00000097438' => 'predicted gene, 26784',
'ENSMUSG00000097783' => 'predicted gene, 26747',
'ENSMUSG00000097987' => 'predicted gene, 17786',
'ENSMUSG00000098211' => 'predicted gene, 27045',
'ENSMUSG00000098560' => 'predicted gene, 27530',
'ENSMUSG00000101886' => 'predicted gene 28324'
),
'gene_name_arr' => array(
'ENSG00000232190' => 'RP11-134D3.1',
'ENSG00000260026' => 'CTD-2015G9.1',
'ENSG00000260387' => 'RP11-463O9.6',
'ENSG00000260456' => 'C16orf95',
'ENSG00000260795' => 'RP11-107C10.1',
'ENSG00000261095' => 'RP11-899L11.1',
'ENSG00000261161' => 'RP11-58A18.1',
'ENSG00000261175' => 'CTD-2015G9.2',
'ENSG00000261363' => 'RP11-134D3.2',
'ENSG00000274478' => 'RP11-58A18.2',
'ENSG00000275934' => 'AC009108.1',
'ENSMUSG00000031809' => '1700018B08Rik',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000042812' => 'Foxf1',
'ENSMUSG00000046714' => 'Foxc2',
'ENSMUSG00000052934' => 'Fbxo31',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000096952' => 'Gm26572',
'ENSMUSG00000097084' => 'Foxl1',
'ENSMUSG00000097097' => '5033426O07Rik',
'ENSMUSG00000097336' => 'Fendrr',
'ENSMUSG00000097384' => 'Gm26815',
'ENSMUSG00000097424' => '1700030M09Rik',
'ENSMUSG00000097438' => 'Gm26784',
'ENSMUSG00000097783' => 'Gm26747',
'ENSMUSG00000097987' => 'Gm17786',
'ENSMUSG00000098211' => 'Gm27045',
'ENSMUSG00000098560' => 'Gm27530',
'ENSMUSG00000101886' => 'RP23-80D9.2'
),
'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) 4 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 12 => 'Brain',
(int) 15 => 'Breast',
(int) 18 => 'Colon',
(int) 21 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 42 => 'Placenta',
(int) 44 => '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) 67,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000430050' => array(
'start' => '87057784',
'end' => '87063991',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.1-001'
),
'ENST00000563331' => array(
'start' => '86720688',
'end' => '86721954',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.1-001'
),
'ENST00000566485' => array(
'start' => '86636328',
'end' => '86637145',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-463O9.6-001'
),
'ENST00000253461' => array(
'start' => '87302814',
'end' => '87317416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-002'
),
'ENST00000562840' => array(
'start' => '87083562',
'end' => '87302762',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-006'
),
'ENST00000564821' => array(
'start' => '87293011',
'end' => '87303073',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-005'
),
'ENST00000565212' => array(
'start' => '87302814',
'end' => '87306125',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-004'
),
'ENST00000567970' => array(
'start' => '87302884',
'end' => '87317380',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-003'
),
'ENST00000618367' => array(
'start' => '87302801',
'end' => '87317420',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-201'
),
'ENST00000618912' => array(
'start' => '87302814',
'end' => '87303655',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'C16orf95-001'
),
'ENST00000566109' => array(
'start' => '86906175',
'end' => '86906472',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-107C10.1-001'
),
'ENST00000566092' => array(
'start' => '87212122',
'end' => '87226430',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-899L11.1-001'
),
'ENST00000565822' => array(
'start' => '86646301',
'end' => '86668923',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.1-001'
),
'ENST00000562064' => array(
'start' => '86722092',
'end' => '86737719',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-001'
),
'ENST00000569740' => array(
'start' => '86722091',
'end' => '86741059',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-002'
),
'ENST00000566798' => array(
'start' => '87066705',
'end' => '87069752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.2-001'
),
'ENST00000621177' => array(
'start' => '86698118',
'end' => '86698841',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.2-001'
),
'ENST00000613364' => array(
'start' => '86613416',
'end' => '86613498',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC009108.1-201'
),
'ENSMUST00000034265' => array(
'start' => '121530780',
'end' => '121541954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-001'
),
'ENSMUST00000182460' => array(
'start' => '121531814',
'end' => '121544320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-004'
),
'ENSMUST00000182739' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-002'
),
'ENSMUST00000183280' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-003'
),
'ENSMUST00000034270' => array(
'start' => '121590361',
'end' => '121598760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-001'
),
'ENSMUST00000180548' => array(
'start' => '121590481',
'end' => '121598046',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-002'
),
'ENSMUST00000181521' => array(
'start' => '121590712',
'end' => '121596995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-005'
),
'ENSMUST00000181826' => array(
'start' => '121590477',
'end' => '121593109',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-004'
),
'ENSMUST00000181948' => array(
'start' => '121590484',
'end' => '121597012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-003'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000181504' => array(
'start' => '121084386',
'end' => '121088144',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxf1-001'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
),
'ENSMUST00000059018' => array(
'start' => '121549440',
'end' => '121578806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-001'
),
'ENSMUST00000180539' => array(
'start' => '121555623',
'end' => '121559963',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fbxo31-003'
),
'ENSMUST00000180979' => array(
'start' => '121553999',
'end' => '121559099',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fbxo31-004'
),
'ENSMUST00000181663' => array(
'start' => '121564331',
'end' => '121578790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-002'
),
'ENSMUST00000046386' => array(
'start' => '121598703',
'end' => '121652901',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-001'
),
'ENSMUST00000134212' => array(
'start' => '121608585',
'end' => '121628610',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-003'
),
'ENSMUST00000139379' => array(
'start' => '121606214',
'end' => '121607218',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-004'
),
'ENSMUST00000154725' => array(
'start' => '121600350',
'end' => '121604514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-002'
),
'ENSMUST00000181096' => array(
'start' => '121091628',
'end' => '121094858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26572-001'
),
'ENSMUST00000181609' => array(
'start' => '121127940',
'end' => '121130644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxl1-001'
),
'ENSMUST00000180796' => array(
'start' => '121198714',
'end' => '121201835',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '5033426O07Rik-001'
),
'ENSMUST00000181231' => array(
'start' => '121058803',
'end' => '121060413',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-002'
),
'ENSMUST00000181530' => array(
'start' => '121054882',
'end' => '121083032',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-001'
),
'ENSMUST00000182264' => array(
'start' => '121059119',
'end' => '121083110',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-003'
),
'ENSMUST00000181200' => array(
'start' => '121256747',
'end' => '121356836',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26815-001'
),
'ENSMUST00000181133' => array(
'start' => '121544382',
'end' => '121548342',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-002'
),
'ENSMUST00000181679' => array(
'start' => '121544388',
'end' => '121547652',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-001'
),
'ENSMUST00000181666' => array(
'start' => '121434980',
'end' => '121435389',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26784-001'
),
'ENSMUST00000180597' => array(
'start' => '121421345',
'end' => '121427188',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26747-001'
),
'ENSMUST00000182000' => array(
'start' => '121581765',
'end' => '121582191',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17786-001'
),
'ENSMUST00000182145' => array(
'start' => '121542122',
'end' => '121543481',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27045-001'
),
'ENSMUST00000184096' => array(
'start' => '121084609',
'end' => '121084706',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm27530-201'
),
'ENSMUST00000187913' => array(
'start' => '121002927',
'end' => '121003190',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-80D9.2-001'
)
),
'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_0008VY_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008VY_0001' => array(
'genes_in_region' => array(
'ENSG00000232190' => array(
[maximum depth reached]
),
'ENSG00000260026' => array(
[maximum depth reached]
),
'ENSG00000260795' => array(
[maximum depth reached]
),
'ENSG00000261095' => array(
[maximum depth reached]
),
'ENSG00000261161' => array(
[maximum depth reached]
),
'ENSG00000261175' => array(
[maximum depth reached]
),
'ENSG00000261363' => array(
[maximum depth reached]
),
'ENSG00000274478' => array(
[maximum depth reached]
),
'ENSG00000275934' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Heart',
(int) 14 => 'Ovary',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Ovary',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Testis',
(int) 37 => 'Adrenal',
(int) 38 => 'Kidney',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Kidney',
(int) 45 => 'Lung',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Adipose',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Lung',
(int) 54 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000232190' => null,
'ENSG00000260026' => null,
'ENSG00000260387' => null,
'ENSG00000260456' => 'chromosome 16 open reading frame 95',
'ENSG00000260795' => null,
'ENSG00000261095' => null,
'ENSG00000261161' => null,
'ENSG00000261175' => null,
'ENSG00000261363' => null,
'ENSG00000274478' => null,
'ENSG00000275934' => null,
'ENSMUSG00000031809' => 'RIKEN cDNA 1700018B08 gene',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000042812' => 'forkhead box F1',
'ENSMUSG00000046714' => 'forkhead box C2',
'ENSMUSG00000052934' => 'F-box protein 31',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000096952' => 'predicted gene, 26572',
'ENSMUSG00000097084' => 'forkhead box L1',
'ENSMUSG00000097097' => 'RIKEN cDNA 5033426O07 gene',
'ENSMUSG00000097336' => 'Foxf1 adjacent non-coding developmental regulatory RNA',
'ENSMUSG00000097384' => 'predicted gene, 26815',
'ENSMUSG00000097424' => 'RIKEN cDNA 1700030M09 gene',
'ENSMUSG00000097438' => 'predicted gene, 26784',
'ENSMUSG00000097783' => 'predicted gene, 26747',
'ENSMUSG00000097987' => 'predicted gene, 17786',
'ENSMUSG00000098211' => 'predicted gene, 27045',
'ENSMUSG00000098560' => 'predicted gene, 27530',
'ENSMUSG00000101886' => 'predicted gene 28324'
)
$gene_name_arr = array(
'ENSG00000232190' => 'RP11-134D3.1',
'ENSG00000260026' => 'CTD-2015G9.1',
'ENSG00000260387' => 'RP11-463O9.6',
'ENSG00000260456' => 'C16orf95',
'ENSG00000260795' => 'RP11-107C10.1',
'ENSG00000261095' => 'RP11-899L11.1',
'ENSG00000261161' => 'RP11-58A18.1',
'ENSG00000261175' => 'CTD-2015G9.2',
'ENSG00000261363' => 'RP11-134D3.2',
'ENSG00000274478' => 'RP11-58A18.2',
'ENSG00000275934' => 'AC009108.1',
'ENSMUSG00000031809' => '1700018B08Rik',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000042812' => 'Foxf1',
'ENSMUSG00000046714' => 'Foxc2',
'ENSMUSG00000052934' => 'Fbxo31',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000096952' => 'Gm26572',
'ENSMUSG00000097084' => 'Foxl1',
'ENSMUSG00000097097' => '5033426O07Rik',
'ENSMUSG00000097336' => 'Fendrr',
'ENSMUSG00000097384' => 'Gm26815',
'ENSMUSG00000097424' => '1700030M09Rik',
'ENSMUSG00000097438' => 'Gm26784',
'ENSMUSG00000097783' => 'Gm26747',
'ENSMUSG00000097987' => 'Gm17786',
'ENSMUSG00000098211' => 'Gm27045',
'ENSMUSG00000098560' => 'Gm27530',
'ENSMUSG00000101886' => 'RP23-80D9.2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008VY_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '86609761',
'seq_end' => '87212569',
'region_length' => '602808',
'region_type' => 'VISTA',
'el_id' => 'hs1613'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008VY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121000361',
'seq_end' => '121603557',
'region_length' => '603196',
'region_type' => 'VISTA',
'el_id' => 'hs1613'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 12 => 'Brain',
(int) 15 => 'Breast',
(int) 18 => 'Colon',
(int) 21 => 'Heart',
(int) 25 => 'Kidney',
(int) 28 => 'Liver',
(int) 29 => 'Lung',
(int) 34 => 'Muscle',
(int) 37 => 'Ovary',
(int) 42 => 'Placenta',
(int) 44 => '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) 67
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000430050' => array(
'start' => '87057784',
'end' => '87063991',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.1-001'
),
'ENST00000563331' => array(
'start' => '86720688',
'end' => '86721954',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.1-001'
),
'ENST00000566485' => array(
'start' => '86636328',
'end' => '86637145',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-463O9.6-001'
),
'ENST00000253461' => array(
'start' => '87302814',
'end' => '87317416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-002'
),
'ENST00000562840' => array(
'start' => '87083562',
'end' => '87302762',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-006'
),
'ENST00000564821' => array(
'start' => '87293011',
'end' => '87303073',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-005'
),
'ENST00000565212' => array(
'start' => '87302814',
'end' => '87306125',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'C16orf95-004'
),
'ENST00000567970' => array(
'start' => '87302884',
'end' => '87317380',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-003'
),
'ENST00000618367' => array(
'start' => '87302801',
'end' => '87317420',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'C16orf95-201'
),
'ENST00000618912' => array(
'start' => '87302814',
'end' => '87303655',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'C16orf95-001'
),
'ENST00000566109' => array(
'start' => '86906175',
'end' => '86906472',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-107C10.1-001'
),
'ENST00000566092' => array(
'start' => '87212122',
'end' => '87226430',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-899L11.1-001'
),
'ENST00000565822' => array(
'start' => '86646301',
'end' => '86668923',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.1-001'
),
'ENST00000562064' => array(
'start' => '86722092',
'end' => '86737719',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-001'
),
'ENST00000569740' => array(
'start' => '86722091',
'end' => '86741059',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2015G9.2-002'
),
'ENST00000566798' => array(
'start' => '87066705',
'end' => '87069752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-134D3.2-001'
),
'ENST00000621177' => array(
'start' => '86698118',
'end' => '86698841',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-58A18.2-001'
),
'ENST00000613364' => array(
'start' => '86613416',
'end' => '86613498',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC009108.1-201'
),
'ENSMUST00000034265' => array(
'start' => '121530780',
'end' => '121541954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-001'
),
'ENSMUST00000182460' => array(
'start' => '121531814',
'end' => '121544320',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700018B08Rik-004'
),
'ENSMUST00000182739' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-002'
),
'ENSMUST00000183280' => array(
'start' => '121530828',
'end' => '121541869',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => '1700018B08Rik-003'
),
'ENSMUST00000034270' => array(
'start' => '121590361',
'end' => '121598760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-001'
),
'ENSMUST00000180548' => array(
'start' => '121590481',
'end' => '121598046',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-002'
),
'ENSMUST00000181521' => array(
'start' => '121590712',
'end' => '121596995',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-005'
),
'ENSMUST00000181826' => array(
'start' => '121590477',
'end' => '121593109',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Map1lc3b-004'
),
'ENSMUST00000181948' => array(
'start' => '121590484',
'end' => '121597012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Map1lc3b-003'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000181504' => array(
'start' => '121084386',
'end' => '121088144',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxf1-001'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
),
'ENSMUST00000059018' => array(
'start' => '121549440',
'end' => '121578806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-001'
),
'ENSMUST00000180539' => array(
'start' => '121555623',
'end' => '121559963',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Fbxo31-003'
),
'ENSMUST00000180979' => array(
'start' => '121553999',
'end' => '121559099',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Fbxo31-004'
),
'ENSMUST00000181663' => array(
'start' => '121564331',
'end' => '121578790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Fbxo31-002'
),
'ENSMUST00000046386' => array(
'start' => '121598703',
'end' => '121652901',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-001'
),
'ENSMUST00000134212' => array(
'start' => '121608585',
'end' => '121628610',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-003'
),
'ENSMUST00000139379' => array(
'start' => '121606214',
'end' => '121607218',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Zcchc14-004'
),
'ENSMUST00000154725' => array(
'start' => '121600350',
'end' => '121604514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Zcchc14-002'
),
'ENSMUST00000181096' => array(
'start' => '121091628',
'end' => '121094858',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26572-001'
),
'ENSMUST00000181609' => array(
'start' => '121127940',
'end' => '121130644',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxl1-001'
),
'ENSMUST00000180796' => array(
'start' => '121198714',
'end' => '121201835',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '5033426O07Rik-001'
),
'ENSMUST00000181231' => array(
'start' => '121058803',
'end' => '121060413',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-002'
),
'ENSMUST00000181530' => array(
'start' => '121054882',
'end' => '121083032',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-001'
),
'ENSMUST00000182264' => array(
'start' => '121059119',
'end' => '121083110',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Fendrr-003'
),
'ENSMUST00000181200' => array(
'start' => '121256747',
'end' => '121356836',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26815-001'
),
'ENSMUST00000181133' => array(
'start' => '121544382',
'end' => '121548342',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-002'
),
'ENSMUST00000181679' => array(
'start' => '121544388',
'end' => '121547652',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '1700030M09Rik-001'
),
'ENSMUST00000181666' => array(
'start' => '121434980',
'end' => '121435389',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26784-001'
),
'ENSMUST00000180597' => array(
'start' => '121421345',
'end' => '121427188',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26747-001'
),
'ENSMUST00000182000' => array(
'start' => '121581765',
'end' => '121582191',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm17786-001'
),
'ENSMUST00000182145' => array(
'start' => '121542122',
'end' => '121543481',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm27045-001'
),
'ENSMUST00000184096' => array(
'start' => '121084609',
'end' => '121084706',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm27530-201'
),
'ENSMUST00000187913' => array(
'start' => '121002927',
'end' => '121003190',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-80D9.2-001'
)
)
$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_0008VY_0001' => array(
'genes_in_region' => array(
'ENSG00000232190' => array(
[maximum depth reached]
),
'ENSG00000260026' => array(
[maximum depth reached]
),
'ENSG00000260795' => array(
[maximum depth reached]
),
'ENSG00000261095' => array(
[maximum depth reached]
),
'ENSG00000261161' => array(
[maximum depth reached]
),
'ENSG00000261175' => array(
[maximum depth reached]
),
'ENSG00000261363' => array(
[maximum depth reached]
),
'ENSG00000274478' => array(
[maximum depth reached]
),
'ENSG00000275934' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Testis',
(int) 12 => 'Adrenal',
(int) 13 => 'Heart',
(int) 14 => 'Ovary',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Ovary',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Lung',
(int) 24 => 'Testis',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Testis',
(int) 37 => 'Adrenal',
(int) 38 => 'Kidney',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Brain',
(int) 43 => 'Breast',
(int) 44 => 'Kidney',
(int) 45 => 'Lung',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Adipose',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Heart',
(int) 53 => 'Lung',
(int) 54 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008VY_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121000361',
'seq_end' => '121603557',
'region_length' => '603196',
'region_type' => 'VISTA',
'el_id' => 'hs1613'
)
)
$gene_el = array(
'ENST00000613364' => array(
'Adipose' => array(
'average_FPKM' => '0.431',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.332',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.849',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.403',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.408',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000275934'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.431',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.332',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.849',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.403',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.408',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000613364'
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 |
| hs1613 |
VISTA |
10090 |
8:121000361-121603557  |
| Gene | Transcript | Position | Biotype |
|---|
(RP11-134D3.1)