Notice (8): Undefined index: CIL_00032T_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_00032T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000131165' => 'charged multivesicular body protein 1A',
'ENSG00000158792' => 'spermatogenesis associated 2-like',
'ENSG00000167523' => 'spermatogenesis associated 33',
'ENSG00000185324' => 'cyclin-dependent kinase 10',
'ENSG00000260259' => null,
'ENSG00000275734' => null,
'ENSMUSG00000033862' => 'cyclin-dependent kinase 10',
'ENSMUSG00000048478' => 'spermatogenesis associated 33'
),
'gene_name_arr' => array(
'ENSG00000131165' => 'CHMP1A',
'ENSG00000158792' => 'SPATA2L',
'ENSG00000167523' => 'SPATA33',
'ENSG00000185324' => 'CDK10',
'ENSG00000260259' => 'RP11-368I7.4',
'ENSG00000275734' => 'RP11-368I7.6',
'ENSMUSG00000033862' => 'Cdk10',
'ENSMUSG00000048478' => 'Spata33'
),
'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) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 47 => 'Kidney',
(int) 58 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 97 => 'Placenta',
(int) 104 => '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) 48,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000397901' => array(
'start' => '89644431',
'end' => '89657845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-001'
),
'ENST00000535997' => array(
'start' => '89644463',
'end' => '89657709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-002'
),
'ENST00000547614' => array(
'start' => '89647044',
'end' => '89657721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CHMP1A-010'
),
'ENST00000547687' => array(
'start' => '89644435',
'end' => '89646880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-004'
),
'ENST00000548650' => array(
'start' => '89646955',
'end' => '89649539',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-007'
),
'ENST00000549139' => array(
'start' => '89645836',
'end' => '89649593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-008'
),
'ENST00000549328' => array(
'start' => '89645955',
'end' => '89657721',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CHMP1A-009'
),
'ENST00000550102' => array(
'start' => '89645889',
'end' => '89657650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-011'
),
'ENST00000550872' => array(
'start' => '89649179',
'end' => '89657697',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-005'
),
'ENST00000551981' => array(
'start' => '89646912',
'end' => '89657605',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-006'
),
'ENST00000289805' => array(
'start' => '89696343',
'end' => '89701695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-001'
),
'ENST00000335360' => array(
'start' => '89696357',
'end' => '89701705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-002'
),
'ENST00000569918' => array(
'start' => '89698068',
'end' => '89701640',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-003'
),
'ENST00000301031' => array(
'start' => '89657802',
'end' => '89671267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-001'
),
'ENST00000457689' => array(
'start' => '89657838',
'end' => '89670297',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-003'
),
'ENST00000564238' => array(
'start' => '89657871',
'end' => '89661508',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-004'
),
'ENST00000565890' => array(
'start' => '89657829',
'end' => '89671272',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-002'
),
'ENST00000566204' => array(
'start' => '89657812',
'end' => '89669631',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-006'
),
'ENST00000566857' => array(
'start' => '89660828',
'end' => '89661508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPATA33-008'
),
'ENST00000567827' => array(
'start' => '89657861',
'end' => '89668044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-007'
),
'ENST00000568929' => array(
'start' => '89658102',
'end' => '89661483',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-005'
),
'ENST00000579310' => array(
'start' => '89657804',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-201'
),
'ENST00000611218' => array(
'start' => '89658047',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-202'
),
'ENST00000331006' => array(
'start' => '89680737',
'end' => '89696353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-016'
),
'ENST00000353379' => array(
'start' => '89686668',
'end' => '89696364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-001'
),
'ENST00000378277' => array(
'start' => '89686713',
'end' => '89692682',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-015'
),
'ENST00000472018' => array(
'start' => '89686700',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-002'
),
'ENST00000502547' => array(
'start' => '89686684',
'end' => '89691507',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-009'
),
'ENST00000503560' => array(
'start' => '89686951',
'end' => '89690557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-013'
),
'ENST00000504473' => array(
'start' => '89686972',
'end' => '89693495',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-014'
),
'ENST00000505473' => array(
'start' => '89686670',
'end' => '89696164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-003'
),
'ENST00000505733' => array(
'start' => '89686690',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-006'
),
'ENST00000507205' => array(
'start' => '89686692',
'end' => '89694040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-005'
),
'ENST00000508723' => array(
'start' => '89686670',
'end' => '89691535',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-008'
),
'ENST00000510811' => array(
'start' => '89686691',
'end' => '89696038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-019'
),
'ENST00000511415' => array(
'start' => '89686680',
'end' => '89693402',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-012'
),
'ENST00000512912' => array(
'start' => '89686690',
'end' => '89692514',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-011'
),
'ENST00000514965' => array(
'start' => '89686728',
'end' => '89691512',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-010'
),
'ENST00000561477' => array(
'start' => '89691826',
'end' => '89694454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-021'
),
'ENST00000564192' => array(
'start' => '89686706',
'end' => '89694972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-022'
),
'ENST00000565470' => array(
'start' => '89694184',
'end' => '89696094',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-017'
),
'ENST00000567932' => array(
'start' => '89692237',
'end' => '89693718',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-020'
),
'ENST00000568456' => array(
'start' => '89689503',
'end' => '89691845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-004'
),
'ENST00000617879' => array(
'start' => '89690606',
'end' => '89695775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-201'
),
'ENST00000567544' => array(
'start' => '89682620',
'end' => '89686569',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-368I7.4-001'
),
'ENST00000615131' => array(
'start' => '89684642',
'end' => '89685304',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-368I7.6-001'
),
'ENSMUST00000036880' => array(
'start' => '123224841',
'end' => '123232250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdk10-201'
),
'ENSMUST00000060133' => array(
'start' => '123212858',
'end' => '123222045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spata33-201'
)
),
'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_00032T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00032T_0001' => array(
'genes_in_region' => array(
'ENSG00000131165' => array(
[maximum depth reached]
),
'ENSG00000158792' => array(
[maximum depth reached]
),
'ENSG00000167523' => array(
[maximum depth reached]
),
'ENSG00000185324' => array(
[maximum depth reached]
),
'ENSG00000260259' => array(
[maximum depth reached]
),
'ENSG00000275734' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adrenal',
(int) 26 => 'Liver',
(int) 27 => 'Ovary',
(int) 28 => 'Ovary',
(int) 29 => 'Ovary',
(int) 30 => 'Kidney',
(int) 31 => 'Adipose',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Lung',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Testis',
(int) 44 => 'Heart',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(int) 47 => 'Testis',
(int) 48 => 'Breast',
(int) 49 => 'Heart',
(int) 50 => 'Muscle',
(int) 51 => 'Adipose',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Placenta',
(int) 62 => 'Testis',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Liver',
(int) 77 => 'Brain',
(int) 78 => 'Liver',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Lung',
(int) 82 => 'Kidney',
(int) 83 => 'Liver',
(int) 84 => 'Placenta',
(int) 85 => 'Breast',
(int) 86 => 'Colon',
(int) 87 => 'Liver',
(int) 88 => 'Kidney',
(int) 89 => 'Ovary',
(int) 90 => 'Adipose',
(int) 91 => 'Adrenal',
(int) 92 => 'Brain',
(int) 93 => 'Breast',
(int) 94 => 'Colon',
(int) 95 => 'Heart',
(int) 96 => 'Kidney',
(int) 97 => 'Liver',
(int) 98 => 'Lung',
(int) 99 => 'Ovary',
(int) 100 => 'Testis',
(int) 101 => 'Adipose',
(int) 102 => 'Adrenal',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta',
(int) 113 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000131165' => 'charged multivesicular body protein 1A',
'ENSG00000158792' => 'spermatogenesis associated 2-like',
'ENSG00000167523' => 'spermatogenesis associated 33',
'ENSG00000185324' => 'cyclin-dependent kinase 10',
'ENSG00000260259' => null,
'ENSG00000275734' => null,
'ENSMUSG00000033862' => 'cyclin-dependent kinase 10',
'ENSMUSG00000048478' => 'spermatogenesis associated 33'
)
$gene_name_arr = array(
'ENSG00000131165' => 'CHMP1A',
'ENSG00000158792' => 'SPATA2L',
'ENSG00000167523' => 'SPATA33',
'ENSG00000185324' => 'CDK10',
'ENSG00000260259' => 'RP11-368I7.4',
'ENSG00000275734' => 'RP11-368I7.6',
'ENSMUSG00000033862' => 'Cdk10',
'ENSMUSG00000048478' => 'Spata33'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032T_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89657802',
'seq_end' => '89696364',
'region_length' => '38562',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167523-ENSG00000185324'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123212858',
'seq_end' => '123232250',
'region_length' => '19392',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000048478-ENSMUSG00000033862'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 47 => 'Kidney',
(int) 58 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 97 => 'Placenta',
(int) 104 => '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) 48
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000397901' => array(
'start' => '89644431',
'end' => '89657845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-001'
),
'ENST00000535997' => array(
'start' => '89644463',
'end' => '89657709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-002'
),
'ENST00000547614' => array(
'start' => '89647044',
'end' => '89657721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CHMP1A-010'
),
'ENST00000547687' => array(
'start' => '89644435',
'end' => '89646880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-004'
),
'ENST00000548650' => array(
'start' => '89646955',
'end' => '89649539',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-007'
),
'ENST00000549139' => array(
'start' => '89645836',
'end' => '89649593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-008'
),
'ENST00000549328' => array(
'start' => '89645955',
'end' => '89657721',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CHMP1A-009'
),
'ENST00000550102' => array(
'start' => '89645889',
'end' => '89657650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-011'
),
'ENST00000550872' => array(
'start' => '89649179',
'end' => '89657697',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-005'
),
'ENST00000551981' => array(
'start' => '89646912',
'end' => '89657605',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-006'
),
'ENST00000289805' => array(
'start' => '89696343',
'end' => '89701695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-001'
),
'ENST00000335360' => array(
'start' => '89696357',
'end' => '89701705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-002'
),
'ENST00000569918' => array(
'start' => '89698068',
'end' => '89701640',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-003'
),
'ENST00000301031' => array(
'start' => '89657802',
'end' => '89671267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-001'
),
'ENST00000457689' => array(
'start' => '89657838',
'end' => '89670297',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-003'
),
'ENST00000564238' => array(
'start' => '89657871',
'end' => '89661508',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-004'
),
'ENST00000565890' => array(
'start' => '89657829',
'end' => '89671272',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-002'
),
'ENST00000566204' => array(
'start' => '89657812',
'end' => '89669631',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-006'
),
'ENST00000566857' => array(
'start' => '89660828',
'end' => '89661508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPATA33-008'
),
'ENST00000567827' => array(
'start' => '89657861',
'end' => '89668044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-007'
),
'ENST00000568929' => array(
'start' => '89658102',
'end' => '89661483',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-005'
),
'ENST00000579310' => array(
'start' => '89657804',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-201'
),
'ENST00000611218' => array(
'start' => '89658047',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-202'
),
'ENST00000331006' => array(
'start' => '89680737',
'end' => '89696353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-016'
),
'ENST00000353379' => array(
'start' => '89686668',
'end' => '89696364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-001'
),
'ENST00000378277' => array(
'start' => '89686713',
'end' => '89692682',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-015'
),
'ENST00000472018' => array(
'start' => '89686700',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-002'
),
'ENST00000502547' => array(
'start' => '89686684',
'end' => '89691507',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-009'
),
'ENST00000503560' => array(
'start' => '89686951',
'end' => '89690557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-013'
),
'ENST00000504473' => array(
'start' => '89686972',
'end' => '89693495',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-014'
),
'ENST00000505473' => array(
'start' => '89686670',
'end' => '89696164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-003'
),
'ENST00000505733' => array(
'start' => '89686690',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-006'
),
'ENST00000507205' => array(
'start' => '89686692',
'end' => '89694040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-005'
),
'ENST00000508723' => array(
'start' => '89686670',
'end' => '89691535',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-008'
),
'ENST00000510811' => array(
'start' => '89686691',
'end' => '89696038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-019'
),
'ENST00000511415' => array(
'start' => '89686680',
'end' => '89693402',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-012'
),
'ENST00000512912' => array(
'start' => '89686690',
'end' => '89692514',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-011'
),
'ENST00000514965' => array(
'start' => '89686728',
'end' => '89691512',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-010'
),
'ENST00000561477' => array(
'start' => '89691826',
'end' => '89694454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-021'
),
'ENST00000564192' => array(
'start' => '89686706',
'end' => '89694972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-022'
),
'ENST00000565470' => array(
'start' => '89694184',
'end' => '89696094',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-017'
),
'ENST00000567932' => array(
'start' => '89692237',
'end' => '89693718',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-020'
),
'ENST00000568456' => array(
'start' => '89689503',
'end' => '89691845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-004'
),
'ENST00000617879' => array(
'start' => '89690606',
'end' => '89695775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-201'
),
'ENST00000567544' => array(
'start' => '89682620',
'end' => '89686569',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-368I7.4-001'
),
'ENST00000615131' => array(
'start' => '89684642',
'end' => '89685304',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-368I7.6-001'
),
'ENSMUST00000036880' => array(
'start' => '123224841',
'end' => '123232250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdk10-201'
),
'ENSMUST00000060133' => array(
'start' => '123212858',
'end' => '123222045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spata33-201'
)
)
$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_00032T_0001' => array(
'genes_in_region' => array(
'ENSG00000131165' => array(
[maximum depth reached]
),
'ENSG00000158792' => array(
[maximum depth reached]
),
'ENSG00000167523' => array(
[maximum depth reached]
),
'ENSG00000185324' => array(
[maximum depth reached]
),
'ENSG00000260259' => array(
[maximum depth reached]
),
'ENSG00000275734' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adrenal',
(int) 26 => 'Liver',
(int) 27 => 'Ovary',
(int) 28 => 'Ovary',
(int) 29 => 'Ovary',
(int) 30 => 'Kidney',
(int) 31 => 'Adipose',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Lung',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Testis',
(int) 44 => 'Heart',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(int) 47 => 'Testis',
(int) 48 => 'Breast',
(int) 49 => 'Heart',
(int) 50 => 'Muscle',
(int) 51 => 'Adipose',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Placenta',
(int) 62 => 'Testis',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Liver',
(int) 77 => 'Brain',
(int) 78 => 'Liver',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Lung',
(int) 82 => 'Kidney',
(int) 83 => 'Liver',
(int) 84 => 'Placenta',
(int) 85 => 'Breast',
(int) 86 => 'Colon',
(int) 87 => 'Liver',
(int) 88 => 'Kidney',
(int) 89 => 'Ovary',
(int) 90 => 'Adipose',
(int) 91 => 'Adrenal',
(int) 92 => 'Brain',
(int) 93 => 'Breast',
(int) 94 => 'Colon',
(int) 95 => 'Heart',
(int) 96 => 'Kidney',
(int) 97 => 'Liver',
(int) 98 => 'Lung',
(int) 99 => 'Ovary',
(int) 100 => 'Testis',
(int) 101 => 'Adipose',
(int) 102 => 'Adrenal',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta',
(int) 113 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00032T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123212858',
'seq_end' => '123232250',
'region_length' => '19392',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000048478-ENSMUSG00000033862'
)
)
$gene_el = array(
'ENST00000615131' => array(
'Adipose' => array(
'average_FPKM' => '0.220',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.378',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.433',
'stddev_FPKM' => '0.27'
),
'Breast' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.365',
'stddev_FPKM' => '0.11'
),
'Heart' => array(
'average_FPKM' => '0.520',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.999',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.254',
'stddev_FPKM' => '0.14'
),
'Lung' => array(
'average_FPKM' => '0.768',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1.233',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.843',
'stddev_FPKM' => '0.39'
),
'Placenta' => array(
'average_FPKM' => '0.253',
'stddev_FPKM' => '0.02'
),
'Testis' => array(
'average_FPKM' => '1.614',
'stddev_FPKM' => '0.71'
)
)
)
$gene_key = 'ENSG00000275734'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.220',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.378',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.433',
'stddev_FPKM' => '0.27'
),
'Breast' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.365',
'stddev_FPKM' => '0.11'
),
'Heart' => array(
'average_FPKM' => '0.520',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.999',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.254',
'stddev_FPKM' => '0.14'
),
'Lung' => array(
'average_FPKM' => '0.768',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1.233',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.843',
'stddev_FPKM' => '0.39'
),
'Placenta' => array(
'average_FPKM' => '0.253',
'stddev_FPKM' => '0.02'
),
'Testis' => array(
'average_FPKM' => '1.614',
'stddev_FPKM' => '0.71'
)
)
$tran_key = 'ENST00000615131'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00032T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000131165' => 'charged multivesicular body protein 1A',
'ENSG00000158792' => 'spermatogenesis associated 2-like',
'ENSG00000167523' => 'spermatogenesis associated 33',
'ENSG00000185324' => 'cyclin-dependent kinase 10',
'ENSG00000260259' => null,
'ENSG00000275734' => null,
'ENSMUSG00000033862' => 'cyclin-dependent kinase 10',
'ENSMUSG00000048478' => 'spermatogenesis associated 33'
),
'gene_name_arr' => array(
'ENSG00000131165' => 'CHMP1A',
'ENSG00000158792' => 'SPATA2L',
'ENSG00000167523' => 'SPATA33',
'ENSG00000185324' => 'CDK10',
'ENSG00000260259' => 'RP11-368I7.4',
'ENSG00000275734' => 'RP11-368I7.6',
'ENSMUSG00000033862' => 'Cdk10',
'ENSMUSG00000048478' => 'Spata33'
),
'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) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 47 => 'Kidney',
(int) 58 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 97 => 'Placenta',
(int) 104 => '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) 48,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000397901' => array(
'start' => '89644431',
'end' => '89657845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-001'
),
'ENST00000535997' => array(
'start' => '89644463',
'end' => '89657709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-002'
),
'ENST00000547614' => array(
'start' => '89647044',
'end' => '89657721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CHMP1A-010'
),
'ENST00000547687' => array(
'start' => '89644435',
'end' => '89646880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-004'
),
'ENST00000548650' => array(
'start' => '89646955',
'end' => '89649539',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-007'
),
'ENST00000549139' => array(
'start' => '89645836',
'end' => '89649593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-008'
),
'ENST00000549328' => array(
'start' => '89645955',
'end' => '89657721',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CHMP1A-009'
),
'ENST00000550102' => array(
'start' => '89645889',
'end' => '89657650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-011'
),
'ENST00000550872' => array(
'start' => '89649179',
'end' => '89657697',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-005'
),
'ENST00000551981' => array(
'start' => '89646912',
'end' => '89657605',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-006'
),
'ENST00000289805' => array(
'start' => '89696343',
'end' => '89701695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-001'
),
'ENST00000335360' => array(
'start' => '89696357',
'end' => '89701705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-002'
),
'ENST00000569918' => array(
'start' => '89698068',
'end' => '89701640',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-003'
),
'ENST00000301031' => array(
'start' => '89657802',
'end' => '89671267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-001'
),
'ENST00000457689' => array(
'start' => '89657838',
'end' => '89670297',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-003'
),
'ENST00000564238' => array(
'start' => '89657871',
'end' => '89661508',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-004'
),
'ENST00000565890' => array(
'start' => '89657829',
'end' => '89671272',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-002'
),
'ENST00000566204' => array(
'start' => '89657812',
'end' => '89669631',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-006'
),
'ENST00000566857' => array(
'start' => '89660828',
'end' => '89661508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPATA33-008'
),
'ENST00000567827' => array(
'start' => '89657861',
'end' => '89668044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-007'
),
'ENST00000568929' => array(
'start' => '89658102',
'end' => '89661483',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-005'
),
'ENST00000579310' => array(
'start' => '89657804',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-201'
),
'ENST00000611218' => array(
'start' => '89658047',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-202'
),
'ENST00000331006' => array(
'start' => '89680737',
'end' => '89696353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-016'
),
'ENST00000353379' => array(
'start' => '89686668',
'end' => '89696364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-001'
),
'ENST00000378277' => array(
'start' => '89686713',
'end' => '89692682',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-015'
),
'ENST00000472018' => array(
'start' => '89686700',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-002'
),
'ENST00000502547' => array(
'start' => '89686684',
'end' => '89691507',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-009'
),
'ENST00000503560' => array(
'start' => '89686951',
'end' => '89690557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-013'
),
'ENST00000504473' => array(
'start' => '89686972',
'end' => '89693495',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-014'
),
'ENST00000505473' => array(
'start' => '89686670',
'end' => '89696164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-003'
),
'ENST00000505733' => array(
'start' => '89686690',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-006'
),
'ENST00000507205' => array(
'start' => '89686692',
'end' => '89694040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-005'
),
'ENST00000508723' => array(
'start' => '89686670',
'end' => '89691535',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-008'
),
'ENST00000510811' => array(
'start' => '89686691',
'end' => '89696038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-019'
),
'ENST00000511415' => array(
'start' => '89686680',
'end' => '89693402',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-012'
),
'ENST00000512912' => array(
'start' => '89686690',
'end' => '89692514',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-011'
),
'ENST00000514965' => array(
'start' => '89686728',
'end' => '89691512',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-010'
),
'ENST00000561477' => array(
'start' => '89691826',
'end' => '89694454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-021'
),
'ENST00000564192' => array(
'start' => '89686706',
'end' => '89694972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-022'
),
'ENST00000565470' => array(
'start' => '89694184',
'end' => '89696094',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-017'
),
'ENST00000567932' => array(
'start' => '89692237',
'end' => '89693718',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-020'
),
'ENST00000568456' => array(
'start' => '89689503',
'end' => '89691845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-004'
),
'ENST00000617879' => array(
'start' => '89690606',
'end' => '89695775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-201'
),
'ENST00000567544' => array(
'start' => '89682620',
'end' => '89686569',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-368I7.4-001'
),
'ENST00000615131' => array(
'start' => '89684642',
'end' => '89685304',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-368I7.6-001'
),
'ENSMUST00000036880' => array(
'start' => '123224841',
'end' => '123232250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdk10-201'
),
'ENSMUST00000060133' => array(
'start' => '123212858',
'end' => '123222045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spata33-201'
)
),
'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_00032T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00032T_0001' => array(
'genes_in_region' => array(
'ENSG00000131165' => array(
[maximum depth reached]
),
'ENSG00000158792' => array(
[maximum depth reached]
),
'ENSG00000167523' => array(
[maximum depth reached]
),
'ENSG00000185324' => array(
[maximum depth reached]
),
'ENSG00000260259' => array(
[maximum depth reached]
),
'ENSG00000275734' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adrenal',
(int) 26 => 'Liver',
(int) 27 => 'Ovary',
(int) 28 => 'Ovary',
(int) 29 => 'Ovary',
(int) 30 => 'Kidney',
(int) 31 => 'Adipose',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Lung',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Testis',
(int) 44 => 'Heart',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(int) 47 => 'Testis',
(int) 48 => 'Breast',
(int) 49 => 'Heart',
(int) 50 => 'Muscle',
(int) 51 => 'Adipose',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Placenta',
(int) 62 => 'Testis',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Liver',
(int) 77 => 'Brain',
(int) 78 => 'Liver',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Lung',
(int) 82 => 'Kidney',
(int) 83 => 'Liver',
(int) 84 => 'Placenta',
(int) 85 => 'Breast',
(int) 86 => 'Colon',
(int) 87 => 'Liver',
(int) 88 => 'Kidney',
(int) 89 => 'Ovary',
(int) 90 => 'Adipose',
(int) 91 => 'Adrenal',
(int) 92 => 'Brain',
(int) 93 => 'Breast',
(int) 94 => 'Colon',
(int) 95 => 'Heart',
(int) 96 => 'Kidney',
(int) 97 => 'Liver',
(int) 98 => 'Lung',
(int) 99 => 'Ovary',
(int) 100 => 'Testis',
(int) 101 => 'Adipose',
(int) 102 => 'Adrenal',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta',
(int) 113 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000131165' => 'charged multivesicular body protein 1A',
'ENSG00000158792' => 'spermatogenesis associated 2-like',
'ENSG00000167523' => 'spermatogenesis associated 33',
'ENSG00000185324' => 'cyclin-dependent kinase 10',
'ENSG00000260259' => null,
'ENSG00000275734' => null,
'ENSMUSG00000033862' => 'cyclin-dependent kinase 10',
'ENSMUSG00000048478' => 'spermatogenesis associated 33'
)
$gene_name_arr = array(
'ENSG00000131165' => 'CHMP1A',
'ENSG00000158792' => 'SPATA2L',
'ENSG00000167523' => 'SPATA33',
'ENSG00000185324' => 'CDK10',
'ENSG00000260259' => 'RP11-368I7.4',
'ENSG00000275734' => 'RP11-368I7.6',
'ENSMUSG00000033862' => 'Cdk10',
'ENSMUSG00000048478' => 'Spata33'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032T_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89657802',
'seq_end' => '89696364',
'region_length' => '38562',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167523-ENSG00000185324'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00032T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123212858',
'seq_end' => '123232250',
'region_length' => '19392',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000048478-ENSMUSG00000033862'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 23 => 'Breast',
(int) 31 => 'Colon',
(int) 38 => 'Heart',
(int) 47 => 'Kidney',
(int) 58 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 97 => 'Placenta',
(int) 104 => '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) 48
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000397901' => array(
'start' => '89644431',
'end' => '89657845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-001'
),
'ENST00000535997' => array(
'start' => '89644463',
'end' => '89657709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-002'
),
'ENST00000547614' => array(
'start' => '89647044',
'end' => '89657721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CHMP1A-010'
),
'ENST00000547687' => array(
'start' => '89644435',
'end' => '89646880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-004'
),
'ENST00000548650' => array(
'start' => '89646955',
'end' => '89649539',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-007'
),
'ENST00000549139' => array(
'start' => '89645836',
'end' => '89649593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-008'
),
'ENST00000549328' => array(
'start' => '89645955',
'end' => '89657721',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CHMP1A-009'
),
'ENST00000550102' => array(
'start' => '89645889',
'end' => '89657650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CHMP1A-011'
),
'ENST00000550872' => array(
'start' => '89649179',
'end' => '89657697',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-005'
),
'ENST00000551981' => array(
'start' => '89646912',
'end' => '89657605',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CHMP1A-006'
),
'ENST00000289805' => array(
'start' => '89696343',
'end' => '89701695',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-001'
),
'ENST00000335360' => array(
'start' => '89696357',
'end' => '89701705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-002'
),
'ENST00000569918' => array(
'start' => '89698068',
'end' => '89701640',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA2L-003'
),
'ENST00000301031' => array(
'start' => '89657802',
'end' => '89671267',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-001'
),
'ENST00000457689' => array(
'start' => '89657838',
'end' => '89670297',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-003'
),
'ENST00000564238' => array(
'start' => '89657871',
'end' => '89661508',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-004'
),
'ENST00000565890' => array(
'start' => '89657829',
'end' => '89671272',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-002'
),
'ENST00000566204' => array(
'start' => '89657812',
'end' => '89669631',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-006'
),
'ENST00000566857' => array(
'start' => '89660828',
'end' => '89661508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPATA33-008'
),
'ENST00000567827' => array(
'start' => '89657861',
'end' => '89668044',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPATA33-007'
),
'ENST00000568929' => array(
'start' => '89658102',
'end' => '89661483',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-005'
),
'ENST00000579310' => array(
'start' => '89657804',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-201'
),
'ENST00000611218' => array(
'start' => '89658047',
'end' => '89670456',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPATA33-202'
),
'ENST00000331006' => array(
'start' => '89680737',
'end' => '89696353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-016'
),
'ENST00000353379' => array(
'start' => '89686668',
'end' => '89696364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-001'
),
'ENST00000378277' => array(
'start' => '89686713',
'end' => '89692682',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-015'
),
'ENST00000472018' => array(
'start' => '89686700',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-002'
),
'ENST00000502547' => array(
'start' => '89686684',
'end' => '89691507',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-009'
),
'ENST00000503560' => array(
'start' => '89686951',
'end' => '89690557',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-013'
),
'ENST00000504473' => array(
'start' => '89686972',
'end' => '89693495',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-014'
),
'ENST00000505473' => array(
'start' => '89686670',
'end' => '89696164',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-003'
),
'ENST00000505733' => array(
'start' => '89686690',
'end' => '89696354',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-006'
),
'ENST00000507205' => array(
'start' => '89686692',
'end' => '89694040',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-005'
),
'ENST00000508723' => array(
'start' => '89686670',
'end' => '89691535',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-008'
),
'ENST00000510811' => array(
'start' => '89686691',
'end' => '89696038',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-019'
),
'ENST00000511415' => array(
'start' => '89686680',
'end' => '89693402',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-012'
),
'ENST00000512912' => array(
'start' => '89686690',
'end' => '89692514',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-011'
),
'ENST00000514965' => array(
'start' => '89686728',
'end' => '89691512',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDK10-010'
),
'ENST00000561477' => array(
'start' => '89691826',
'end' => '89694454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-021'
),
'ENST00000564192' => array(
'start' => '89686706',
'end' => '89694972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-022'
),
'ENST00000565470' => array(
'start' => '89694184',
'end' => '89696094',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'CDK10-017'
),
'ENST00000567932' => array(
'start' => '89692237',
'end' => '89693718',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-020'
),
'ENST00000568456' => array(
'start' => '89689503',
'end' => '89691845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDK10-004'
),
'ENST00000617879' => array(
'start' => '89690606',
'end' => '89695775',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDK10-201'
),
'ENST00000567544' => array(
'start' => '89682620',
'end' => '89686569',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-368I7.4-001'
),
'ENST00000615131' => array(
'start' => '89684642',
'end' => '89685304',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-368I7.6-001'
),
'ENSMUST00000036880' => array(
'start' => '123224841',
'end' => '123232250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdk10-201'
),
'ENSMUST00000060133' => array(
'start' => '123212858',
'end' => '123222045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spata33-201'
)
)
$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_00032T_0001' => array(
'genes_in_region' => array(
'ENSG00000131165' => array(
[maximum depth reached]
),
'ENSG00000158792' => array(
[maximum depth reached]
),
'ENSG00000167523' => array(
[maximum depth reached]
),
'ENSG00000185324' => array(
[maximum depth reached]
),
'ENSG00000260259' => array(
[maximum depth reached]
),
'ENSG00000275734' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Brain',
(int) 17 => 'Colon',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Adrenal',
(int) 26 => 'Liver',
(int) 27 => 'Ovary',
(int) 28 => 'Ovary',
(int) 29 => 'Ovary',
(int) 30 => 'Kidney',
(int) 31 => 'Adipose',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Lung',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Testis',
(int) 44 => 'Heart',
(int) 45 => 'Ovary',
(int) 46 => 'Testis',
(int) 47 => 'Testis',
(int) 48 => 'Breast',
(int) 49 => 'Heart',
(int) 50 => 'Muscle',
(int) 51 => 'Adipose',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Placenta',
(int) 62 => 'Testis',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Lung',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis',
(int) 74 => 'Bladder',
(int) 75 => 'Liver',
(int) 76 => 'Liver',
(int) 77 => 'Brain',
(int) 78 => 'Liver',
(int) 79 => 'Muscle',
(int) 80 => 'Ovary',
(int) 81 => 'Lung',
(int) 82 => 'Kidney',
(int) 83 => 'Liver',
(int) 84 => 'Placenta',
(int) 85 => 'Breast',
(int) 86 => 'Colon',
(int) 87 => 'Liver',
(int) 88 => 'Kidney',
(int) 89 => 'Ovary',
(int) 90 => 'Adipose',
(int) 91 => 'Adrenal',
(int) 92 => 'Brain',
(int) 93 => 'Breast',
(int) 94 => 'Colon',
(int) 95 => 'Heart',
(int) 96 => 'Kidney',
(int) 97 => 'Liver',
(int) 98 => 'Lung',
(int) 99 => 'Ovary',
(int) 100 => 'Testis',
(int) 101 => 'Adipose',
(int) 102 => 'Adrenal',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta',
(int) 113 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00032T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123212858',
'seq_end' => '123232250',
'region_length' => '19392',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000048478-ENSMUSG00000033862'
)
)
$gene_el = array(
'ENST00000615131' => array(
'Adipose' => array(
'average_FPKM' => '0.220',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.378',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.433',
'stddev_FPKM' => '0.27'
),
'Breast' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.365',
'stddev_FPKM' => '0.11'
),
'Heart' => array(
'average_FPKM' => '0.520',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.999',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.254',
'stddev_FPKM' => '0.14'
),
'Lung' => array(
'average_FPKM' => '0.768',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1.233',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.843',
'stddev_FPKM' => '0.39'
),
'Placenta' => array(
'average_FPKM' => '0.253',
'stddev_FPKM' => '0.02'
),
'Testis' => array(
'average_FPKM' => '1.614',
'stddev_FPKM' => '0.71'
)
)
)
$gene_key = 'ENSG00000275734'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.220',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '1.378',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.433',
'stddev_FPKM' => '0.27'
),
'Breast' => array(
'average_FPKM' => '0.467',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.365',
'stddev_FPKM' => '0.11'
),
'Heart' => array(
'average_FPKM' => '0.520',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.999',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.254',
'stddev_FPKM' => '0.14'
),
'Lung' => array(
'average_FPKM' => '0.768',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '1.233',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.843',
'stddev_FPKM' => '0.39'
),
'Placenta' => array(
'average_FPKM' => '0.253',
'stddev_FPKM' => '0.02'
),
'Testis' => array(
'average_FPKM' => '1.614',
'stddev_FPKM' => '0.71'
)
)
$tran_key = 'ENST00000615131'
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 |
| ENSMUSG00000048478-ENSMUSG00000033862 |
CGP |
10090 |
8:123212858-123232250  |
| Gene | Transcript | Position | Biotype |
|---|
(CHMP1A)