| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000061410-ENSMUSG00000025318 |
CGP |
10090 |
8:121598703-121794276  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00070Q_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_00070Q_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000140948' => 'zinc finger, CCHC domain containing 14',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000226180' => null,
'ENSG00000260750' => null,
'ENSG00000269935' => null,
'ENSG00000276337' => null,
'ENSG00000276393' => null,
'ENSG00000277504' => null,
'ENSMUSG00000025318' => 'junctophilin 3',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000064642' => 'predicted gene, 23299',
'ENSMUSG00000098221' => 'predicted gene, 27030'
),
'gene_name_arr' => array(
'ENSG00000104731' => 'KLHDC4',
'ENSG00000140948' => 'ZCCHC14',
'ENSG00000154118' => 'JPH3',
'ENSG00000226180' => 'RP11-278A23.1',
'ENSG00000260750' => 'RP11-482M8.1',
'ENSG00000269935' => 'RP11-482M8.3',
'ENSG00000276337' => 'RP11-106D4.2',
'ENSG00000276393' => 'RP11-106D4.3',
'ENSG00000277504' => 'RP11-278A23.4',
'ENSMUSG00000025318' => 'Jph3',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000064642' => 'Gm23299',
'ENSMUSG00000098221' => 'Gm27030'
),
'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) 18 => 'Brain',
(int) 24 => 'Breast',
(int) 29 => 'Colon',
(int) 37 => 'Heart',
(int) 46 => 'Kidney',
(int) 55 => 'Liver',
(int) 66 => 'Lung',
(int) 73 => 'Muscle',
(int) 80 => 'Ovary',
(int) 88 => 'Placenta',
(int) 97 => '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) 58,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000270583' => array(
'start' => '87707813',
'end' => '87765949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-001'
),
'ENST00000316853' => array(
'start' => '87707812',
'end' => '87750942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-008'
),
'ENST00000347925' => array(
'start' => '87707812',
'end' => '87765976',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-004'
),
'ENST00000353170' => array(
'start' => '87707812',
'end' => '87765899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-002'
),
'ENST00000446344' => array(
'start' => '87701639',
'end' => '87702514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-201'
),
'ENST00000561825' => array(
'start' => '87748799',
'end' => '87765931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-015'
),
'ENST00000562155' => array(
'start' => '87707840',
'end' => '87765929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-003'
),
'ENST00000562261' => array(
'start' => '87709438',
'end' => '87765951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-019'
),
'ENST00000562872' => array(
'start' => '87726821',
'end' => '87731006',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-023'
),
'ENST00000562913' => array(
'start' => '87710798',
'end' => '87726917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-024'
),
'ENST00000563845' => array(
'start' => '87761958',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-014'
),
'ENST00000564396' => array(
'start' => '87730636',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-018'
),
'ENST00000564484' => array(
'start' => '87726899',
'end' => '87765933',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-020'
),
'ENST00000565328' => array(
'start' => '87729318',
'end' => '87762154',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-021'
),
'ENST00000566349' => array(
'start' => '87707813',
'end' => '87743044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-009'
),
'ENST00000566561' => array(
'start' => '87763485',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-013'
),
'ENST00000566661' => array(
'start' => '87709463',
'end' => '87762016',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-007'
),
'ENST00000567298' => array(
'start' => '87698149',
'end' => '87765972',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-005'
),
'ENST00000567513' => array(
'start' => '87711236',
'end' => '87740964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-022'
),
'ENST00000568338' => array(
'start' => '87755198',
'end' => '87765992',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-012'
),
'ENST00000568346' => array(
'start' => '87700778',
'end' => '87701724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-026'
),
'ENST00000568444' => array(
'start' => '87696485',
'end' => '87699415',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-027'
),
'ENST00000568499' => array(
'start' => '87703026',
'end' => '87708387',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-025'
),
'ENST00000568502' => array(
'start' => '87748738',
'end' => '87765964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-016'
),
'ENST00000569487' => array(
'start' => '87707816',
'end' => '87710877',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-010'
),
'ENST00000569747' => array(
'start' => '87730607',
'end' => '87765967',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-017'
),
'ENST00000622456' => array(
'start' => '87707914',
'end' => '87765992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-202'
),
'ENST00000268616' => array(
'start' => '87406246',
'end' => '87492045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-001'
),
'ENST00000561928' => array(
'start' => '87411412',
'end' => '87433134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-003'
),
'ENST00000565193' => array(
'start' => '87415312',
'end' => '87417926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZCCHC14-004'
),
'ENST00000568020' => array(
'start' => '87406257',
'end' => '87491859',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZCCHC14-002'
),
'ENST00000284262' => array(
'start' => '87602905',
'end' => '87698156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'JPH3-001'
),
'ENST00000301008' => array(
'start' => '87602887',
'end' => '87604627',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-003'
),
'ENST00000537256' => array(
'start' => '87601835',
'end' => '87697927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-002'
),
'ENST00000563609' => array(
'start' => '87653562',
'end' => '87698142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-004'
),
'ENST00000538868' => array(
'start' => '87693537',
'end' => '87696147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-278A23.1-001'
),
'ENST00000562466' => array(
'start' => '87492555',
'end' => '87496998',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-002'
),
'ENST00000563921' => array(
'start' => '87494187',
'end' => '87515635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-003'
),
'ENST00000565824' => array(
'start' => '87493274',
'end' => '87497166',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-001'
),
'ENST00000602388' => array(
'start' => '87600526',
'end' => '87602190',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-482M8.3-001'
),
'ENST00000612833' => array(
'start' => '87470370',
'end' => '87474370',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-106D4.2-001'
),
'ENST00000610567' => array(
'start' => '87467138',
'end' => '87467654',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-106D4.3-001'
),
'ENST00000620306' => array(
'start' => '87683945',
'end' => '87684477',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-278A23.4-001'
),
'ENSMUST00000026357' => array(
'start' => '121730563',
'end' => '121790821',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Jph3-001'
),
'ENSMUST00000167439' => array(
'start' => '121730567',
'end' => '121794276',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Jph3-002'
),
'ENSMUST00000169735' => array(
'start' => '121729623',
'end' => '121789617',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Jph3-003'
),
'ENSMUST00000172209' => array(
'start' => '121753476',
'end' => '121782570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Jph3-004'
),
'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'
),
'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'
),
'ENSMUST00000082708' => array(
'start' => '121666628',
'end' => '121666706',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23299-201'
),
'ENSMUST00000182551' => array(
'start' => '121654054',
'end' => '121654517',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm27030-001'
)
),
'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_00070Q_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00070Q_0001' => array(
'genes_in_region' => array(
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000140948' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000226180' => array(
[maximum depth reached]
),
'ENSG00000260750' => array(
[maximum depth reached]
),
'ENSG00000276337' => array(
[maximum depth reached]
),
'ENSG00000276393' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Adipose',
(int) 9 => 'Heart',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Kidney',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Breast',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Muscle',
(int) 26 => 'Ovary',
(int) 27 => 'Placenta',
(int) 28 => 'Testis',
(int) 29 => 'Colon',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adrenal',
(int) 33 => 'Liver',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Muscle',
(int) 37 => 'Muscle',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Bladder',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Placenta',
(int) 59 => 'Brain',
(int) 60 => 'Colon',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Kidney',
(int) 79 => 'Liver',
(int) 80 => 'Lung',
(int) 81 => 'Testis',
(int) 82 => 'Kidney',
(int) 83 => 'Placenta',
(int) 84 => 'Testis',
(int) 85 => 'Brain',
(int) 86 => 'Heart',
(int) 87 => 'Kidney',
(int) 88 => 'Liver',
(int) 89 => 'Ovary',
(int) 90 => 'Testis',
(int) 91 => 'Adipose',
(int) 92 => 'Adrenal',
(int) 93 => 'Bladder',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Kidney',
(int) 99 => 'Liver',
(int) 100 => 'Lung',
(int) 101 => 'Muscle',
(int) 102 => 'Ovary',
(int) 103 => 'Placenta',
(int) 104 => 'Testis',
(int) 105 => 'Adrenal',
(int) 106 => 'Colon'
)
)
)
$gene_desc_arr = array(
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000140948' => 'zinc finger, CCHC domain containing 14',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000226180' => null,
'ENSG00000260750' => null,
'ENSG00000269935' => null,
'ENSG00000276337' => null,
'ENSG00000276393' => null,
'ENSG00000277504' => null,
'ENSMUSG00000025318' => 'junctophilin 3',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000064642' => 'predicted gene, 23299',
'ENSMUSG00000098221' => 'predicted gene, 27030'
)
$gene_name_arr = array(
'ENSG00000104731' => 'KLHDC4',
'ENSG00000140948' => 'ZCCHC14',
'ENSG00000154118' => 'JPH3',
'ENSG00000226180' => 'RP11-278A23.1',
'ENSG00000260750' => 'RP11-482M8.1',
'ENSG00000269935' => 'RP11-482M8.3',
'ENSG00000276337' => 'RP11-106D4.2',
'ENSG00000276393' => 'RP11-106D4.3',
'ENSG00000277504' => 'RP11-278A23.4',
'ENSMUSG00000025318' => 'Jph3',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000064642' => 'Gm23299',
'ENSMUSG00000098221' => 'Gm27030'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00070Q_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '87406246',
'seq_end' => '87698156',
'region_length' => '291910',
'region_type' => 'CGP',
'el_id' => 'ENSG00000140948-ENSG00000154118'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00070Q_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121598703',
'seq_end' => '121794276',
'region_length' => '195573',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000061410-ENSMUSG00000025318'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 18 => 'Brain',
(int) 24 => 'Breast',
(int) 29 => 'Colon',
(int) 37 => 'Heart',
(int) 46 => 'Kidney',
(int) 55 => 'Liver',
(int) 66 => 'Lung',
(int) 73 => 'Muscle',
(int) 80 => 'Ovary',
(int) 88 => 'Placenta',
(int) 97 => '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) 58
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000270583' => array(
'start' => '87707813',
'end' => '87765949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-001'
),
'ENST00000316853' => array(
'start' => '87707812',
'end' => '87750942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-008'
),
'ENST00000347925' => array(
'start' => '87707812',
'end' => '87765976',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-004'
),
'ENST00000353170' => array(
'start' => '87707812',
'end' => '87765899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-002'
),
'ENST00000446344' => array(
'start' => '87701639',
'end' => '87702514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-201'
),
'ENST00000561825' => array(
'start' => '87748799',
'end' => '87765931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-015'
),
'ENST00000562155' => array(
'start' => '87707840',
'end' => '87765929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-003'
),
'ENST00000562261' => array(
'start' => '87709438',
'end' => '87765951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-019'
),
'ENST00000562872' => array(
'start' => '87726821',
'end' => '87731006',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-023'
),
'ENST00000562913' => array(
'start' => '87710798',
'end' => '87726917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-024'
),
'ENST00000563845' => array(
'start' => '87761958',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-014'
),
'ENST00000564396' => array(
'start' => '87730636',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-018'
),
'ENST00000564484' => array(
'start' => '87726899',
'end' => '87765933',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-020'
),
'ENST00000565328' => array(
'start' => '87729318',
'end' => '87762154',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-021'
),
'ENST00000566349' => array(
'start' => '87707813',
'end' => '87743044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-009'
),
'ENST00000566561' => array(
'start' => '87763485',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-013'
),
'ENST00000566661' => array(
'start' => '87709463',
'end' => '87762016',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-007'
),
'ENST00000567298' => array(
'start' => '87698149',
'end' => '87765972',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-005'
),
'ENST00000567513' => array(
'start' => '87711236',
'end' => '87740964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-022'
),
'ENST00000568338' => array(
'start' => '87755198',
'end' => '87765992',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-012'
),
'ENST00000568346' => array(
'start' => '87700778',
'end' => '87701724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-026'
),
'ENST00000568444' => array(
'start' => '87696485',
'end' => '87699415',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-027'
),
'ENST00000568499' => array(
'start' => '87703026',
'end' => '87708387',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-025'
),
'ENST00000568502' => array(
'start' => '87748738',
'end' => '87765964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-016'
),
'ENST00000569487' => array(
'start' => '87707816',
'end' => '87710877',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-010'
),
'ENST00000569747' => array(
'start' => '87730607',
'end' => '87765967',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-017'
),
'ENST00000622456' => array(
'start' => '87707914',
'end' => '87765992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-202'
),
'ENST00000268616' => array(
'start' => '87406246',
'end' => '87492045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-001'
),
'ENST00000561928' => array(
'start' => '87411412',
'end' => '87433134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-003'
),
'ENST00000565193' => array(
'start' => '87415312',
'end' => '87417926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZCCHC14-004'
),
'ENST00000568020' => array(
'start' => '87406257',
'end' => '87491859',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZCCHC14-002'
),
'ENST00000284262' => array(
'start' => '87602905',
'end' => '87698156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'JPH3-001'
),
'ENST00000301008' => array(
'start' => '87602887',
'end' => '87604627',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-003'
),
'ENST00000537256' => array(
'start' => '87601835',
'end' => '87697927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-002'
),
'ENST00000563609' => array(
'start' => '87653562',
'end' => '87698142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-004'
),
'ENST00000538868' => array(
'start' => '87693537',
'end' => '87696147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-278A23.1-001'
),
'ENST00000562466' => array(
'start' => '87492555',
'end' => '87496998',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-002'
),
'ENST00000563921' => array(
'start' => '87494187',
'end' => '87515635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-003'
),
'ENST00000565824' => array(
'start' => '87493274',
'end' => '87497166',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-001'
),
'ENST00000602388' => array(
'start' => '87600526',
'end' => '87602190',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-482M8.3-001'
),
'ENST00000612833' => array(
'start' => '87470370',
'end' => '87474370',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-106D4.2-001'
),
'ENST00000610567' => array(
'start' => '87467138',
'end' => '87467654',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-106D4.3-001'
),
'ENST00000620306' => array(
'start' => '87683945',
'end' => '87684477',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-278A23.4-001'
),
'ENSMUST00000026357' => array(
'start' => '121730563',
'end' => '121790821',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Jph3-001'
),
'ENSMUST00000167439' => array(
'start' => '121730567',
'end' => '121794276',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Jph3-002'
),
'ENSMUST00000169735' => array(
'start' => '121729623',
'end' => '121789617',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Jph3-003'
),
'ENSMUST00000172209' => array(
'start' => '121753476',
'end' => '121782570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Jph3-004'
),
'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'
),
'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'
),
'ENSMUST00000082708' => array(
'start' => '121666628',
'end' => '121666706',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23299-201'
),
'ENSMUST00000182551' => array(
'start' => '121654054',
'end' => '121654517',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm27030-001'
)
)
$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_00070Q_0001' => array(
'genes_in_region' => array(
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000140948' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000226180' => array(
[maximum depth reached]
),
'ENSG00000260750' => array(
[maximum depth reached]
),
'ENSG00000276337' => array(
[maximum depth reached]
),
'ENSG00000276393' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Adipose',
(int) 9 => 'Heart',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Kidney',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Breast',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Muscle',
(int) 26 => 'Ovary',
(int) 27 => 'Placenta',
(int) 28 => 'Testis',
(int) 29 => 'Colon',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adrenal',
(int) 33 => 'Liver',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Muscle',
(int) 37 => 'Muscle',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Bladder',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Placenta',
(int) 59 => 'Brain',
(int) 60 => 'Colon',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Kidney',
(int) 79 => 'Liver',
(int) 80 => 'Lung',
(int) 81 => 'Testis',
(int) 82 => 'Kidney',
(int) 83 => 'Placenta',
(int) 84 => 'Testis',
(int) 85 => 'Brain',
(int) 86 => 'Heart',
(int) 87 => 'Kidney',
(int) 88 => 'Liver',
(int) 89 => 'Ovary',
(int) 90 => 'Testis',
(int) 91 => 'Adipose',
(int) 92 => 'Adrenal',
(int) 93 => 'Bladder',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Kidney',
(int) 99 => 'Liver',
(int) 100 => 'Lung',
(int) 101 => 'Muscle',
(int) 102 => 'Ovary',
(int) 103 => 'Placenta',
(int) 104 => 'Testis',
(int) 105 => 'Adrenal',
(int) 106 => 'Colon'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00070Q_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121598703',
'seq_end' => '121794276',
'region_length' => '195573',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000061410-ENSMUSG00000025318'
)
)
$gene_el = array(
'ENST00000610567' => array(
'Adrenal' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.204',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000276393'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.204',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000610567'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00070Q_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000140948' => 'zinc finger, CCHC domain containing 14',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000226180' => null,
'ENSG00000260750' => null,
'ENSG00000269935' => null,
'ENSG00000276337' => null,
'ENSG00000276393' => null,
'ENSG00000277504' => null,
'ENSMUSG00000025318' => 'junctophilin 3',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000064642' => 'predicted gene, 23299',
'ENSMUSG00000098221' => 'predicted gene, 27030'
),
'gene_name_arr' => array(
'ENSG00000104731' => 'KLHDC4',
'ENSG00000140948' => 'ZCCHC14',
'ENSG00000154118' => 'JPH3',
'ENSG00000226180' => 'RP11-278A23.1',
'ENSG00000260750' => 'RP11-482M8.1',
'ENSG00000269935' => 'RP11-482M8.3',
'ENSG00000276337' => 'RP11-106D4.2',
'ENSG00000276393' => 'RP11-106D4.3',
'ENSG00000277504' => 'RP11-278A23.4',
'ENSMUSG00000025318' => 'Jph3',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000064642' => 'Gm23299',
'ENSMUSG00000098221' => 'Gm27030'
),
'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) 18 => 'Brain',
(int) 24 => 'Breast',
(int) 29 => 'Colon',
(int) 37 => 'Heart',
(int) 46 => 'Kidney',
(int) 55 => 'Liver',
(int) 66 => 'Lung',
(int) 73 => 'Muscle',
(int) 80 => 'Ovary',
(int) 88 => 'Placenta',
(int) 97 => '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) 58,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000270583' => array(
'start' => '87707813',
'end' => '87765949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-001'
),
'ENST00000316853' => array(
'start' => '87707812',
'end' => '87750942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-008'
),
'ENST00000347925' => array(
'start' => '87707812',
'end' => '87765976',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-004'
),
'ENST00000353170' => array(
'start' => '87707812',
'end' => '87765899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-002'
),
'ENST00000446344' => array(
'start' => '87701639',
'end' => '87702514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-201'
),
'ENST00000561825' => array(
'start' => '87748799',
'end' => '87765931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-015'
),
'ENST00000562155' => array(
'start' => '87707840',
'end' => '87765929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-003'
),
'ENST00000562261' => array(
'start' => '87709438',
'end' => '87765951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-019'
),
'ENST00000562872' => array(
'start' => '87726821',
'end' => '87731006',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-023'
),
'ENST00000562913' => array(
'start' => '87710798',
'end' => '87726917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-024'
),
'ENST00000563845' => array(
'start' => '87761958',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-014'
),
'ENST00000564396' => array(
'start' => '87730636',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-018'
),
'ENST00000564484' => array(
'start' => '87726899',
'end' => '87765933',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-020'
),
'ENST00000565328' => array(
'start' => '87729318',
'end' => '87762154',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-021'
),
'ENST00000566349' => array(
'start' => '87707813',
'end' => '87743044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-009'
),
'ENST00000566561' => array(
'start' => '87763485',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-013'
),
'ENST00000566661' => array(
'start' => '87709463',
'end' => '87762016',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-007'
),
'ENST00000567298' => array(
'start' => '87698149',
'end' => '87765972',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-005'
),
'ENST00000567513' => array(
'start' => '87711236',
'end' => '87740964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-022'
),
'ENST00000568338' => array(
'start' => '87755198',
'end' => '87765992',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-012'
),
'ENST00000568346' => array(
'start' => '87700778',
'end' => '87701724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-026'
),
'ENST00000568444' => array(
'start' => '87696485',
'end' => '87699415',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-027'
),
'ENST00000568499' => array(
'start' => '87703026',
'end' => '87708387',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-025'
),
'ENST00000568502' => array(
'start' => '87748738',
'end' => '87765964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-016'
),
'ENST00000569487' => array(
'start' => '87707816',
'end' => '87710877',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-010'
),
'ENST00000569747' => array(
'start' => '87730607',
'end' => '87765967',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-017'
),
'ENST00000622456' => array(
'start' => '87707914',
'end' => '87765992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-202'
),
'ENST00000268616' => array(
'start' => '87406246',
'end' => '87492045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-001'
),
'ENST00000561928' => array(
'start' => '87411412',
'end' => '87433134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-003'
),
'ENST00000565193' => array(
'start' => '87415312',
'end' => '87417926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZCCHC14-004'
),
'ENST00000568020' => array(
'start' => '87406257',
'end' => '87491859',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZCCHC14-002'
),
'ENST00000284262' => array(
'start' => '87602905',
'end' => '87698156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'JPH3-001'
),
'ENST00000301008' => array(
'start' => '87602887',
'end' => '87604627',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-003'
),
'ENST00000537256' => array(
'start' => '87601835',
'end' => '87697927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-002'
),
'ENST00000563609' => array(
'start' => '87653562',
'end' => '87698142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-004'
),
'ENST00000538868' => array(
'start' => '87693537',
'end' => '87696147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-278A23.1-001'
),
'ENST00000562466' => array(
'start' => '87492555',
'end' => '87496998',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-002'
),
'ENST00000563921' => array(
'start' => '87494187',
'end' => '87515635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-003'
),
'ENST00000565824' => array(
'start' => '87493274',
'end' => '87497166',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-001'
),
'ENST00000602388' => array(
'start' => '87600526',
'end' => '87602190',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-482M8.3-001'
),
'ENST00000612833' => array(
'start' => '87470370',
'end' => '87474370',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-106D4.2-001'
),
'ENST00000610567' => array(
'start' => '87467138',
'end' => '87467654',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-106D4.3-001'
),
'ENST00000620306' => array(
'start' => '87683945',
'end' => '87684477',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-278A23.4-001'
),
'ENSMUST00000026357' => array(
'start' => '121730563',
'end' => '121790821',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Jph3-001'
),
'ENSMUST00000167439' => array(
'start' => '121730567',
'end' => '121794276',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Jph3-002'
),
'ENSMUST00000169735' => array(
'start' => '121729623',
'end' => '121789617',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Jph3-003'
),
'ENSMUST00000172209' => array(
'start' => '121753476',
'end' => '121782570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Jph3-004'
),
'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'
),
'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'
),
'ENSMUST00000082708' => array(
'start' => '121666628',
'end' => '121666706',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23299-201'
),
'ENSMUST00000182551' => array(
'start' => '121654054',
'end' => '121654517',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm27030-001'
)
),
'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_00070Q_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00070Q_0001' => array(
'genes_in_region' => array(
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000140948' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000226180' => array(
[maximum depth reached]
),
'ENSG00000260750' => array(
[maximum depth reached]
),
'ENSG00000276337' => array(
[maximum depth reached]
),
'ENSG00000276393' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Adipose',
(int) 9 => 'Heart',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Kidney',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Breast',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Muscle',
(int) 26 => 'Ovary',
(int) 27 => 'Placenta',
(int) 28 => 'Testis',
(int) 29 => 'Colon',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adrenal',
(int) 33 => 'Liver',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Muscle',
(int) 37 => 'Muscle',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Bladder',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Placenta',
(int) 59 => 'Brain',
(int) 60 => 'Colon',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Kidney',
(int) 79 => 'Liver',
(int) 80 => 'Lung',
(int) 81 => 'Testis',
(int) 82 => 'Kidney',
(int) 83 => 'Placenta',
(int) 84 => 'Testis',
(int) 85 => 'Brain',
(int) 86 => 'Heart',
(int) 87 => 'Kidney',
(int) 88 => 'Liver',
(int) 89 => 'Ovary',
(int) 90 => 'Testis',
(int) 91 => 'Adipose',
(int) 92 => 'Adrenal',
(int) 93 => 'Bladder',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Kidney',
(int) 99 => 'Liver',
(int) 100 => 'Lung',
(int) 101 => 'Muscle',
(int) 102 => 'Ovary',
(int) 103 => 'Placenta',
(int) 104 => 'Testis',
(int) 105 => 'Adrenal',
(int) 106 => 'Colon'
)
)
)
$gene_desc_arr = array(
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000140948' => 'zinc finger, CCHC domain containing 14',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000226180' => null,
'ENSG00000260750' => null,
'ENSG00000269935' => null,
'ENSG00000276337' => null,
'ENSG00000276393' => null,
'ENSG00000277504' => null,
'ENSMUSG00000025318' => 'junctophilin 3',
'ENSMUSG00000031812' => 'microtubule-associated protein 1 light chain 3 beta',
'ENSMUSG00000061410' => 'zinc finger, CCHC domain containing 14',
'ENSMUSG00000064642' => 'predicted gene, 23299',
'ENSMUSG00000098221' => 'predicted gene, 27030'
)
$gene_name_arr = array(
'ENSG00000104731' => 'KLHDC4',
'ENSG00000140948' => 'ZCCHC14',
'ENSG00000154118' => 'JPH3',
'ENSG00000226180' => 'RP11-278A23.1',
'ENSG00000260750' => 'RP11-482M8.1',
'ENSG00000269935' => 'RP11-482M8.3',
'ENSG00000276337' => 'RP11-106D4.2',
'ENSG00000276393' => 'RP11-106D4.3',
'ENSG00000277504' => 'RP11-278A23.4',
'ENSMUSG00000025318' => 'Jph3',
'ENSMUSG00000031812' => 'Map1lc3b',
'ENSMUSG00000061410' => 'Zcchc14',
'ENSMUSG00000064642' => 'Gm23299',
'ENSMUSG00000098221' => 'Gm27030'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00070Q_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '87406246',
'seq_end' => '87698156',
'region_length' => '291910',
'region_type' => 'CGP',
'el_id' => 'ENSG00000140948-ENSG00000154118'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00070Q_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121598703',
'seq_end' => '121794276',
'region_length' => '195573',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000061410-ENSMUSG00000025318'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 18 => 'Brain',
(int) 24 => 'Breast',
(int) 29 => 'Colon',
(int) 37 => 'Heart',
(int) 46 => 'Kidney',
(int) 55 => 'Liver',
(int) 66 => 'Lung',
(int) 73 => 'Muscle',
(int) 80 => 'Ovary',
(int) 88 => 'Placenta',
(int) 97 => '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) 58
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000270583' => array(
'start' => '87707813',
'end' => '87765949',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-001'
),
'ENST00000316853' => array(
'start' => '87707812',
'end' => '87750942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-008'
),
'ENST00000347925' => array(
'start' => '87707812',
'end' => '87765976',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-004'
),
'ENST00000353170' => array(
'start' => '87707812',
'end' => '87765899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-002'
),
'ENST00000446344' => array(
'start' => '87701639',
'end' => '87702514',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-201'
),
'ENST00000561825' => array(
'start' => '87748799',
'end' => '87765931',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-015'
),
'ENST00000562155' => array(
'start' => '87707840',
'end' => '87765929',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-003'
),
'ENST00000562261' => array(
'start' => '87709438',
'end' => '87765951',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-019'
),
'ENST00000562872' => array(
'start' => '87726821',
'end' => '87731006',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-023'
),
'ENST00000562913' => array(
'start' => '87710798',
'end' => '87726917',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-024'
),
'ENST00000563845' => array(
'start' => '87761958',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-014'
),
'ENST00000564396' => array(
'start' => '87730636',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-018'
),
'ENST00000564484' => array(
'start' => '87726899',
'end' => '87765933',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-020'
),
'ENST00000565328' => array(
'start' => '87729318',
'end' => '87762154',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-021'
),
'ENST00000566349' => array(
'start' => '87707813',
'end' => '87743044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-009'
),
'ENST00000566561' => array(
'start' => '87763485',
'end' => '87765961',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-013'
),
'ENST00000566661' => array(
'start' => '87709463',
'end' => '87762016',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-007'
),
'ENST00000567298' => array(
'start' => '87698149',
'end' => '87765972',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-005'
),
'ENST00000567513' => array(
'start' => '87711236',
'end' => '87740964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-022'
),
'ENST00000568338' => array(
'start' => '87755198',
'end' => '87765992',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-012'
),
'ENST00000568346' => array(
'start' => '87700778',
'end' => '87701724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-026'
),
'ENST00000568444' => array(
'start' => '87696485',
'end' => '87699415',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-027'
),
'ENST00000568499' => array(
'start' => '87703026',
'end' => '87708387',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-025'
),
'ENST00000568502' => array(
'start' => '87748738',
'end' => '87765964',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'KLHDC4-016'
),
'ENST00000569487' => array(
'start' => '87707816',
'end' => '87710877',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'KLHDC4-010'
),
'ENST00000569747' => array(
'start' => '87730607',
'end' => '87765967',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'KLHDC4-017'
),
'ENST00000622456' => array(
'start' => '87707914',
'end' => '87765992',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'KLHDC4-202'
),
'ENST00000268616' => array(
'start' => '87406246',
'end' => '87492045',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-001'
),
'ENST00000561928' => array(
'start' => '87411412',
'end' => '87433134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZCCHC14-003'
),
'ENST00000565193' => array(
'start' => '87415312',
'end' => '87417926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZCCHC14-004'
),
'ENST00000568020' => array(
'start' => '87406257',
'end' => '87491859',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ZCCHC14-002'
),
'ENST00000284262' => array(
'start' => '87602905',
'end' => '87698156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'JPH3-001'
),
'ENST00000301008' => array(
'start' => '87602887',
'end' => '87604627',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-003'
),
'ENST00000537256' => array(
'start' => '87601835',
'end' => '87697927',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-002'
),
'ENST00000563609' => array(
'start' => '87653562',
'end' => '87698142',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'JPH3-004'
),
'ENST00000538868' => array(
'start' => '87693537',
'end' => '87696147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-278A23.1-001'
),
'ENST00000562466' => array(
'start' => '87492555',
'end' => '87496998',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-002'
),
'ENST00000563921' => array(
'start' => '87494187',
'end' => '87515635',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-003'
),
'ENST00000565824' => array(
'start' => '87493274',
'end' => '87497166',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-482M8.1-001'
),
'ENST00000602388' => array(
'start' => '87600526',
'end' => '87602190',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-482M8.3-001'
),
'ENST00000612833' => array(
'start' => '87470370',
'end' => '87474370',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-106D4.2-001'
),
'ENST00000610567' => array(
'start' => '87467138',
'end' => '87467654',
'transcript_biotype' => 'unprocessed_pseudogene',
'transcript_name' => 'RP11-106D4.3-001'
),
'ENST00000620306' => array(
'start' => '87683945',
'end' => '87684477',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-278A23.4-001'
),
'ENSMUST00000026357' => array(
'start' => '121730563',
'end' => '121790821',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Jph3-001'
),
'ENSMUST00000167439' => array(
'start' => '121730567',
'end' => '121794276',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Jph3-002'
),
'ENSMUST00000169735' => array(
'start' => '121729623',
'end' => '121789617',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Jph3-003'
),
'ENSMUST00000172209' => array(
'start' => '121753476',
'end' => '121782570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Jph3-004'
),
'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'
),
'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'
),
'ENSMUST00000082708' => array(
'start' => '121666628',
'end' => '121666706',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23299-201'
),
'ENSMUST00000182551' => array(
'start' => '121654054',
'end' => '121654517',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm27030-001'
)
)
$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_00070Q_0001' => array(
'genes_in_region' => array(
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000140948' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000226180' => array(
[maximum depth reached]
),
'ENSG00000260750' => array(
[maximum depth reached]
),
'ENSG00000276337' => array(
[maximum depth reached]
),
'ENSG00000276393' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Ovary',
(int) 7 => 'Placenta',
(int) 8 => 'Adipose',
(int) 9 => 'Heart',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Kidney',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Breast',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Muscle',
(int) 26 => 'Ovary',
(int) 27 => 'Placenta',
(int) 28 => 'Testis',
(int) 29 => 'Colon',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adrenal',
(int) 33 => 'Liver',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Muscle',
(int) 37 => 'Muscle',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Brain',
(int) 44 => 'Breast',
(int) 45 => 'Colon',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Lung',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Testis',
(int) 55 => 'Bladder',
(int) 56 => 'Lung',
(int) 57 => 'Muscle',
(int) 58 => 'Placenta',
(int) 59 => 'Brain',
(int) 60 => 'Colon',
(int) 61 => 'Testis',
(int) 62 => 'Adipose',
(int) 63 => 'Adrenal',
(int) 64 => 'Bladder',
(int) 65 => 'Brain',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Ovary',
(int) 74 => 'Placenta',
(int) 75 => 'Testis',
(int) 76 => 'Adipose',
(int) 77 => 'Brain',
(int) 78 => 'Kidney',
(int) 79 => 'Liver',
(int) 80 => 'Lung',
(int) 81 => 'Testis',
(int) 82 => 'Kidney',
(int) 83 => 'Placenta',
(int) 84 => 'Testis',
(int) 85 => 'Brain',
(int) 86 => 'Heart',
(int) 87 => 'Kidney',
(int) 88 => 'Liver',
(int) 89 => 'Ovary',
(int) 90 => 'Testis',
(int) 91 => 'Adipose',
(int) 92 => 'Adrenal',
(int) 93 => 'Bladder',
(int) 94 => 'Brain',
(int) 95 => 'Breast',
(int) 96 => 'Colon',
(int) 97 => 'Heart',
(int) 98 => 'Kidney',
(int) 99 => 'Liver',
(int) 100 => 'Lung',
(int) 101 => 'Muscle',
(int) 102 => 'Ovary',
(int) 103 => 'Placenta',
(int) 104 => 'Testis',
(int) 105 => 'Adrenal',
(int) 106 => 'Colon'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00070Q_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121598703',
'seq_end' => '121794276',
'region_length' => '195573',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000061410-ENSMUSG00000025318'
)
)
$gene_el = array(
'ENST00000610567' => array(
'Adrenal' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.204',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000276393'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.204',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000610567'
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
(KLHDC4)