| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000040263-ENSMUSG00000040010 |
CGP |
10090 |
8:121796313-121907694  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0002T0_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_0002T0_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000103257' => 'solute carrier family 7 (amino acid transporter light chain, L system), member 5',
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000260177' => null,
'ENSG00000260466' => null,
'ENSG00000260498' => null,
'ENSG00000260671' => null,
'ENSG00000278598' => 'microRNA 6775',
'ENSMUSG00000040010' => 'solute carrier family 7 (cationic amino acid transporter, y+ system), member 5',
'ENSMUSG00000040263' => 'kelch domain containing 4',
'ENSMUSG00000077421' => 'predicted gene, 24283',
'ENSMUSG00000092418' => 'predicted gene 20406',
'ENSMUSG00000097812' => 'predicted gene, 26812',
'ENSMUSG00000098109' => 'RIKEN cDNA 9530085P06 gene'
),
'gene_name_arr' => array(
'ENSG00000103257' => 'SLC7A5',
'ENSG00000104731' => 'KLHDC4',
'ENSG00000154118' => 'JPH3',
'ENSG00000260177' => 'RP4-536B24.3',
'ENSG00000260466' => 'RP4-536B24.2',
'ENSG00000260498' => 'RP4-536B24.4',
'ENSG00000260671' => 'RP11-278A23.2',
'ENSG00000278598' => 'MIR6775',
'ENSMUSG00000040010' => 'Slc7a5',
'ENSMUSG00000040263' => 'Klhdc4',
'ENSMUSG00000077421' => 'Gm24283',
'ENSMUSG00000092418' => 'Gm20406',
'ENSMUSG00000097812' => 'Gm26812',
'ENSMUSG00000098109' => '9530085P06Rik'
),
'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) 5 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 21 => 'Breast',
(int) 26 => 'Colon',
(int) 32 => 'Heart',
(int) 41 => 'Kidney',
(int) 48 => 'Liver',
(int) 56 => 'Lung',
(int) 60 => 'Muscle',
(int) 67 => 'Ovary',
(int) 74 => 'Placenta',
(int) 82 => '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(
'ENST00000261622' => array(
'start' => '87830023',
'end' => '87869488',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-001'
),
'ENST00000563489' => array(
'start' => '87832732',
'end' => '87836805',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC7A5-003'
),
'ENST00000565644' => array(
'start' => '87830023',
'end' => '87863639',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-002'
),
'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'
),
'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'
),
'ENST00000561567' => array(
'start' => '87780134',
'end' => '87806476',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.3-001'
),
'ENST00000563687' => array(
'start' => '87836532',
'end' => '87837663',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-536B24.2-001'
),
'ENST00000563993' => array(
'start' => '87773488',
'end' => '87779374',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-001'
),
'ENST00000570159' => array(
'start' => '87773511',
'end' => '87779148',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-002'
),
'ENST00000563036' => array(
'start' => '87739771',
'end' => '87747706',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-278A23.2-001'
),
'ENST00000617557' => array(
'start' => '87834592',
'end' => '87834660',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6775-201'
),
'ENSMUST00000045557' => array(
'start' => '121881150',
'end' => '121907694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc7a5-001'
),
'ENSMUST00000182165' => array(
'start' => '121882802',
'end' => '121883914',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc7a5-003'
),
'ENSMUST00000183015' => array(
'start' => '121888374',
'end' => '121896502',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc7a5-002'
),
'ENSMUST00000045884' => array(
'start' => '121796313',
'end' => '121829569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-001'
),
'ENSMUST00000172470' => array(
'start' => '121821009',
'end' => '121829509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-007'
),
'ENSMUST00000172507' => array(
'start' => '121798183',
'end' => '121805320',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Klhdc4-008'
),
'ENSMUST00000172954' => array(
'start' => '121799485',
'end' => '121801599',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-009'
),
'ENSMUST00000174192' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-005'
),
'ENSMUST00000174206' => array(
'start' => '121796344',
'end' => '121797428',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-010'
),
'ENSMUST00000174255' => array(
'start' => '121821303',
'end' => '121829504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-006'
),
'ENSMUST00000174665' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-004'
),
'ENSMUST00000174709' => array(
'start' => '121796333',
'end' => '121829540',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-002'
),
'ENSMUST00000174717' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-003'
),
'ENSMUST00000104233' => array(
'start' => '121830436',
'end' => '121830542',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm24283-201'
),
'ENSMUST00000173993' => array(
'start' => '121806415',
'end' => '121807369',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm20406-001'
),
'ENSMUST00000181647' => array(
'start' => '121851883',
'end' => '121860325',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-002'
),
'ENSMUST00000181776' => array(
'start' => '121850194',
'end' => '121860621',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-001'
),
'ENSMUST00000182121' => array(
'start' => '121856777',
'end' => '121857603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '9530085P06Rik-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_0002T0_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0002T0_0001' => array(
'genes_in_region' => array(
'ENSG00000103257' => array(
[maximum depth reached]
),
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000260177' => array(
[maximum depth reached]
),
'ENSG00000260466' => array(
[maximum depth reached]
),
'ENSG00000260498' => array(
[maximum depth reached]
),
'ENSG00000260671' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Adipose',
(int) 33 => 'Heart',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Kidney',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Heart',
(int) 42 => 'Liver',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary',
(int) 56 => 'Adrenal',
(int) 57 => 'Liver',
(int) 58 => 'Placenta',
(int) 59 => 'Testis',
(int) 60 => 'Muscle',
(int) 61 => 'Muscle',
(int) 62 => 'Heart',
(int) 63 => 'Liver',
(int) 64 => 'Brain',
(int) 65 => 'Colon',
(int) 66 => 'Testis',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis',
(int) 75 => 'Colon',
(int) 76 => 'Brain',
(int) 77 => 'Testis',
(int) 78 => 'Adipose',
(int) 79 => 'Adrenal',
(int) 80 => 'Ovary',
(int) 81 => 'Testis',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Liver',
(int) 88 => 'Muscle',
(int) 89 => 'Placenta',
(int) 90 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000103257' => 'solute carrier family 7 (amino acid transporter light chain, L system), member 5',
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000260177' => null,
'ENSG00000260466' => null,
'ENSG00000260498' => null,
'ENSG00000260671' => null,
'ENSG00000278598' => 'microRNA 6775',
'ENSMUSG00000040010' => 'solute carrier family 7 (cationic amino acid transporter, y+ system), member 5',
'ENSMUSG00000040263' => 'kelch domain containing 4',
'ENSMUSG00000077421' => 'predicted gene, 24283',
'ENSMUSG00000092418' => 'predicted gene 20406',
'ENSMUSG00000097812' => 'predicted gene, 26812',
'ENSMUSG00000098109' => 'RIKEN cDNA 9530085P06 gene'
)
$gene_name_arr = array(
'ENSG00000103257' => 'SLC7A5',
'ENSG00000104731' => 'KLHDC4',
'ENSG00000154118' => 'JPH3',
'ENSG00000260177' => 'RP4-536B24.3',
'ENSG00000260466' => 'RP4-536B24.2',
'ENSG00000260498' => 'RP4-536B24.4',
'ENSG00000260671' => 'RP11-278A23.2',
'ENSG00000278598' => 'MIR6775',
'ENSMUSG00000040010' => 'Slc7a5',
'ENSMUSG00000040263' => 'Klhdc4',
'ENSMUSG00000077421' => 'Gm24283',
'ENSMUSG00000092418' => 'Gm20406',
'ENSMUSG00000097812' => 'Gm26812',
'ENSMUSG00000098109' => '9530085P06Rik'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002T0_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '87696485',
'seq_end' => '87869488',
'region_length' => '173003',
'region_type' => 'CGP',
'el_id' => 'ENSG00000104731-ENSG00000103257'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002T0_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121796313',
'seq_end' => '121907694',
'region_length' => '111381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000040263-ENSMUSG00000040010'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 21 => 'Breast',
(int) 26 => 'Colon',
(int) 32 => 'Heart',
(int) 41 => 'Kidney',
(int) 48 => 'Liver',
(int) 56 => 'Lung',
(int) 60 => 'Muscle',
(int) 67 => 'Ovary',
(int) 74 => 'Placenta',
(int) 82 => '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(
'ENST00000261622' => array(
'start' => '87830023',
'end' => '87869488',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-001'
),
'ENST00000563489' => array(
'start' => '87832732',
'end' => '87836805',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC7A5-003'
),
'ENST00000565644' => array(
'start' => '87830023',
'end' => '87863639',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-002'
),
'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'
),
'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'
),
'ENST00000561567' => array(
'start' => '87780134',
'end' => '87806476',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.3-001'
),
'ENST00000563687' => array(
'start' => '87836532',
'end' => '87837663',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-536B24.2-001'
),
'ENST00000563993' => array(
'start' => '87773488',
'end' => '87779374',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-001'
),
'ENST00000570159' => array(
'start' => '87773511',
'end' => '87779148',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-002'
),
'ENST00000563036' => array(
'start' => '87739771',
'end' => '87747706',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-278A23.2-001'
),
'ENST00000617557' => array(
'start' => '87834592',
'end' => '87834660',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6775-201'
),
'ENSMUST00000045557' => array(
'start' => '121881150',
'end' => '121907694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc7a5-001'
),
'ENSMUST00000182165' => array(
'start' => '121882802',
'end' => '121883914',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc7a5-003'
),
'ENSMUST00000183015' => array(
'start' => '121888374',
'end' => '121896502',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc7a5-002'
),
'ENSMUST00000045884' => array(
'start' => '121796313',
'end' => '121829569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-001'
),
'ENSMUST00000172470' => array(
'start' => '121821009',
'end' => '121829509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-007'
),
'ENSMUST00000172507' => array(
'start' => '121798183',
'end' => '121805320',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Klhdc4-008'
),
'ENSMUST00000172954' => array(
'start' => '121799485',
'end' => '121801599',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-009'
),
'ENSMUST00000174192' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-005'
),
'ENSMUST00000174206' => array(
'start' => '121796344',
'end' => '121797428',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-010'
),
'ENSMUST00000174255' => array(
'start' => '121821303',
'end' => '121829504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-006'
),
'ENSMUST00000174665' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-004'
),
'ENSMUST00000174709' => array(
'start' => '121796333',
'end' => '121829540',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-002'
),
'ENSMUST00000174717' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-003'
),
'ENSMUST00000104233' => array(
'start' => '121830436',
'end' => '121830542',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm24283-201'
),
'ENSMUST00000173993' => array(
'start' => '121806415',
'end' => '121807369',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm20406-001'
),
'ENSMUST00000181647' => array(
'start' => '121851883',
'end' => '121860325',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-002'
),
'ENSMUST00000181776' => array(
'start' => '121850194',
'end' => '121860621',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-001'
),
'ENSMUST00000182121' => array(
'start' => '121856777',
'end' => '121857603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '9530085P06Rik-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_0002T0_0001' => array(
'genes_in_region' => array(
'ENSG00000103257' => array(
[maximum depth reached]
),
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000260177' => array(
[maximum depth reached]
),
'ENSG00000260466' => array(
[maximum depth reached]
),
'ENSG00000260498' => array(
[maximum depth reached]
),
'ENSG00000260671' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Adipose',
(int) 33 => 'Heart',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Kidney',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Heart',
(int) 42 => 'Liver',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary',
(int) 56 => 'Adrenal',
(int) 57 => 'Liver',
(int) 58 => 'Placenta',
(int) 59 => 'Testis',
(int) 60 => 'Muscle',
(int) 61 => 'Muscle',
(int) 62 => 'Heart',
(int) 63 => 'Liver',
(int) 64 => 'Brain',
(int) 65 => 'Colon',
(int) 66 => 'Testis',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis',
(int) 75 => 'Colon',
(int) 76 => 'Brain',
(int) 77 => 'Testis',
(int) 78 => 'Adipose',
(int) 79 => 'Adrenal',
(int) 80 => 'Ovary',
(int) 81 => 'Testis',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Liver',
(int) 88 => 'Muscle',
(int) 89 => 'Placenta',
(int) 90 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0002T0_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121796313',
'seq_end' => '121907694',
'region_length' => '111381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000040263-ENSMUSG00000040010'
)
)
$gene_el = array(
'ENST00000563036' => array(
'Adrenal' => array(
'average_FPKM' => '1.465',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.305',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.351',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.374',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.312',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.100',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.605',
'stddev_FPKM' => '0.11'
)
)
)
$gene_key = 'ENSG00000260671'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '1.465',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.305',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.351',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.374',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.312',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.100',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.605',
'stddev_FPKM' => '0.11'
)
)
$tran_key = 'ENST00000563036'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0002T0_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000103257' => 'solute carrier family 7 (amino acid transporter light chain, L system), member 5',
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000260177' => null,
'ENSG00000260466' => null,
'ENSG00000260498' => null,
'ENSG00000260671' => null,
'ENSG00000278598' => 'microRNA 6775',
'ENSMUSG00000040010' => 'solute carrier family 7 (cationic amino acid transporter, y+ system), member 5',
'ENSMUSG00000040263' => 'kelch domain containing 4',
'ENSMUSG00000077421' => 'predicted gene, 24283',
'ENSMUSG00000092418' => 'predicted gene 20406',
'ENSMUSG00000097812' => 'predicted gene, 26812',
'ENSMUSG00000098109' => 'RIKEN cDNA 9530085P06 gene'
),
'gene_name_arr' => array(
'ENSG00000103257' => 'SLC7A5',
'ENSG00000104731' => 'KLHDC4',
'ENSG00000154118' => 'JPH3',
'ENSG00000260177' => 'RP4-536B24.3',
'ENSG00000260466' => 'RP4-536B24.2',
'ENSG00000260498' => 'RP4-536B24.4',
'ENSG00000260671' => 'RP11-278A23.2',
'ENSG00000278598' => 'MIR6775',
'ENSMUSG00000040010' => 'Slc7a5',
'ENSMUSG00000040263' => 'Klhdc4',
'ENSMUSG00000077421' => 'Gm24283',
'ENSMUSG00000092418' => 'Gm20406',
'ENSMUSG00000097812' => 'Gm26812',
'ENSMUSG00000098109' => '9530085P06Rik'
),
'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) 5 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 21 => 'Breast',
(int) 26 => 'Colon',
(int) 32 => 'Heart',
(int) 41 => 'Kidney',
(int) 48 => 'Liver',
(int) 56 => 'Lung',
(int) 60 => 'Muscle',
(int) 67 => 'Ovary',
(int) 74 => 'Placenta',
(int) 82 => '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(
'ENST00000261622' => array(
'start' => '87830023',
'end' => '87869488',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-001'
),
'ENST00000563489' => array(
'start' => '87832732',
'end' => '87836805',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC7A5-003'
),
'ENST00000565644' => array(
'start' => '87830023',
'end' => '87863639',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-002'
),
'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'
),
'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'
),
'ENST00000561567' => array(
'start' => '87780134',
'end' => '87806476',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.3-001'
),
'ENST00000563687' => array(
'start' => '87836532',
'end' => '87837663',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-536B24.2-001'
),
'ENST00000563993' => array(
'start' => '87773488',
'end' => '87779374',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-001'
),
'ENST00000570159' => array(
'start' => '87773511',
'end' => '87779148',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-002'
),
'ENST00000563036' => array(
'start' => '87739771',
'end' => '87747706',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-278A23.2-001'
),
'ENST00000617557' => array(
'start' => '87834592',
'end' => '87834660',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6775-201'
),
'ENSMUST00000045557' => array(
'start' => '121881150',
'end' => '121907694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc7a5-001'
),
'ENSMUST00000182165' => array(
'start' => '121882802',
'end' => '121883914',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc7a5-003'
),
'ENSMUST00000183015' => array(
'start' => '121888374',
'end' => '121896502',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc7a5-002'
),
'ENSMUST00000045884' => array(
'start' => '121796313',
'end' => '121829569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-001'
),
'ENSMUST00000172470' => array(
'start' => '121821009',
'end' => '121829509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-007'
),
'ENSMUST00000172507' => array(
'start' => '121798183',
'end' => '121805320',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Klhdc4-008'
),
'ENSMUST00000172954' => array(
'start' => '121799485',
'end' => '121801599',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-009'
),
'ENSMUST00000174192' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-005'
),
'ENSMUST00000174206' => array(
'start' => '121796344',
'end' => '121797428',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-010'
),
'ENSMUST00000174255' => array(
'start' => '121821303',
'end' => '121829504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-006'
),
'ENSMUST00000174665' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-004'
),
'ENSMUST00000174709' => array(
'start' => '121796333',
'end' => '121829540',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-002'
),
'ENSMUST00000174717' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-003'
),
'ENSMUST00000104233' => array(
'start' => '121830436',
'end' => '121830542',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm24283-201'
),
'ENSMUST00000173993' => array(
'start' => '121806415',
'end' => '121807369',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm20406-001'
),
'ENSMUST00000181647' => array(
'start' => '121851883',
'end' => '121860325',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-002'
),
'ENSMUST00000181776' => array(
'start' => '121850194',
'end' => '121860621',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-001'
),
'ENSMUST00000182121' => array(
'start' => '121856777',
'end' => '121857603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '9530085P06Rik-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_0002T0_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0002T0_0001' => array(
'genes_in_region' => array(
'ENSG00000103257' => array(
[maximum depth reached]
),
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000260177' => array(
[maximum depth reached]
),
'ENSG00000260466' => array(
[maximum depth reached]
),
'ENSG00000260498' => array(
[maximum depth reached]
),
'ENSG00000260671' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Adipose',
(int) 33 => 'Heart',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Kidney',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Heart',
(int) 42 => 'Liver',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary',
(int) 56 => 'Adrenal',
(int) 57 => 'Liver',
(int) 58 => 'Placenta',
(int) 59 => 'Testis',
(int) 60 => 'Muscle',
(int) 61 => 'Muscle',
(int) 62 => 'Heart',
(int) 63 => 'Liver',
(int) 64 => 'Brain',
(int) 65 => 'Colon',
(int) 66 => 'Testis',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis',
(int) 75 => 'Colon',
(int) 76 => 'Brain',
(int) 77 => 'Testis',
(int) 78 => 'Adipose',
(int) 79 => 'Adrenal',
(int) 80 => 'Ovary',
(int) 81 => 'Testis',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Liver',
(int) 88 => 'Muscle',
(int) 89 => 'Placenta',
(int) 90 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000103257' => 'solute carrier family 7 (amino acid transporter light chain, L system), member 5',
'ENSG00000104731' => 'kelch domain containing 4',
'ENSG00000154118' => 'junctophilin 3',
'ENSG00000260177' => null,
'ENSG00000260466' => null,
'ENSG00000260498' => null,
'ENSG00000260671' => null,
'ENSG00000278598' => 'microRNA 6775',
'ENSMUSG00000040010' => 'solute carrier family 7 (cationic amino acid transporter, y+ system), member 5',
'ENSMUSG00000040263' => 'kelch domain containing 4',
'ENSMUSG00000077421' => 'predicted gene, 24283',
'ENSMUSG00000092418' => 'predicted gene 20406',
'ENSMUSG00000097812' => 'predicted gene, 26812',
'ENSMUSG00000098109' => 'RIKEN cDNA 9530085P06 gene'
)
$gene_name_arr = array(
'ENSG00000103257' => 'SLC7A5',
'ENSG00000104731' => 'KLHDC4',
'ENSG00000154118' => 'JPH3',
'ENSG00000260177' => 'RP4-536B24.3',
'ENSG00000260466' => 'RP4-536B24.2',
'ENSG00000260498' => 'RP4-536B24.4',
'ENSG00000260671' => 'RP11-278A23.2',
'ENSG00000278598' => 'MIR6775',
'ENSMUSG00000040010' => 'Slc7a5',
'ENSMUSG00000040263' => 'Klhdc4',
'ENSMUSG00000077421' => 'Gm24283',
'ENSMUSG00000092418' => 'Gm20406',
'ENSMUSG00000097812' => 'Gm26812',
'ENSMUSG00000098109' => '9530085P06Rik'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002T0_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '87696485',
'seq_end' => '87869488',
'region_length' => '173003',
'region_type' => 'CGP',
'el_id' => 'ENSG00000104731-ENSG00000103257'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0002T0_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121796313',
'seq_end' => '121907694',
'region_length' => '111381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000040263-ENSMUSG00000040010'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 15 => 'Brain',
(int) 21 => 'Breast',
(int) 26 => 'Colon',
(int) 32 => 'Heart',
(int) 41 => 'Kidney',
(int) 48 => 'Liver',
(int) 56 => 'Lung',
(int) 60 => 'Muscle',
(int) 67 => 'Ovary',
(int) 74 => 'Placenta',
(int) 82 => '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(
'ENST00000261622' => array(
'start' => '87830023',
'end' => '87869488',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-001'
),
'ENST00000563489' => array(
'start' => '87832732',
'end' => '87836805',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SLC7A5-003'
),
'ENST00000565644' => array(
'start' => '87830023',
'end' => '87863639',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SLC7A5-002'
),
'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'
),
'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'
),
'ENST00000561567' => array(
'start' => '87780134',
'end' => '87806476',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.3-001'
),
'ENST00000563687' => array(
'start' => '87836532',
'end' => '87837663',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP4-536B24.2-001'
),
'ENST00000563993' => array(
'start' => '87773488',
'end' => '87779374',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-001'
),
'ENST00000570159' => array(
'start' => '87773511',
'end' => '87779148',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP4-536B24.4-002'
),
'ENST00000563036' => array(
'start' => '87739771',
'end' => '87747706',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-278A23.2-001'
),
'ENST00000617557' => array(
'start' => '87834592',
'end' => '87834660',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR6775-201'
),
'ENSMUST00000045557' => array(
'start' => '121881150',
'end' => '121907694',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Slc7a5-001'
),
'ENSMUST00000182165' => array(
'start' => '121882802',
'end' => '121883914',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Slc7a5-003'
),
'ENSMUST00000183015' => array(
'start' => '121888374',
'end' => '121896502',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Slc7a5-002'
),
'ENSMUST00000045884' => array(
'start' => '121796313',
'end' => '121829569',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-001'
),
'ENSMUST00000172470' => array(
'start' => '121821009',
'end' => '121829509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-007'
),
'ENSMUST00000172507' => array(
'start' => '121798183',
'end' => '121805320',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Klhdc4-008'
),
'ENSMUST00000172954' => array(
'start' => '121799485',
'end' => '121801599',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-009'
),
'ENSMUST00000174192' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-005'
),
'ENSMUST00000174206' => array(
'start' => '121796344',
'end' => '121797428',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-010'
),
'ENSMUST00000174255' => array(
'start' => '121821303',
'end' => '121829504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-006'
),
'ENSMUST00000174665' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Klhdc4-004'
),
'ENSMUST00000174709' => array(
'start' => '121796333',
'end' => '121829540',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Klhdc4-002'
),
'ENSMUST00000174717' => array(
'start' => '121796547',
'end' => '121829480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Klhdc4-003'
),
'ENSMUST00000104233' => array(
'start' => '121830436',
'end' => '121830542',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm24283-201'
),
'ENSMUST00000173993' => array(
'start' => '121806415',
'end' => '121807369',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm20406-001'
),
'ENSMUST00000181647' => array(
'start' => '121851883',
'end' => '121860325',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-002'
),
'ENSMUST00000181776' => array(
'start' => '121850194',
'end' => '121860621',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm26812-001'
),
'ENSMUST00000182121' => array(
'start' => '121856777',
'end' => '121857603',
'transcript_biotype' => 'lincRNA',
'transcript_name' => '9530085P06Rik-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_0002T0_0001' => array(
'genes_in_region' => array(
'ENSG00000103257' => array(
[maximum depth reached]
),
'ENSG00000104731' => array(
[maximum depth reached]
),
'ENSG00000154118' => array(
[maximum depth reached]
),
'ENSG00000260177' => array(
[maximum depth reached]
),
'ENSG00000260466' => array(
[maximum depth reached]
),
'ENSG00000260498' => array(
[maximum depth reached]
),
'ENSG00000260671' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Lung',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Placenta',
(int) 23 => 'Testis',
(int) 24 => 'Adipose',
(int) 25 => 'Bladder',
(int) 26 => 'Colon',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Liver',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Adipose',
(int) 33 => 'Heart',
(int) 34 => 'Ovary',
(int) 35 => 'Placenta',
(int) 36 => 'Kidney',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Heart',
(int) 42 => 'Liver',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Breast',
(int) 46 => 'Heart',
(int) 47 => 'Kidney',
(int) 48 => 'Liver',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary',
(int) 56 => 'Adrenal',
(int) 57 => 'Liver',
(int) 58 => 'Placenta',
(int) 59 => 'Testis',
(int) 60 => 'Muscle',
(int) 61 => 'Muscle',
(int) 62 => 'Heart',
(int) 63 => 'Liver',
(int) 64 => 'Brain',
(int) 65 => 'Colon',
(int) 66 => 'Testis',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis',
(int) 75 => 'Colon',
(int) 76 => 'Brain',
(int) 77 => 'Testis',
(int) 78 => 'Adipose',
(int) 79 => 'Adrenal',
(int) 80 => 'Ovary',
(int) 81 => 'Testis',
(int) 82 => 'Adrenal',
(int) 83 => 'Brain',
(int) 84 => 'Breast',
(int) 85 => 'Heart',
(int) 86 => 'Kidney',
(int) 87 => 'Liver',
(int) 88 => 'Muscle',
(int) 89 => 'Placenta',
(int) 90 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0002T0_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121796313',
'seq_end' => '121907694',
'region_length' => '111381',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000040263-ENSMUSG00000040010'
)
)
$gene_el = array(
'ENST00000563036' => array(
'Adrenal' => array(
'average_FPKM' => '1.465',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.305',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.351',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.374',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.312',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.100',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.605',
'stddev_FPKM' => '0.11'
)
)
)
$gene_key = 'ENSG00000260671'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '1.465',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.305',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.351',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.374',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.058',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.312',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.100',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.605',
'stddev_FPKM' => '0.11'
)
)
$tran_key = 'ENST00000563036'
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
(SLC7A5)