| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000000738-ENSMUSG00000000740 |
CGP |
10090 |
8:123062942-123105244  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000331_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_000331_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000197912' => 'spastic paraplegia 7 (pure and complicated autosomal recessive)',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSG00000261118' => null,
'ENSG00000274627' => null,
'ENSMUSG00000000738' => 'spastic paraplegia 7 homolog (human)',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079'
),
'gene_name_arr' => array(
'ENSG00000167526' => 'RPL13',
'ENSG00000197912' => 'SPG7',
'ENSG00000200084' => 'SNORD68',
'ENSG00000261118' => 'RP11-104N10.1',
'ENSG00000274627' => 'RP11-104N10.2',
'ENSMUSG00000000738' => 'Spg7',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079'
),
'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) 8 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 33 => 'Colon',
(int) 41 => 'Heart',
(int) 48 => 'Kidney',
(int) 58 => 'Liver',
(int) 64 => 'Lung',
(int) 74 => 'Muscle',
(int) 81 => 'Ovary',
(int) 90 => 'Placenta',
(int) 100 => '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) 60,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268704' => array(
'start' => '89508403',
'end' => '89557766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-001'
),
'ENST00000341316' => array(
'start' => '89508411',
'end' => '89537721',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-002'
),
'ENST00000561702' => array(
'start' => '89549846',
'end' => '89557762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-006'
),
'ENST00000561911' => array(
'start' => '89546664',
'end' => '89557130',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-018'
),
'ENST00000561945' => array(
'start' => '89531873',
'end' => '89544690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-015'
),
'ENST00000562775' => array(
'start' => '89522720',
'end' => '89526395',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-003'
),
'ENST00000563218' => array(
'start' => '89532587',
'end' => '89548378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-016'
),
'ENST00000563783' => array(
'start' => '89490917',
'end' => '89510592',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-007'
),
'ENST00000564047' => array(
'start' => '89524204',
'end' => '89529714',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-010'
),
'ENST00000564409' => array(
'start' => '89529205',
'end' => '89532570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-011'
),
'ENST00000565370' => array(
'start' => '89548889',
'end' => '89553100',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-014'
),
'ENST00000565891' => array(
'start' => '89555864',
'end' => '89557542',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-021'
),
'ENST00000566221' => array(
'start' => '89544726',
'end' => '89553079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-013'
),
'ENST00000566371' => array(
'start' => '89507502',
'end' => '89524154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-009'
),
'ENST00000566682' => array(
'start' => '89553064',
'end' => '89555002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-019'
),
'ENST00000567138' => array(
'start' => '89532035',
'end' => '89533791',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-012'
),
'ENST00000568151' => array(
'start' => '89508713',
'end' => '89524077',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-008'
),
'ENST00000568205' => array(
'start' => '89550536',
'end' => '89553367',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-017'
),
'ENST00000568509' => array(
'start' => '89491218',
'end' => '89499285',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-023'
),
'ENST00000569363' => array(
'start' => '89508577',
'end' => '89514571',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-022'
),
'ENST00000569720' => array(
'start' => '89553667',
'end' => '89557423',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-020'
),
'ENST00000569820' => array(
'start' => '89544648',
'end' => '89557768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-005'
),
'ENST00000620811' => array(
'start' => '89508397',
'end' => '89557765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-201'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENST00000565310' => array(
'start' => '89492403',
'end' => '89493793',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-002'
),
'ENST00000565623' => array(
'start' => '89492017',
'end' => '89504460',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-001'
),
'ENST00000611189' => array(
'start' => '89516797',
'end' => '89522217',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-104N10.2-001'
),
'ENSMUST00000108868' => array(
'start' => '123065281',
'end' => '123097649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-201'
),
'ENSMUST00000125975' => array(
'start' => '123062988',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-003'
),
'ENSMUST00000128234' => array(
'start' => '123080781',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-005'
),
'ENSMUST00000128803' => array(
'start' => '123065508',
'end' => '123097751',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-002'
),
'ENSMUST00000130787' => array(
'start' => '123087238',
'end' => '123093658',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-009'
),
'ENSMUST00000135991' => array(
'start' => '123091676',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-006'
),
'ENSMUST00000142150' => array(
'start' => '123080409',
'end' => '123088988',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-010'
),
'ENSMUST00000142541' => array(
'start' => '123062942',
'end' => '123079987',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-004'
),
'ENSMUST00000149248' => array(
'start' => '123065179',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-001'
),
'ENSMUST00000152972' => array(
'start' => '123087408',
'end' => '123091716',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Spg7-008'
),
'ENSMUST00000153285' => array(
'start' => '123065476',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-011'
),
'ENSMUST00000153492' => array(
'start' => '123073794',
'end' => '123088962',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Spg7-007'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_000331_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000331_0001' => array(
'genes_in_region' => array(
'ENSG00000197912' => array(
[maximum depth reached]
),
'ENSG00000261118' => array(
[maximum depth reached]
),
'ENSG00000274627' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Breast',
(int) 4 => 'Ovary',
(int) 5 => 'Placenta',
(int) 6 => 'Testis',
(int) 7 => 'Ovary',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Kidney',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Adipose',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Brain',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Bladder',
(int) 63 => 'Breast',
(int) 64 => 'Heart',
(int) 65 => 'Lung',
(int) 66 => 'Placenta',
(int) 67 => 'Testis',
(int) 68 => 'Muscle',
(int) 69 => 'Brain',
(int) 70 => 'Colon',
(int) 71 => 'Kidney',
(int) 72 => 'Adipose',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Kidney',
(int) 76 => 'Lung',
(int) 77 => 'Lung',
(int) 78 => 'Testis',
(int) 79 => 'Adipose',
(int) 80 => 'Brain',
(int) 81 => 'Breast',
(int) 82 => 'Colon',
(int) 83 => 'Heart',
(int) 84 => 'Kidney',
(int) 85 => 'Liver',
(int) 86 => 'Lung',
(int) 87 => 'Placenta',
(int) 88 => 'Testis',
(int) 89 => 'Brain',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Placenta',
(int) 96 => 'Testis',
(int) 97 => 'Adipose',
(int) 98 => 'Bladder',
(int) 99 => 'Brain',
(int) 100 => 'Breast',
(int) 101 => 'Colon',
(int) 102 => 'Heart',
(int) 103 => 'Kidney',
(int) 104 => 'Liver',
(int) 105 => 'Lung',
(int) 106 => 'Muscle',
(int) 107 => 'Ovary',
(int) 108 => 'Placenta',
(int) 109 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000197912' => 'spastic paraplegia 7 (pure and complicated autosomal recessive)',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSG00000261118' => null,
'ENSG00000274627' => null,
'ENSMUSG00000000738' => 'spastic paraplegia 7 homolog (human)',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079'
)
$gene_name_arr = array(
'ENSG00000167526' => 'RPL13',
'ENSG00000197912' => 'SPG7',
'ENSG00000200084' => 'SNORD68',
'ENSG00000261118' => 'RP11-104N10.1',
'ENSG00000274627' => 'RP11-104N10.2',
'ENSMUSG00000000738' => 'Spg7',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000331_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89490917',
'seq_end' => '89566828',
'region_length' => '75911',
'region_type' => 'CGP',
'el_id' => 'ENSG00000197912-ENSG00000167526'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000331_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123062942',
'seq_end' => '123105244',
'region_length' => '42302',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000738-ENSMUSG00000000740'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 33 => 'Colon',
(int) 41 => 'Heart',
(int) 48 => 'Kidney',
(int) 58 => 'Liver',
(int) 64 => 'Lung',
(int) 74 => 'Muscle',
(int) 81 => 'Ovary',
(int) 90 => 'Placenta',
(int) 100 => '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) 60
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268704' => array(
'start' => '89508403',
'end' => '89557766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-001'
),
'ENST00000341316' => array(
'start' => '89508411',
'end' => '89537721',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-002'
),
'ENST00000561702' => array(
'start' => '89549846',
'end' => '89557762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-006'
),
'ENST00000561911' => array(
'start' => '89546664',
'end' => '89557130',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-018'
),
'ENST00000561945' => array(
'start' => '89531873',
'end' => '89544690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-015'
),
'ENST00000562775' => array(
'start' => '89522720',
'end' => '89526395',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-003'
),
'ENST00000563218' => array(
'start' => '89532587',
'end' => '89548378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-016'
),
'ENST00000563783' => array(
'start' => '89490917',
'end' => '89510592',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-007'
),
'ENST00000564047' => array(
'start' => '89524204',
'end' => '89529714',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-010'
),
'ENST00000564409' => array(
'start' => '89529205',
'end' => '89532570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-011'
),
'ENST00000565370' => array(
'start' => '89548889',
'end' => '89553100',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-014'
),
'ENST00000565891' => array(
'start' => '89555864',
'end' => '89557542',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-021'
),
'ENST00000566221' => array(
'start' => '89544726',
'end' => '89553079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-013'
),
'ENST00000566371' => array(
'start' => '89507502',
'end' => '89524154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-009'
),
'ENST00000566682' => array(
'start' => '89553064',
'end' => '89555002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-019'
),
'ENST00000567138' => array(
'start' => '89532035',
'end' => '89533791',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-012'
),
'ENST00000568151' => array(
'start' => '89508713',
'end' => '89524077',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-008'
),
'ENST00000568205' => array(
'start' => '89550536',
'end' => '89553367',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-017'
),
'ENST00000568509' => array(
'start' => '89491218',
'end' => '89499285',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-023'
),
'ENST00000569363' => array(
'start' => '89508577',
'end' => '89514571',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-022'
),
'ENST00000569720' => array(
'start' => '89553667',
'end' => '89557423',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-020'
),
'ENST00000569820' => array(
'start' => '89544648',
'end' => '89557768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-005'
),
'ENST00000620811' => array(
'start' => '89508397',
'end' => '89557765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-201'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENST00000565310' => array(
'start' => '89492403',
'end' => '89493793',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-002'
),
'ENST00000565623' => array(
'start' => '89492017',
'end' => '89504460',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-001'
),
'ENST00000611189' => array(
'start' => '89516797',
'end' => '89522217',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-104N10.2-001'
),
'ENSMUST00000108868' => array(
'start' => '123065281',
'end' => '123097649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-201'
),
'ENSMUST00000125975' => array(
'start' => '123062988',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-003'
),
'ENSMUST00000128234' => array(
'start' => '123080781',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-005'
),
'ENSMUST00000128803' => array(
'start' => '123065508',
'end' => '123097751',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-002'
),
'ENSMUST00000130787' => array(
'start' => '123087238',
'end' => '123093658',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-009'
),
'ENSMUST00000135991' => array(
'start' => '123091676',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-006'
),
'ENSMUST00000142150' => array(
'start' => '123080409',
'end' => '123088988',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-010'
),
'ENSMUST00000142541' => array(
'start' => '123062942',
'end' => '123079987',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-004'
),
'ENSMUST00000149248' => array(
'start' => '123065179',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-001'
),
'ENSMUST00000152972' => array(
'start' => '123087408',
'end' => '123091716',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Spg7-008'
),
'ENSMUST00000153285' => array(
'start' => '123065476',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-011'
),
'ENSMUST00000153492' => array(
'start' => '123073794',
'end' => '123088962',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Spg7-007'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_000331_0001' => array(
'genes_in_region' => array(
'ENSG00000197912' => array(
[maximum depth reached]
),
'ENSG00000261118' => array(
[maximum depth reached]
),
'ENSG00000274627' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Breast',
(int) 4 => 'Ovary',
(int) 5 => 'Placenta',
(int) 6 => 'Testis',
(int) 7 => 'Ovary',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Kidney',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Adipose',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Brain',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Bladder',
(int) 63 => 'Breast',
(int) 64 => 'Heart',
(int) 65 => 'Lung',
(int) 66 => 'Placenta',
(int) 67 => 'Testis',
(int) 68 => 'Muscle',
(int) 69 => 'Brain',
(int) 70 => 'Colon',
(int) 71 => 'Kidney',
(int) 72 => 'Adipose',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Kidney',
(int) 76 => 'Lung',
(int) 77 => 'Lung',
(int) 78 => 'Testis',
(int) 79 => 'Adipose',
(int) 80 => 'Brain',
(int) 81 => 'Breast',
(int) 82 => 'Colon',
(int) 83 => 'Heart',
(int) 84 => 'Kidney',
(int) 85 => 'Liver',
(int) 86 => 'Lung',
(int) 87 => 'Placenta',
(int) 88 => 'Testis',
(int) 89 => 'Brain',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Placenta',
(int) 96 => 'Testis',
(int) 97 => 'Adipose',
(int) 98 => 'Bladder',
(int) 99 => 'Brain',
(int) 100 => 'Breast',
(int) 101 => 'Colon',
(int) 102 => 'Heart',
(int) 103 => 'Kidney',
(int) 104 => 'Liver',
(int) 105 => 'Lung',
(int) 106 => 'Muscle',
(int) 107 => 'Ovary',
(int) 108 => 'Placenta',
(int) 109 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000331_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123062942',
'seq_end' => '123105244',
'region_length' => '42302',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000738-ENSMUSG00000000740'
)
)
$gene_el = array(
'ENST00000611189' => array(
'Adipose' => array(
'average_FPKM' => '0.495',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.737',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.578',
'stddev_FPKM' => '0.23'
),
'Breast' => array(
'average_FPKM' => '1.059',
'stddev_FPKM' => '0.50'
),
'Colon' => array(
'average_FPKM' => '0.683',
'stddev_FPKM' => '0.42'
),
'Heart' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.10'
),
'Kidney' => array(
'average_FPKM' => '0.689',
'stddev_FPKM' => '0.04'
),
'Liver' => array(
'average_FPKM' => '0.349',
'stddev_FPKM' => '0.21'
),
'Lung' => array(
'average_FPKM' => '0.466',
'stddev_FPKM' => '0.13'
),
'Muscle' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.15'
),
'Ovary' => array(
'average_FPKM' => '0.810',
'stddev_FPKM' => '0.38'
),
'Placenta' => array(
'average_FPKM' => '0.276',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '1.153',
'stddev_FPKM' => '0.50'
)
)
)
$gene_key = 'ENSG00000274627'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.495',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.737',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.578',
'stddev_FPKM' => '0.23'
),
'Breast' => array(
'average_FPKM' => '1.059',
'stddev_FPKM' => '0.50'
),
'Colon' => array(
'average_FPKM' => '0.683',
'stddev_FPKM' => '0.42'
),
'Heart' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.10'
),
'Kidney' => array(
'average_FPKM' => '0.689',
'stddev_FPKM' => '0.04'
),
'Liver' => array(
'average_FPKM' => '0.349',
'stddev_FPKM' => '0.21'
),
'Lung' => array(
'average_FPKM' => '0.466',
'stddev_FPKM' => '0.13'
),
'Muscle' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.15'
),
'Ovary' => array(
'average_FPKM' => '0.810',
'stddev_FPKM' => '0.38'
),
'Placenta' => array(
'average_FPKM' => '0.276',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '1.153',
'stddev_FPKM' => '0.50'
)
)
$tran_key = 'ENST00000611189'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000331_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000197912' => 'spastic paraplegia 7 (pure and complicated autosomal recessive)',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSG00000261118' => null,
'ENSG00000274627' => null,
'ENSMUSG00000000738' => 'spastic paraplegia 7 homolog (human)',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079'
),
'gene_name_arr' => array(
'ENSG00000167526' => 'RPL13',
'ENSG00000197912' => 'SPG7',
'ENSG00000200084' => 'SNORD68',
'ENSG00000261118' => 'RP11-104N10.1',
'ENSG00000274627' => 'RP11-104N10.2',
'ENSMUSG00000000738' => 'Spg7',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079'
),
'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) 8 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 33 => 'Colon',
(int) 41 => 'Heart',
(int) 48 => 'Kidney',
(int) 58 => 'Liver',
(int) 64 => 'Lung',
(int) 74 => 'Muscle',
(int) 81 => 'Ovary',
(int) 90 => 'Placenta',
(int) 100 => '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) 60,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268704' => array(
'start' => '89508403',
'end' => '89557766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-001'
),
'ENST00000341316' => array(
'start' => '89508411',
'end' => '89537721',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-002'
),
'ENST00000561702' => array(
'start' => '89549846',
'end' => '89557762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-006'
),
'ENST00000561911' => array(
'start' => '89546664',
'end' => '89557130',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-018'
),
'ENST00000561945' => array(
'start' => '89531873',
'end' => '89544690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-015'
),
'ENST00000562775' => array(
'start' => '89522720',
'end' => '89526395',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-003'
),
'ENST00000563218' => array(
'start' => '89532587',
'end' => '89548378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-016'
),
'ENST00000563783' => array(
'start' => '89490917',
'end' => '89510592',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-007'
),
'ENST00000564047' => array(
'start' => '89524204',
'end' => '89529714',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-010'
),
'ENST00000564409' => array(
'start' => '89529205',
'end' => '89532570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-011'
),
'ENST00000565370' => array(
'start' => '89548889',
'end' => '89553100',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-014'
),
'ENST00000565891' => array(
'start' => '89555864',
'end' => '89557542',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-021'
),
'ENST00000566221' => array(
'start' => '89544726',
'end' => '89553079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-013'
),
'ENST00000566371' => array(
'start' => '89507502',
'end' => '89524154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-009'
),
'ENST00000566682' => array(
'start' => '89553064',
'end' => '89555002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-019'
),
'ENST00000567138' => array(
'start' => '89532035',
'end' => '89533791',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-012'
),
'ENST00000568151' => array(
'start' => '89508713',
'end' => '89524077',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-008'
),
'ENST00000568205' => array(
'start' => '89550536',
'end' => '89553367',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-017'
),
'ENST00000568509' => array(
'start' => '89491218',
'end' => '89499285',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-023'
),
'ENST00000569363' => array(
'start' => '89508577',
'end' => '89514571',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-022'
),
'ENST00000569720' => array(
'start' => '89553667',
'end' => '89557423',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-020'
),
'ENST00000569820' => array(
'start' => '89544648',
'end' => '89557768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-005'
),
'ENST00000620811' => array(
'start' => '89508397',
'end' => '89557765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-201'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENST00000565310' => array(
'start' => '89492403',
'end' => '89493793',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-002'
),
'ENST00000565623' => array(
'start' => '89492017',
'end' => '89504460',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-001'
),
'ENST00000611189' => array(
'start' => '89516797',
'end' => '89522217',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-104N10.2-001'
),
'ENSMUST00000108868' => array(
'start' => '123065281',
'end' => '123097649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-201'
),
'ENSMUST00000125975' => array(
'start' => '123062988',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-003'
),
'ENSMUST00000128234' => array(
'start' => '123080781',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-005'
),
'ENSMUST00000128803' => array(
'start' => '123065508',
'end' => '123097751',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-002'
),
'ENSMUST00000130787' => array(
'start' => '123087238',
'end' => '123093658',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-009'
),
'ENSMUST00000135991' => array(
'start' => '123091676',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-006'
),
'ENSMUST00000142150' => array(
'start' => '123080409',
'end' => '123088988',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-010'
),
'ENSMUST00000142541' => array(
'start' => '123062942',
'end' => '123079987',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-004'
),
'ENSMUST00000149248' => array(
'start' => '123065179',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-001'
),
'ENSMUST00000152972' => array(
'start' => '123087408',
'end' => '123091716',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Spg7-008'
),
'ENSMUST00000153285' => array(
'start' => '123065476',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-011'
),
'ENSMUST00000153492' => array(
'start' => '123073794',
'end' => '123088962',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Spg7-007'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_000331_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000331_0001' => array(
'genes_in_region' => array(
'ENSG00000197912' => array(
[maximum depth reached]
),
'ENSG00000261118' => array(
[maximum depth reached]
),
'ENSG00000274627' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Breast',
(int) 4 => 'Ovary',
(int) 5 => 'Placenta',
(int) 6 => 'Testis',
(int) 7 => 'Ovary',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Kidney',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Adipose',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Brain',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Bladder',
(int) 63 => 'Breast',
(int) 64 => 'Heart',
(int) 65 => 'Lung',
(int) 66 => 'Placenta',
(int) 67 => 'Testis',
(int) 68 => 'Muscle',
(int) 69 => 'Brain',
(int) 70 => 'Colon',
(int) 71 => 'Kidney',
(int) 72 => 'Adipose',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Kidney',
(int) 76 => 'Lung',
(int) 77 => 'Lung',
(int) 78 => 'Testis',
(int) 79 => 'Adipose',
(int) 80 => 'Brain',
(int) 81 => 'Breast',
(int) 82 => 'Colon',
(int) 83 => 'Heart',
(int) 84 => 'Kidney',
(int) 85 => 'Liver',
(int) 86 => 'Lung',
(int) 87 => 'Placenta',
(int) 88 => 'Testis',
(int) 89 => 'Brain',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Placenta',
(int) 96 => 'Testis',
(int) 97 => 'Adipose',
(int) 98 => 'Bladder',
(int) 99 => 'Brain',
(int) 100 => 'Breast',
(int) 101 => 'Colon',
(int) 102 => 'Heart',
(int) 103 => 'Kidney',
(int) 104 => 'Liver',
(int) 105 => 'Lung',
(int) 106 => 'Muscle',
(int) 107 => 'Ovary',
(int) 108 => 'Placenta',
(int) 109 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000167526' => 'ribosomal protein L13',
'ENSG00000197912' => 'spastic paraplegia 7 (pure and complicated autosomal recessive)',
'ENSG00000200084' => 'small nucleolar RNA, C/D box 68',
'ENSG00000261118' => null,
'ENSG00000274627' => null,
'ENSMUSG00000000738' => 'spastic paraplegia 7 homolog (human)',
'ENSMUSG00000000740' => 'ribosomal protein L13',
'ENSMUSG00000064450' => 'small nucleolar RNA, C/D box 68',
'ENSMUSG00000098550' => 'microRNA 7079'
)
$gene_name_arr = array(
'ENSG00000167526' => 'RPL13',
'ENSG00000197912' => 'SPG7',
'ENSG00000200084' => 'SNORD68',
'ENSG00000261118' => 'RP11-104N10.1',
'ENSG00000274627' => 'RP11-104N10.2',
'ENSMUSG00000000738' => 'Spg7',
'ENSMUSG00000000740' => 'Rpl13',
'ENSMUSG00000064450' => 'Snord68',
'ENSMUSG00000098550' => 'Mir7079'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000331_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89490917',
'seq_end' => '89566828',
'region_length' => '75911',
'region_type' => 'CGP',
'el_id' => 'ENSG00000197912-ENSG00000167526'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000331_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123062942',
'seq_end' => '123105244',
'region_length' => '42302',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000738-ENSMUSG00000000740'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 12 => 'Bladder',
(int) 17 => 'Brain',
(int) 24 => 'Breast',
(int) 33 => 'Colon',
(int) 41 => 'Heart',
(int) 48 => 'Kidney',
(int) 58 => 'Liver',
(int) 64 => 'Lung',
(int) 74 => 'Muscle',
(int) 81 => 'Ovary',
(int) 90 => 'Placenta',
(int) 100 => '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) 60
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000311528' => array(
'start' => '89560657',
'end' => '89566828',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-001'
),
'ENST00000393099' => array(
'start' => '89560711',
'end' => '89564542',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-002'
),
'ENST00000399461' => array(
'start' => '89560904',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-003'
),
'ENST00000452368' => array(
'start' => '89560683',
'end' => '89563952',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-015'
),
'ENST00000467736' => array(
'start' => '89560711',
'end' => '89561710',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-006'
),
'ENST00000472354' => array(
'start' => '89562370',
'end' => '89563438',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-008'
),
'ENST00000484610' => array(
'start' => '89560679',
'end' => '89563067',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-004'
),
'ENST00000487034' => array(
'start' => '89560682',
'end' => '89561523',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-007'
),
'ENST00000491523' => array(
'start' => '89560677',
'end' => '89562393',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-005'
),
'ENST00000562879' => array(
'start' => '89560682',
'end' => '89563473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'RPL13-011'
),
'ENST00000563270' => array(
'start' => '89560681',
'end' => '89563032',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-016'
),
'ENST00000563749' => array(
'start' => '89560677',
'end' => '89563043',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-010'
),
'ENST00000565571' => array(
'start' => '89560683',
'end' => '89561849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-018'
),
'ENST00000567815' => array(
'start' => '89560681',
'end' => '89563080',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL13-009'
),
'ENST00000570149' => array(
'start' => '89562140',
'end' => '89563066',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL13-017'
),
'ENST00000268704' => array(
'start' => '89508403',
'end' => '89557766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-001'
),
'ENST00000341316' => array(
'start' => '89508411',
'end' => '89537721',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-002'
),
'ENST00000561702' => array(
'start' => '89549846',
'end' => '89557762',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-006'
),
'ENST00000561911' => array(
'start' => '89546664',
'end' => '89557130',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-018'
),
'ENST00000561945' => array(
'start' => '89531873',
'end' => '89544690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-015'
),
'ENST00000562775' => array(
'start' => '89522720',
'end' => '89526395',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-003'
),
'ENST00000563218' => array(
'start' => '89532587',
'end' => '89548378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-016'
),
'ENST00000563783' => array(
'start' => '89490917',
'end' => '89510592',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-007'
),
'ENST00000564047' => array(
'start' => '89524204',
'end' => '89529714',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-010'
),
'ENST00000564409' => array(
'start' => '89529205',
'end' => '89532570',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-011'
),
'ENST00000565370' => array(
'start' => '89548889',
'end' => '89553100',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-014'
),
'ENST00000565891' => array(
'start' => '89555864',
'end' => '89557542',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-021'
),
'ENST00000566221' => array(
'start' => '89544726',
'end' => '89553079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-013'
),
'ENST00000566371' => array(
'start' => '89507502',
'end' => '89524154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-009'
),
'ENST00000566682' => array(
'start' => '89553064',
'end' => '89555002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-019'
),
'ENST00000567138' => array(
'start' => '89532035',
'end' => '89533791',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-012'
),
'ENST00000568151' => array(
'start' => '89508713',
'end' => '89524077',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-008'
),
'ENST00000568205' => array(
'start' => '89550536',
'end' => '89553367',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-017'
),
'ENST00000568509' => array(
'start' => '89491218',
'end' => '89499285',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-023'
),
'ENST00000569363' => array(
'start' => '89508577',
'end' => '89514571',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPG7-022'
),
'ENST00000569720' => array(
'start' => '89553667',
'end' => '89557423',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPG7-020'
),
'ENST00000569820' => array(
'start' => '89544648',
'end' => '89557768',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPG7-005'
),
'ENST00000620811' => array(
'start' => '89508397',
'end' => '89557765',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPG7-201'
),
'ENST00000363214' => array(
'start' => '89561434',
'end' => '89561517',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORD68-201'
),
'ENST00000565310' => array(
'start' => '89492403',
'end' => '89493793',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-002'
),
'ENST00000565623' => array(
'start' => '89492017',
'end' => '89504460',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-104N10.1-001'
),
'ENST00000611189' => array(
'start' => '89516797',
'end' => '89522217',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-104N10.2-001'
),
'ENSMUST00000108868' => array(
'start' => '123065281',
'end' => '123097649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-201'
),
'ENSMUST00000125975' => array(
'start' => '123062988',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-003'
),
'ENSMUST00000128234' => array(
'start' => '123080781',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-005'
),
'ENSMUST00000128803' => array(
'start' => '123065508',
'end' => '123097751',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-002'
),
'ENSMUST00000130787' => array(
'start' => '123087238',
'end' => '123093658',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-009'
),
'ENSMUST00000135991' => array(
'start' => '123091676',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-006'
),
'ENSMUST00000142150' => array(
'start' => '123080409',
'end' => '123088988',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Spg7-010'
),
'ENSMUST00000142541' => array(
'start' => '123062942',
'end' => '123079987',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-004'
),
'ENSMUST00000149248' => array(
'start' => '123065179',
'end' => '123097760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-001'
),
'ENSMUST00000152972' => array(
'start' => '123087408',
'end' => '123091716',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Spg7-008'
),
'ENSMUST00000153285' => array(
'start' => '123065476',
'end' => '123097753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spg7-011'
),
'ENSMUST00000153492' => array(
'start' => '123073794',
'end' => '123088962',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Spg7-007'
),
'ENSMUST00000000756' => array(
'start' => '123102350',
'end' => '123105244',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Rpl13-001'
),
'ENSMUST00000129311' => array(
'start' => '123102653',
'end' => '123105244',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-002'
),
'ENSMUST00000132275' => array(
'start' => '123102653',
'end' => '123104464',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-004'
),
'ENSMUST00000152444' => array(
'start' => '123102651',
'end' => '123103641',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Rpl13-003'
),
'ENSMUST00000082516' => array(
'start' => '123103038',
'end' => '123103123',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Snord68-201'
),
'ENSMUST00000184697' => array(
'start' => '123104975',
'end' => '123105043',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir7079-201'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_000331_0001' => array(
'genes_in_region' => array(
'ENSG00000197912' => array(
[maximum depth reached]
),
'ENSG00000261118' => array(
[maximum depth reached]
),
'ENSG00000274627' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Ovary',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Breast',
(int) 4 => 'Ovary',
(int) 5 => 'Placenta',
(int) 6 => 'Testis',
(int) 7 => 'Ovary',
(int) 8 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 12 => 'Breast',
(int) 13 => 'Colon',
(int) 14 => 'Heart',
(int) 15 => 'Kidney',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Muscle',
(int) 19 => 'Ovary',
(int) 20 => 'Placenta',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Colon',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Kidney',
(int) 34 => 'Adipose',
(int) 35 => 'Adrenal',
(int) 36 => 'Bladder',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Adipose',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Brain',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Heart',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Lung',
(int) 58 => 'Muscle',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Bladder',
(int) 63 => 'Breast',
(int) 64 => 'Heart',
(int) 65 => 'Lung',
(int) 66 => 'Placenta',
(int) 67 => 'Testis',
(int) 68 => 'Muscle',
(int) 69 => 'Brain',
(int) 70 => 'Colon',
(int) 71 => 'Kidney',
(int) 72 => 'Adipose',
(int) 73 => 'Breast',
(int) 74 => 'Colon',
(int) 75 => 'Kidney',
(int) 76 => 'Lung',
(int) 77 => 'Lung',
(int) 78 => 'Testis',
(int) 79 => 'Adipose',
(int) 80 => 'Brain',
(int) 81 => 'Breast',
(int) 82 => 'Colon',
(int) 83 => 'Heart',
(int) 84 => 'Kidney',
(int) 85 => 'Liver',
(int) 86 => 'Lung',
(int) 87 => 'Placenta',
(int) 88 => 'Testis',
(int) 89 => 'Brain',
(int) 90 => 'Heart',
(int) 91 => 'Kidney',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Placenta',
(int) 96 => 'Testis',
(int) 97 => 'Adipose',
(int) 98 => 'Bladder',
(int) 99 => 'Brain',
(int) 100 => 'Breast',
(int) 101 => 'Colon',
(int) 102 => 'Heart',
(int) 103 => 'Kidney',
(int) 104 => 'Liver',
(int) 105 => 'Lung',
(int) 106 => 'Muscle',
(int) 107 => 'Ovary',
(int) 108 => 'Placenta',
(int) 109 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000331_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123062942',
'seq_end' => '123105244',
'region_length' => '42302',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000000738-ENSMUSG00000000740'
)
)
$gene_el = array(
'ENST00000611189' => array(
'Adipose' => array(
'average_FPKM' => '0.495',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.737',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.578',
'stddev_FPKM' => '0.23'
),
'Breast' => array(
'average_FPKM' => '1.059',
'stddev_FPKM' => '0.50'
),
'Colon' => array(
'average_FPKM' => '0.683',
'stddev_FPKM' => '0.42'
),
'Heart' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.10'
),
'Kidney' => array(
'average_FPKM' => '0.689',
'stddev_FPKM' => '0.04'
),
'Liver' => array(
'average_FPKM' => '0.349',
'stddev_FPKM' => '0.21'
),
'Lung' => array(
'average_FPKM' => '0.466',
'stddev_FPKM' => '0.13'
),
'Muscle' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.15'
),
'Ovary' => array(
'average_FPKM' => '0.810',
'stddev_FPKM' => '0.38'
),
'Placenta' => array(
'average_FPKM' => '0.276',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '1.153',
'stddev_FPKM' => '0.50'
)
)
)
$gene_key = 'ENSG00000274627'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.495',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.737',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.578',
'stddev_FPKM' => '0.23'
),
'Breast' => array(
'average_FPKM' => '1.059',
'stddev_FPKM' => '0.50'
),
'Colon' => array(
'average_FPKM' => '0.683',
'stddev_FPKM' => '0.42'
),
'Heart' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.10'
),
'Kidney' => array(
'average_FPKM' => '0.689',
'stddev_FPKM' => '0.04'
),
'Liver' => array(
'average_FPKM' => '0.349',
'stddev_FPKM' => '0.21'
),
'Lung' => array(
'average_FPKM' => '0.466',
'stddev_FPKM' => '0.13'
),
'Muscle' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.15'
),
'Ovary' => array(
'average_FPKM' => '0.810',
'stddev_FPKM' => '0.38'
),
'Placenta' => array(
'average_FPKM' => '0.276',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '1.153',
'stddev_FPKM' => '0.50'
)
)
$tran_key = 'ENST00000611189'
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
(SPG7)