| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000031976-ENSMUSG00000089704 |
CGP |
10090 |
8:124021508-124345724  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000611_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_000611_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000135763' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSG00000143641' => 'polypeptide N-acetylgalactosaminyltransferase 2',
'ENSG00000211525' => null,
'ENSG00000213028' => null,
'ENSG00000224407' => null,
'ENSG00000225984' => 'high mobility group box 1 pseudogene 26',
'ENSG00000227006' => null,
'ENSG00000227043' => null,
'ENSG00000228058' => null,
'ENSMUSG00000031976' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSMUSG00000088414' => 'microRNA 1967',
'ENSMUSG00000089704' => 'UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2',
'ENSMUSG00000089745' => 'RIKEN cDNA 1810008B01 gene',
'ENSMUSG00000089820' => 'predicted gene 15775',
'ENSMUSG00000092329' => 'predicted gene 20388'
),
'gene_name_arr' => array(
'ENSG00000135763' => 'URB2',
'ENSG00000143641' => 'GALNT2',
'ENSG00000211525' => 'BX323860.1',
'ENSG00000213028' => 'RP11-108F13.2',
'ENSG00000224407' => 'RP5-956O18.3',
'ENSG00000225984' => 'HMGB1P26',
'ENSG00000227006' => 'RP5-956O18.2',
'ENSG00000227043' => 'RP11-286M16.1',
'ENSG00000228058' => 'RP11-552D4.1',
'ENSMUSG00000031976' => 'Urb2',
'ENSMUSG00000088414' => 'Mir1967',
'ENSMUSG00000089704' => 'Galnt2',
'ENSMUSG00000089745' => '1810008B01Rik',
'ENSMUSG00000089820' => 'Gm15775',
'ENSMUSG00000092329' => 'Gm20388'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 12 => 'Brain',
(int) 17 => 'Breast',
(int) 23 => 'Colon',
(int) 28 => 'Heart',
(int) 33 => 'Kidney',
(int) 39 => 'Liver',
(int) 44 => 'Lung',
(int) 49 => 'Muscle',
(int) 55 => 'Ovary',
(int) 62 => 'Placenta',
(int) 69 => '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) 24,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000258243' => array(
'start' => '229626234',
'end' => '229660199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-001'
),
'ENST00000434387' => array(
'start' => '229650847',
'end' => '229659126',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-002'
),
'ENST00000366672' => array(
'start' => '230067209',
'end' => '230282124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GALNT2-001'
),
'ENST00000485438' => array(
'start' => '230255358',
'end' => '230282120',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-002'
),
'ENST00000488903' => array(
'start' => '230067259',
'end' => '230092033',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-005'
),
'ENST00000492568' => array(
'start' => '230261951',
'end' => '230264972',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-003'
),
'ENST00000494106' => array(
'start' => '230057990',
'end' => '230243427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-004'
),
'ENST00000390191' => array(
'start' => '230049182',
'end' => '230049250',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'BX323860.1-201'
),
'ENST00000434580' => array(
'start' => '229688999',
'end' => '229689904',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-108F13.2-001'
),
'ENST00000414640' => array(
'start' => '230280312',
'end' => '230281893',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.3-001'
),
'ENST00000452520' => array(
'start' => '229705234',
'end' => '229705861',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P26-001'
),
'ENST00000440729' => array(
'start' => '230258694',
'end' => '230268483',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.2-001'
),
'ENST00000435973' => array(
'start' => '229875550',
'end' => '229885752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-286M16.1-001'
),
'ENST00000445339' => array(
'start' => '230002730',
'end' => '230007162',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-552D4.1-001'
),
'ENSMUST00000034457' => array(
'start' => '124023394',
'end' => '124048505',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Urb2-001'
),
'ENSMUST00000173168' => array(
'start' => '124021508',
'end' => '124048504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Urb2-002'
),
'ENSMUST00000157789' => array(
'start' => '124022641',
'end' => '124022722',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir1967-201'
),
'ENSMUST00000034458' => array(
'start' => '124231391',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Galnt2-001'
),
'ENSMUST00000142547' => array(
'start' => '124295103',
'end' => '124323729',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-003'
),
'ENSMUST00000142578' => array(
'start' => '124231508',
'end' => '124334310',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-004'
),
'ENSMUST00000147911' => array(
'start' => '124295366',
'end' => '124345724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-005'
),
'ENSMUST00000162325' => array(
'start' => '124305132',
'end' => '124306507',
'transcript_biotype' => 'antisense',
'transcript_name' => '1810008B01Rik-001'
),
'ENSMUST00000159796' => array(
'start' => '124324778',
'end' => '124331795',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15775-001'
),
'ENSMUST00000127664' => array(
'start' => '119910841',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20388-001'
)
),
'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_000611_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000611_0001' => array(
'genes_in_region' => array(
'ENSG00000135763' => array(
[maximum depth reached]
),
'ENSG00000143641' => array(
[maximum depth reached]
),
'ENSG00000213028' => array(
[maximum depth reached]
),
'ENSG00000224407' => array(
[maximum depth reached]
),
'ENSG00000225984' => array(
[maximum depth reached]
),
'ENSG00000227006' => array(
[maximum depth reached]
),
'ENSG00000227043' => array(
[maximum depth reached]
),
'ENSG00000228058' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Lung',
(int) 29 => 'Adrenal',
(int) 30 => 'Breast',
(int) 31 => 'Kidney',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Muscle',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Colon',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Testis',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000135763' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSG00000143641' => 'polypeptide N-acetylgalactosaminyltransferase 2',
'ENSG00000211525' => null,
'ENSG00000213028' => null,
'ENSG00000224407' => null,
'ENSG00000225984' => 'high mobility group box 1 pseudogene 26',
'ENSG00000227006' => null,
'ENSG00000227043' => null,
'ENSG00000228058' => null,
'ENSMUSG00000031976' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSMUSG00000088414' => 'microRNA 1967',
'ENSMUSG00000089704' => 'UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2',
'ENSMUSG00000089745' => 'RIKEN cDNA 1810008B01 gene',
'ENSMUSG00000089820' => 'predicted gene 15775',
'ENSMUSG00000092329' => 'predicted gene 20388'
)
$gene_name_arr = array(
'ENSG00000135763' => 'URB2',
'ENSG00000143641' => 'GALNT2',
'ENSG00000211525' => 'BX323860.1',
'ENSG00000213028' => 'RP11-108F13.2',
'ENSG00000224407' => 'RP5-956O18.3',
'ENSG00000225984' => 'HMGB1P26',
'ENSG00000227006' => 'RP5-956O18.2',
'ENSG00000227043' => 'RP11-286M16.1',
'ENSG00000228058' => 'RP11-552D4.1',
'ENSMUSG00000031976' => 'Urb2',
'ENSMUSG00000088414' => 'Mir1967',
'ENSMUSG00000089704' => 'Galnt2',
'ENSMUSG00000089745' => '1810008B01Rik',
'ENSMUSG00000089820' => 'Gm15775',
'ENSMUSG00000092329' => 'Gm20388'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000611_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '229626234',
'seq_end' => '230282124',
'region_length' => '655890',
'region_type' => 'CGP',
'el_id' => 'ENSG00000135763-ENSG00000143641'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000611_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '124021508',
'seq_end' => '124345724',
'region_length' => '324216',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031976-ENSMUSG00000089704'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 12 => 'Brain',
(int) 17 => 'Breast',
(int) 23 => 'Colon',
(int) 28 => 'Heart',
(int) 33 => 'Kidney',
(int) 39 => 'Liver',
(int) 44 => 'Lung',
(int) 49 => 'Muscle',
(int) 55 => 'Ovary',
(int) 62 => 'Placenta',
(int) 69 => '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) 24
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000258243' => array(
'start' => '229626234',
'end' => '229660199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-001'
),
'ENST00000434387' => array(
'start' => '229650847',
'end' => '229659126',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-002'
),
'ENST00000366672' => array(
'start' => '230067209',
'end' => '230282124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GALNT2-001'
),
'ENST00000485438' => array(
'start' => '230255358',
'end' => '230282120',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-002'
),
'ENST00000488903' => array(
'start' => '230067259',
'end' => '230092033',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-005'
),
'ENST00000492568' => array(
'start' => '230261951',
'end' => '230264972',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-003'
),
'ENST00000494106' => array(
'start' => '230057990',
'end' => '230243427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-004'
),
'ENST00000390191' => array(
'start' => '230049182',
'end' => '230049250',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'BX323860.1-201'
),
'ENST00000434580' => array(
'start' => '229688999',
'end' => '229689904',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-108F13.2-001'
),
'ENST00000414640' => array(
'start' => '230280312',
'end' => '230281893',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.3-001'
),
'ENST00000452520' => array(
'start' => '229705234',
'end' => '229705861',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P26-001'
),
'ENST00000440729' => array(
'start' => '230258694',
'end' => '230268483',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.2-001'
),
'ENST00000435973' => array(
'start' => '229875550',
'end' => '229885752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-286M16.1-001'
),
'ENST00000445339' => array(
'start' => '230002730',
'end' => '230007162',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-552D4.1-001'
),
'ENSMUST00000034457' => array(
'start' => '124023394',
'end' => '124048505',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Urb2-001'
),
'ENSMUST00000173168' => array(
'start' => '124021508',
'end' => '124048504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Urb2-002'
),
'ENSMUST00000157789' => array(
'start' => '124022641',
'end' => '124022722',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir1967-201'
),
'ENSMUST00000034458' => array(
'start' => '124231391',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Galnt2-001'
),
'ENSMUST00000142547' => array(
'start' => '124295103',
'end' => '124323729',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-003'
),
'ENSMUST00000142578' => array(
'start' => '124231508',
'end' => '124334310',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-004'
),
'ENSMUST00000147911' => array(
'start' => '124295366',
'end' => '124345724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-005'
),
'ENSMUST00000162325' => array(
'start' => '124305132',
'end' => '124306507',
'transcript_biotype' => 'antisense',
'transcript_name' => '1810008B01Rik-001'
),
'ENSMUST00000159796' => array(
'start' => '124324778',
'end' => '124331795',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15775-001'
),
'ENSMUST00000127664' => array(
'start' => '119910841',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20388-001'
)
)
$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_000611_0001' => array(
'genes_in_region' => array(
'ENSG00000135763' => array(
[maximum depth reached]
),
'ENSG00000143641' => array(
[maximum depth reached]
),
'ENSG00000213028' => array(
[maximum depth reached]
),
'ENSG00000224407' => array(
[maximum depth reached]
),
'ENSG00000225984' => array(
[maximum depth reached]
),
'ENSG00000227006' => array(
[maximum depth reached]
),
'ENSG00000227043' => array(
[maximum depth reached]
),
'ENSG00000228058' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Lung',
(int) 29 => 'Adrenal',
(int) 30 => 'Breast',
(int) 31 => 'Kidney',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Muscle',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Colon',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Testis',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000611_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '124021508',
'seq_end' => '124345724',
'region_length' => '324216',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031976-ENSMUSG00000089704'
)
)
$gene_el = array(
'ENST00000445339' => array(
'Adrenal' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.07'
),
'Breast' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.134',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.457',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.102',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000228058'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.07'
),
'Breast' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.134',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.457',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.102',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000445339'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000611_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000135763' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSG00000143641' => 'polypeptide N-acetylgalactosaminyltransferase 2',
'ENSG00000211525' => null,
'ENSG00000213028' => null,
'ENSG00000224407' => null,
'ENSG00000225984' => 'high mobility group box 1 pseudogene 26',
'ENSG00000227006' => null,
'ENSG00000227043' => null,
'ENSG00000228058' => null,
'ENSMUSG00000031976' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSMUSG00000088414' => 'microRNA 1967',
'ENSMUSG00000089704' => 'UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2',
'ENSMUSG00000089745' => 'RIKEN cDNA 1810008B01 gene',
'ENSMUSG00000089820' => 'predicted gene 15775',
'ENSMUSG00000092329' => 'predicted gene 20388'
),
'gene_name_arr' => array(
'ENSG00000135763' => 'URB2',
'ENSG00000143641' => 'GALNT2',
'ENSG00000211525' => 'BX323860.1',
'ENSG00000213028' => 'RP11-108F13.2',
'ENSG00000224407' => 'RP5-956O18.3',
'ENSG00000225984' => 'HMGB1P26',
'ENSG00000227006' => 'RP5-956O18.2',
'ENSG00000227043' => 'RP11-286M16.1',
'ENSG00000228058' => 'RP11-552D4.1',
'ENSMUSG00000031976' => 'Urb2',
'ENSMUSG00000088414' => 'Mir1967',
'ENSMUSG00000089704' => 'Galnt2',
'ENSMUSG00000089745' => '1810008B01Rik',
'ENSMUSG00000089820' => 'Gm15775',
'ENSMUSG00000092329' => 'Gm20388'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 12 => 'Brain',
(int) 17 => 'Breast',
(int) 23 => 'Colon',
(int) 28 => 'Heart',
(int) 33 => 'Kidney',
(int) 39 => 'Liver',
(int) 44 => 'Lung',
(int) 49 => 'Muscle',
(int) 55 => 'Ovary',
(int) 62 => 'Placenta',
(int) 69 => '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) 24,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000258243' => array(
'start' => '229626234',
'end' => '229660199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-001'
),
'ENST00000434387' => array(
'start' => '229650847',
'end' => '229659126',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-002'
),
'ENST00000366672' => array(
'start' => '230067209',
'end' => '230282124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GALNT2-001'
),
'ENST00000485438' => array(
'start' => '230255358',
'end' => '230282120',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-002'
),
'ENST00000488903' => array(
'start' => '230067259',
'end' => '230092033',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-005'
),
'ENST00000492568' => array(
'start' => '230261951',
'end' => '230264972',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-003'
),
'ENST00000494106' => array(
'start' => '230057990',
'end' => '230243427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-004'
),
'ENST00000390191' => array(
'start' => '230049182',
'end' => '230049250',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'BX323860.1-201'
),
'ENST00000434580' => array(
'start' => '229688999',
'end' => '229689904',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-108F13.2-001'
),
'ENST00000414640' => array(
'start' => '230280312',
'end' => '230281893',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.3-001'
),
'ENST00000452520' => array(
'start' => '229705234',
'end' => '229705861',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P26-001'
),
'ENST00000440729' => array(
'start' => '230258694',
'end' => '230268483',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.2-001'
),
'ENST00000435973' => array(
'start' => '229875550',
'end' => '229885752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-286M16.1-001'
),
'ENST00000445339' => array(
'start' => '230002730',
'end' => '230007162',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-552D4.1-001'
),
'ENSMUST00000034457' => array(
'start' => '124023394',
'end' => '124048505',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Urb2-001'
),
'ENSMUST00000173168' => array(
'start' => '124021508',
'end' => '124048504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Urb2-002'
),
'ENSMUST00000157789' => array(
'start' => '124022641',
'end' => '124022722',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir1967-201'
),
'ENSMUST00000034458' => array(
'start' => '124231391',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Galnt2-001'
),
'ENSMUST00000142547' => array(
'start' => '124295103',
'end' => '124323729',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-003'
),
'ENSMUST00000142578' => array(
'start' => '124231508',
'end' => '124334310',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-004'
),
'ENSMUST00000147911' => array(
'start' => '124295366',
'end' => '124345724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-005'
),
'ENSMUST00000162325' => array(
'start' => '124305132',
'end' => '124306507',
'transcript_biotype' => 'antisense',
'transcript_name' => '1810008B01Rik-001'
),
'ENSMUST00000159796' => array(
'start' => '124324778',
'end' => '124331795',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15775-001'
),
'ENSMUST00000127664' => array(
'start' => '119910841',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20388-001'
)
),
'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_000611_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000611_0001' => array(
'genes_in_region' => array(
'ENSG00000135763' => array(
[maximum depth reached]
),
'ENSG00000143641' => array(
[maximum depth reached]
),
'ENSG00000213028' => array(
[maximum depth reached]
),
'ENSG00000224407' => array(
[maximum depth reached]
),
'ENSG00000225984' => array(
[maximum depth reached]
),
'ENSG00000227006' => array(
[maximum depth reached]
),
'ENSG00000227043' => array(
[maximum depth reached]
),
'ENSG00000228058' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Lung',
(int) 29 => 'Adrenal',
(int) 30 => 'Breast',
(int) 31 => 'Kidney',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Muscle',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Colon',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Testis',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000135763' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSG00000143641' => 'polypeptide N-acetylgalactosaminyltransferase 2',
'ENSG00000211525' => null,
'ENSG00000213028' => null,
'ENSG00000224407' => null,
'ENSG00000225984' => 'high mobility group box 1 pseudogene 26',
'ENSG00000227006' => null,
'ENSG00000227043' => null,
'ENSG00000228058' => null,
'ENSMUSG00000031976' => 'URB2 ribosome biogenesis 2 homolog (S. cerevisiae)',
'ENSMUSG00000088414' => 'microRNA 1967',
'ENSMUSG00000089704' => 'UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2',
'ENSMUSG00000089745' => 'RIKEN cDNA 1810008B01 gene',
'ENSMUSG00000089820' => 'predicted gene 15775',
'ENSMUSG00000092329' => 'predicted gene 20388'
)
$gene_name_arr = array(
'ENSG00000135763' => 'URB2',
'ENSG00000143641' => 'GALNT2',
'ENSG00000211525' => 'BX323860.1',
'ENSG00000213028' => 'RP11-108F13.2',
'ENSG00000224407' => 'RP5-956O18.3',
'ENSG00000225984' => 'HMGB1P26',
'ENSG00000227006' => 'RP5-956O18.2',
'ENSG00000227043' => 'RP11-286M16.1',
'ENSG00000228058' => 'RP11-552D4.1',
'ENSMUSG00000031976' => 'Urb2',
'ENSMUSG00000088414' => 'Mir1967',
'ENSMUSG00000089704' => 'Galnt2',
'ENSMUSG00000089745' => '1810008B01Rik',
'ENSMUSG00000089820' => 'Gm15775',
'ENSMUSG00000092329' => 'Gm20388'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000611_0001',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '229626234',
'seq_end' => '230282124',
'region_length' => '655890',
'region_type' => 'CGP',
'el_id' => 'ENSG00000135763-ENSG00000143641'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000611_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '124021508',
'seq_end' => '124345724',
'region_length' => '324216',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031976-ENSMUSG00000089704'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 12 => 'Brain',
(int) 17 => 'Breast',
(int) 23 => 'Colon',
(int) 28 => 'Heart',
(int) 33 => 'Kidney',
(int) 39 => 'Liver',
(int) 44 => 'Lung',
(int) 49 => 'Muscle',
(int) 55 => 'Ovary',
(int) 62 => 'Placenta',
(int) 69 => '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) 24
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000258243' => array(
'start' => '229626234',
'end' => '229660199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-001'
),
'ENST00000434387' => array(
'start' => '229650847',
'end' => '229659126',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'URB2-002'
),
'ENST00000366672' => array(
'start' => '230067209',
'end' => '230282124',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GALNT2-001'
),
'ENST00000485438' => array(
'start' => '230255358',
'end' => '230282120',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-002'
),
'ENST00000488903' => array(
'start' => '230067259',
'end' => '230092033',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-005'
),
'ENST00000492568' => array(
'start' => '230261951',
'end' => '230264972',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-003'
),
'ENST00000494106' => array(
'start' => '230057990',
'end' => '230243427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GALNT2-004'
),
'ENST00000390191' => array(
'start' => '230049182',
'end' => '230049250',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'BX323860.1-201'
),
'ENST00000434580' => array(
'start' => '229688999',
'end' => '229689904',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-108F13.2-001'
),
'ENST00000414640' => array(
'start' => '230280312',
'end' => '230281893',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.3-001'
),
'ENST00000452520' => array(
'start' => '229705234',
'end' => '229705861',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P26-001'
),
'ENST00000440729' => array(
'start' => '230258694',
'end' => '230268483',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP5-956O18.2-001'
),
'ENST00000435973' => array(
'start' => '229875550',
'end' => '229885752',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-286M16.1-001'
),
'ENST00000445339' => array(
'start' => '230002730',
'end' => '230007162',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-552D4.1-001'
),
'ENSMUST00000034457' => array(
'start' => '124023394',
'end' => '124048505',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Urb2-001'
),
'ENSMUST00000173168' => array(
'start' => '124021508',
'end' => '124048504',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Urb2-002'
),
'ENSMUST00000157789' => array(
'start' => '124022641',
'end' => '124022722',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir1967-201'
),
'ENSMUST00000034458' => array(
'start' => '124231391',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Galnt2-001'
),
'ENSMUST00000142547' => array(
'start' => '124295103',
'end' => '124323729',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-003'
),
'ENSMUST00000142578' => array(
'start' => '124231508',
'end' => '124334310',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-004'
),
'ENSMUST00000147911' => array(
'start' => '124295366',
'end' => '124345724',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Galnt2-005'
),
'ENSMUST00000162325' => array(
'start' => '124305132',
'end' => '124306507',
'transcript_biotype' => 'antisense',
'transcript_name' => '1810008B01Rik-001'
),
'ENSMUST00000159796' => array(
'start' => '124324778',
'end' => '124331795',
'transcript_biotype' => 'antisense',
'transcript_name' => 'Gm15775-001'
),
'ENSMUST00000127664' => array(
'start' => '119910841',
'end' => '124345722',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20388-001'
)
)
$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_000611_0001' => array(
'genes_in_region' => array(
'ENSG00000135763' => array(
[maximum depth reached]
),
'ENSG00000143641' => array(
[maximum depth reached]
),
'ENSG00000213028' => array(
[maximum depth reached]
),
'ENSG00000224407' => array(
[maximum depth reached]
),
'ENSG00000225984' => array(
[maximum depth reached]
),
'ENSG00000227006' => array(
[maximum depth reached]
),
'ENSG00000227043' => array(
[maximum depth reached]
),
'ENSG00000228058' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Lung',
(int) 29 => 'Adrenal',
(int) 30 => 'Breast',
(int) 31 => 'Kidney',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Colon',
(int) 41 => 'Heart',
(int) 42 => 'Kidney',
(int) 43 => 'Liver',
(int) 44 => 'Lung',
(int) 45 => 'Muscle',
(int) 46 => 'Ovary',
(int) 47 => 'Placenta',
(int) 48 => 'Testis',
(int) 49 => 'Colon',
(int) 50 => 'Muscle',
(int) 51 => 'Ovary',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Bladder',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Testis',
(int) 68 => 'Adrenal',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Heart',
(int) 72 => 'Kidney',
(int) 73 => 'Liver',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000611_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '124021508',
'seq_end' => '124345724',
'region_length' => '324216',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031976-ENSMUSG00000089704'
)
)
$gene_el = array(
'ENST00000445339' => array(
'Adrenal' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.07'
),
'Breast' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.134',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.457',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.102',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000228058'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.030',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.836',
'stddev_FPKM' => '0.07'
),
'Breast' => array(
'average_FPKM' => '0.081',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.134',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.457',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.341',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.01'
),
'Placenta' => array(
'average_FPKM' => '0.102',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.191',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000445339'
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
(URB2)