| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000015016-ENSMUSG00000031962 |
CGP |
10090 |
8:122775505-122867397  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0006AI_0003 [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_0006AI_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000068191' => 'cadherin 15, M-cadherin (myotubule)',
'ENSDARG00000091438' => '5S ribosomal RNA',
'ENSG00000129910' => 'cadherin 15, type 1, M-cadherin (myotubule)',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000180422' => 'long intergenic non-protein coding RNA 304',
'ENSG00000205015' => null,
'ENSG00000261546' => null,
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000031962' => 'cadherin 15',
'ENSMUSG00000095762' => 'predicted gene 16378'
),
'gene_name_arr' => array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000068191' => 'cdh15',
'ENSDARG00000091438' => '5S_rRNA',
'ENSG00000129910' => 'CDH15',
'ENSG00000176715' => 'ACSF3',
'ENSG00000180422' => 'LINC00304',
'ENSG00000205015' => 'RP11-46C24.3',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000031962' => 'Cdh15',
'ENSMUSG00000095762' => 'Gm16378'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 14 => 'Brain',
(int) 26 => 'Breast',
(int) 31 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 57 => 'Liver',
(int) 65 => 'Lung',
(int) 74 => 'Muscle',
(int) 85 => 'Ovary',
(int) 96 => 'Placenta',
(int) 103 => '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) 33,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000098453' => array(
'start' => '57361853',
'end' => '57408934',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-001'
),
'ENSDART00000127046' => array(
'start' => '57361785',
'end' => '57408811',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-201'
),
'ENSDART00000129110' => array(
'start' => '57331429',
'end' => '57331543',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1924-201'
),
'ENST00000289746' => array(
'start' => '89171767',
'end' => '89195492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDH15-001'
),
'ENST00000521087' => array(
'start' => '89171767',
'end' => '89183605',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDH15-002'
),
'ENST00000524089' => array(
'start' => '89171767',
'end' => '89186192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDH15-003'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000321214' => array(
'start' => '89159220',
'end' => '89163675',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-001'
),
'ENST00000562248' => array(
'start' => '89159146',
'end' => '89160562',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-002'
),
'ENST00000565008' => array(
'start' => '89162382',
'end' => '89164245',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-003'
),
'ENST00000378340' => array(
'start' => '89166383',
'end' => '89169147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-46C24.3-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000034443' => array(
'start' => '122848374',
'end' => '122867397',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdh15-201'
),
'ENSMUST00000179168' => array(
'start' => '122841731',
'end' => '122842072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16378-001'
)
),
'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_0006AI_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AI_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000068191' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
'ENSG00000129910' => array(
[maximum depth reached]
),
'ENSG00000180422' => array(
[maximum depth reached]
),
'ENSG00000205015' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Colon',
(int) 13 => 'Kidney',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Bladder',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Muscle',
(int) 50 => 'Heart',
(int) 51 => 'Kidney',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Placenta',
(int) 55 => 'Heart',
(int) 56 => 'Brain',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Heart',
(int) 66 => 'Kidney',
(int) 67 => 'Lung',
(int) 68 => 'Muscle',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis',
(int) 72 => 'Brain',
(int) 73 => 'Bladder',
(int) 74 => 'Ovary',
(int) 75 => 'Adrenal',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Lung',
(int) 79 => 'Ovary',
(int) 80 => 'Liver',
(int) 81 => 'Ovary',
(int) 82 => 'Testis',
(int) 83 => 'Adipose',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Kidney',
(int) 89 => 'Liver',
(int) 90 => 'Lung',
(int) 91 => 'Ovary',
(int) 92 => 'Placenta',
(int) 93 => 'Testis',
(int) 94 => 'Kidney',
(int) 95 => 'Lung',
(int) 96 => 'Placenta',
(int) 97 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000068191' => 'cadherin 15, M-cadherin (myotubule)',
'ENSDARG00000091438' => '5S ribosomal RNA',
'ENSG00000129910' => 'cadherin 15, type 1, M-cadherin (myotubule)',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000180422' => 'long intergenic non-protein coding RNA 304',
'ENSG00000205015' => null,
'ENSG00000261546' => null,
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000031962' => 'cadherin 15',
'ENSMUSG00000095762' => 'predicted gene 16378'
)
$gene_name_arr = array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000068191' => 'cdh15',
'ENSDARG00000091438' => '5S_rRNA',
'ENSG00000129910' => 'CDH15',
'ENSG00000176715' => 'ACSF3',
'ENSG00000180422' => 'LINC00304',
'ENSG00000205015' => 'RP11-46C24.3',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000031962' => 'Cdh15',
'ENSMUSG00000095762' => 'Gm16378'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '57215011',
'seq_end' => '57408934',
'region_length' => '193923',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000059503-ENSDARG00000068191'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89088375',
'seq_end' => '89195492',
'region_length' => '107117',
'region_type' => 'CGP',
'el_id' => 'ENSG00000176715-ENSG00000129910'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122775505',
'seq_end' => '122867397',
'region_length' => '91892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000015016-ENSMUSG00000031962'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 14 => 'Brain',
(int) 26 => 'Breast',
(int) 31 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 57 => 'Liver',
(int) 65 => 'Lung',
(int) 74 => 'Muscle',
(int) 85 => 'Ovary',
(int) 96 => 'Placenta',
(int) 103 => '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) 33
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000098453' => array(
'start' => '57361853',
'end' => '57408934',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-001'
),
'ENSDART00000127046' => array(
'start' => '57361785',
'end' => '57408811',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-201'
),
'ENSDART00000129110' => array(
'start' => '57331429',
'end' => '57331543',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1924-201'
),
'ENST00000289746' => array(
'start' => '89171767',
'end' => '89195492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDH15-001'
),
'ENST00000521087' => array(
'start' => '89171767',
'end' => '89183605',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDH15-002'
),
'ENST00000524089' => array(
'start' => '89171767',
'end' => '89186192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDH15-003'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000321214' => array(
'start' => '89159220',
'end' => '89163675',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-001'
),
'ENST00000562248' => array(
'start' => '89159146',
'end' => '89160562',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-002'
),
'ENST00000565008' => array(
'start' => '89162382',
'end' => '89164245',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-003'
),
'ENST00000378340' => array(
'start' => '89166383',
'end' => '89169147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-46C24.3-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000034443' => array(
'start' => '122848374',
'end' => '122867397',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdh15-201'
),
'ENSMUST00000179168' => array(
'start' => '122841731',
'end' => '122842072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16378-001'
)
)
$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_0006AI_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000068191' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
'ENSG00000129910' => array(
[maximum depth reached]
),
'ENSG00000180422' => array(
[maximum depth reached]
),
'ENSG00000205015' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Colon',
(int) 13 => 'Kidney',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Bladder',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Muscle',
(int) 50 => 'Heart',
(int) 51 => 'Kidney',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Placenta',
(int) 55 => 'Heart',
(int) 56 => 'Brain',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Heart',
(int) 66 => 'Kidney',
(int) 67 => 'Lung',
(int) 68 => 'Muscle',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis',
(int) 72 => 'Brain',
(int) 73 => 'Bladder',
(int) 74 => 'Ovary',
(int) 75 => 'Adrenal',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Lung',
(int) 79 => 'Ovary',
(int) 80 => 'Liver',
(int) 81 => 'Ovary',
(int) 82 => 'Testis',
(int) 83 => 'Adipose',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Kidney',
(int) 89 => 'Liver',
(int) 90 => 'Lung',
(int) 91 => 'Ovary',
(int) 92 => 'Placenta',
(int) 93 => 'Testis',
(int) 94 => 'Kidney',
(int) 95 => 'Lung',
(int) 96 => 'Placenta',
(int) 97 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122775505',
'seq_end' => '122867397',
'region_length' => '91892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000015016-ENSMUSG00000031962'
)
)
$gene_el = array(
'ENST00000378340' => array(
'Kidney' => array(
'average_FPKM' => '0.284',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.144',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.04'
),
'Testis' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000205015'
$is_first = false
$tran_el = array(
'Kidney' => array(
'average_FPKM' => '0.284',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.144',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.04'
),
'Testis' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000378340'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0006AI_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000068191' => 'cadherin 15, M-cadherin (myotubule)',
'ENSDARG00000091438' => '5S ribosomal RNA',
'ENSG00000129910' => 'cadherin 15, type 1, M-cadherin (myotubule)',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000180422' => 'long intergenic non-protein coding RNA 304',
'ENSG00000205015' => null,
'ENSG00000261546' => null,
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000031962' => 'cadherin 15',
'ENSMUSG00000095762' => 'predicted gene 16378'
),
'gene_name_arr' => array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000068191' => 'cdh15',
'ENSDARG00000091438' => '5S_rRNA',
'ENSG00000129910' => 'CDH15',
'ENSG00000176715' => 'ACSF3',
'ENSG00000180422' => 'LINC00304',
'ENSG00000205015' => 'RP11-46C24.3',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000031962' => 'Cdh15',
'ENSMUSG00000095762' => 'Gm16378'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 14 => 'Brain',
(int) 26 => 'Breast',
(int) 31 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 57 => 'Liver',
(int) 65 => 'Lung',
(int) 74 => 'Muscle',
(int) 85 => 'Ovary',
(int) 96 => 'Placenta',
(int) 103 => '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) 33,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000098453' => array(
'start' => '57361853',
'end' => '57408934',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-001'
),
'ENSDART00000127046' => array(
'start' => '57361785',
'end' => '57408811',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-201'
),
'ENSDART00000129110' => array(
'start' => '57331429',
'end' => '57331543',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1924-201'
),
'ENST00000289746' => array(
'start' => '89171767',
'end' => '89195492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDH15-001'
),
'ENST00000521087' => array(
'start' => '89171767',
'end' => '89183605',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDH15-002'
),
'ENST00000524089' => array(
'start' => '89171767',
'end' => '89186192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDH15-003'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000321214' => array(
'start' => '89159220',
'end' => '89163675',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-001'
),
'ENST00000562248' => array(
'start' => '89159146',
'end' => '89160562',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-002'
),
'ENST00000565008' => array(
'start' => '89162382',
'end' => '89164245',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-003'
),
'ENST00000378340' => array(
'start' => '89166383',
'end' => '89169147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-46C24.3-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000034443' => array(
'start' => '122848374',
'end' => '122867397',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdh15-201'
),
'ENSMUST00000179168' => array(
'start' => '122841731',
'end' => '122842072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16378-001'
)
),
'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_0006AI_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0006AI_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000068191' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
'ENSG00000129910' => array(
[maximum depth reached]
),
'ENSG00000180422' => array(
[maximum depth reached]
),
'ENSG00000205015' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Colon',
(int) 13 => 'Kidney',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Bladder',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Muscle',
(int) 50 => 'Heart',
(int) 51 => 'Kidney',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Placenta',
(int) 55 => 'Heart',
(int) 56 => 'Brain',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Heart',
(int) 66 => 'Kidney',
(int) 67 => 'Lung',
(int) 68 => 'Muscle',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis',
(int) 72 => 'Brain',
(int) 73 => 'Bladder',
(int) 74 => 'Ovary',
(int) 75 => 'Adrenal',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Lung',
(int) 79 => 'Ovary',
(int) 80 => 'Liver',
(int) 81 => 'Ovary',
(int) 82 => 'Testis',
(int) 83 => 'Adipose',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Kidney',
(int) 89 => 'Liver',
(int) 90 => 'Lung',
(int) 91 => 'Ovary',
(int) 92 => 'Placenta',
(int) 93 => 'Testis',
(int) 94 => 'Kidney',
(int) 95 => 'Lung',
(int) 96 => 'Placenta',
(int) 97 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000059503' => 'Uncharacterized protein',
'ENSDARG00000068191' => 'cadherin 15, M-cadherin (myotubule)',
'ENSDARG00000091438' => '5S ribosomal RNA',
'ENSG00000129910' => 'cadherin 15, type 1, M-cadherin (myotubule)',
'ENSG00000176715' => 'acyl-CoA synthetase family member 3',
'ENSG00000180422' => 'long intergenic non-protein coding RNA 304',
'ENSG00000205015' => null,
'ENSG00000261546' => null,
'ENSMUSG00000015016' => 'acyl-CoA synthetase family member 3',
'ENSMUSG00000031962' => 'cadherin 15',
'ENSMUSG00000095762' => 'predicted gene 16378'
)
$gene_name_arr = array(
'ENSDARG00000059503' => 'CR848706.1',
'ENSDARG00000068191' => 'cdh15',
'ENSDARG00000091438' => '5S_rRNA',
'ENSG00000129910' => 'CDH15',
'ENSG00000176715' => 'ACSF3',
'ENSG00000180422' => 'LINC00304',
'ENSG00000205015' => 'RP11-46C24.3',
'ENSG00000261546' => 'CTD-2555A7.3',
'ENSMUSG00000015016' => 'Acsf3',
'ENSMUSG00000031962' => 'Cdh15',
'ENSMUSG00000095762' => 'Gm16378'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '57215011',
'seq_end' => '57408934',
'region_length' => '193923',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000059503-ENSDARG00000068191'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89088375',
'seq_end' => '89195492',
'region_length' => '107117',
'region_type' => 'CGP',
'el_id' => 'ENSG00000176715-ENSG00000129910'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122775505',
'seq_end' => '122867397',
'region_length' => '91892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000015016-ENSMUSG00000031962'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 11 => 'Bladder',
(int) 14 => 'Brain',
(int) 26 => 'Breast',
(int) 31 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 57 => 'Liver',
(int) 65 => 'Lung',
(int) 74 => 'Muscle',
(int) 85 => 'Ovary',
(int) 96 => 'Placenta',
(int) 103 => '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) 33
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000082780' => array(
'start' => '57215011',
'end' => '57300831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CR848706.1-201'
),
'ENSDART00000098453' => array(
'start' => '57361853',
'end' => '57408934',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-001'
),
'ENSDART00000127046' => array(
'start' => '57361785',
'end' => '57408811',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdh15-201'
),
'ENSDART00000129110' => array(
'start' => '57331429',
'end' => '57331543',
'transcript_biotype' => 'rRNA',
'transcript_name' => '5S_rRNA.1924-201'
),
'ENST00000289746' => array(
'start' => '89171767',
'end' => '89195492',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDH15-001'
),
'ENST00000521087' => array(
'start' => '89171767',
'end' => '89183605',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CDH15-002'
),
'ENST00000524089' => array(
'start' => '89171767',
'end' => '89186192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDH15-003'
),
'ENST00000317447' => array(
'start' => '89093809',
'end' => '89155763',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-001'
),
'ENST00000378345' => array(
'start' => '89093898',
'end' => '89154588',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-002'
),
'ENST00000393145' => array(
'start' => '89147567',
'end' => '89154586',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-020'
),
'ENST00000406948' => array(
'start' => '89093883',
'end' => '89154589',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-003'
),
'ENST00000535176' => array(
'start' => '89145950',
'end' => '89151348',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-013'
),
'ENST00000537116' => array(
'start' => '89136548',
'end' => '89155846',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-005'
),
'ENST00000537155' => array(
'start' => '89145161',
'end' => '89154584',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ACSF3-016'
),
'ENST00000537290' => array(
'start' => '89093855',
'end' => '89102648',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-009'
),
'ENST00000537895' => array(
'start' => '89088375',
'end' => '89114473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-011'
),
'ENST00000538340' => array(
'start' => '89102613',
'end' => '89122392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-015'
),
'ENST00000540697' => array(
'start' => '89093868',
'end' => '89133262',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-010'
),
'ENST00000541755' => array(
'start' => '89093904',
'end' => '89100767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-023'
),
'ENST00000542688' => array(
'start' => '89098711',
'end' => '89154540',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'ACSF3-006'
),
'ENST00000543676' => array(
'start' => '89102696',
'end' => '89122832',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-014'
),
'ENST00000544543' => array(
'start' => '89102352',
'end' => '89145400',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-012'
),
'ENST00000562204' => array(
'start' => '89112201',
'end' => '89146044',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-021'
),
'ENST00000562750' => array(
'start' => '89150600',
'end' => '89151222',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ACSF3-019'
),
'ENST00000614302' => array(
'start' => '89093809',
'end' => '89155846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ACSF3-201'
),
'ENST00000321214' => array(
'start' => '89159220',
'end' => '89163675',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-001'
),
'ENST00000562248' => array(
'start' => '89159146',
'end' => '89160562',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-002'
),
'ENST00000565008' => array(
'start' => '89162382',
'end' => '89164245',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00304-003'
),
'ENST00000378340' => array(
'start' => '89166383',
'end' => '89169147',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-46C24.3-001'
),
'ENST00000562782' => array(
'start' => '89113175',
'end' => '89115279',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2555A7.3-001'
),
'ENSMUST00000015160' => array(
'start' => '122775505',
'end' => '122817880',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Acsf3-201'
),
'ENSMUST00000034443' => array(
'start' => '122848374',
'end' => '122867397',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdh15-201'
),
'ENSMUST00000179168' => array(
'start' => '122841731',
'end' => '122842072',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm16378-001'
)
)
$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_0006AI_0001' => array(
'genes_in_region' => array(
'ENSDARG00000059503' => array(
[maximum depth reached]
),
'ENSDARG00000068191' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Muscle'
)
),
'CIL_0006AI_0002' => array(
'genes_in_region' => array(
'ENSG00000129910' => array(
[maximum depth reached]
),
'ENSG00000180422' => array(
[maximum depth reached]
),
'ENSG00000205015' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Lung',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Placenta',
(int) 9 => 'Testis',
(int) 10 => 'Adrenal',
(int) 11 => 'Brain',
(int) 12 => 'Colon',
(int) 13 => 'Kidney',
(int) 14 => 'Lung',
(int) 15 => 'Ovary',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Adipose',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Testis',
(int) 25 => 'Adipose',
(int) 26 => 'Adrenal',
(int) 27 => 'Bladder',
(int) 28 => 'Brain',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Placenta',
(int) 38 => 'Testis',
(int) 39 => 'Adipose',
(int) 40 => 'Bladder',
(int) 41 => 'Brain',
(int) 42 => 'Breast',
(int) 43 => 'Heart',
(int) 44 => 'Kidney',
(int) 45 => 'Liver',
(int) 46 => 'Lung',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Muscle',
(int) 50 => 'Heart',
(int) 51 => 'Kidney',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Placenta',
(int) 55 => 'Heart',
(int) 56 => 'Brain',
(int) 57 => 'Kidney',
(int) 58 => 'Muscle',
(int) 59 => 'Muscle',
(int) 60 => 'Ovary',
(int) 61 => 'Adipose',
(int) 62 => 'Adrenal',
(int) 63 => 'Brain',
(int) 64 => 'Breast',
(int) 65 => 'Heart',
(int) 66 => 'Kidney',
(int) 67 => 'Lung',
(int) 68 => 'Muscle',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis',
(int) 72 => 'Brain',
(int) 73 => 'Bladder',
(int) 74 => 'Ovary',
(int) 75 => 'Adrenal',
(int) 76 => 'Brain',
(int) 77 => 'Kidney',
(int) 78 => 'Lung',
(int) 79 => 'Ovary',
(int) 80 => 'Liver',
(int) 81 => 'Ovary',
(int) 82 => 'Testis',
(int) 83 => 'Adipose',
(int) 84 => 'Adrenal',
(int) 85 => 'Brain',
(int) 86 => 'Breast',
(int) 87 => 'Colon',
(int) 88 => 'Kidney',
(int) 89 => 'Liver',
(int) 90 => 'Lung',
(int) 91 => 'Ovary',
(int) 92 => 'Placenta',
(int) 93 => 'Testis',
(int) 94 => 'Kidney',
(int) 95 => 'Lung',
(int) 96 => 'Placenta',
(int) 97 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0006AI_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122775505',
'seq_end' => '122867397',
'region_length' => '91892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000015016-ENSMUSG00000031962'
)
)
$gene_el = array(
'ENST00000378340' => array(
'Kidney' => array(
'average_FPKM' => '0.284',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.144',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.04'
),
'Testis' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000205015'
$is_first = false
$tran_el = array(
'Kidney' => array(
'average_FPKM' => '0.284',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.144',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.04'
),
'Testis' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000378340'
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
(CR848706.1)