| Source ID |
Type |
Tax ID |
Position |
| hs2400 |
VISTA |
10090 |
16:86537654-87139343  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0008OF_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_0008OF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000178457' => 'long intergenic non-protein coding RNA 314',
'ENSG00000226935' => 'long intergenic non-protein coding RNA 161',
'ENSG00000232079' => null,
'ENSG00000232855' => null,
'ENSG00000234083' => null,
'ENSG00000236532' => null,
'ENSMUSG00000089252' => 'predicted gene, 25715'
),
'gene_name_arr' => array(
'ENSG00000178457' => 'LINC00314',
'ENSG00000226935' => 'LINC00161',
'ENSG00000232079' => 'AL035610.1',
'ENSG00000232855' => 'AF131217.1',
'ENSG00000234083' => 'AJ006995.3',
'ENSG00000236532' => 'AL035610.2',
'ENSMUSG00000089252' => 'Gm25715'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 27 => 'Breast',
(int) 36 => 'Colon',
(int) 44 => 'Heart',
(int) 54 => 'Kidney',
(int) 64 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 94 => 'Placenta',
(int) 104 => '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) 17,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000324988' => array(
'start' => '28013363',
'end' => '28023233',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00314-001'
),
'ENST00000412526' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-001'
),
'ENST00000455939' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-002'
),
'ENST00000423808' => array(
'start' => '28090314',
'end' => '28102790',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-003'
),
'ENST00000426534' => array(
'start' => '28048414',
'end' => '28137611',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-001'
),
'ENST00000436878' => array(
'start' => '28090445',
'end' => '28103240',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-002'
),
'ENST00000458316' => array(
'start' => '28048447',
'end' => '28103580',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-004'
),
'ENST00000609782' => array(
'start' => '28130119',
'end' => '28135572',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'AL035610.1-005'
),
'ENST00000616647' => array(
'start' => '28090356',
'end' => '28102639',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-006'
),
'ENST00000430247' => array(
'start' => '28444549',
'end' => '28626604',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-002'
),
'ENST00000433310' => array(
'start' => '28439346',
'end' => '28674848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-001'
),
'ENST00000452028' => array(
'start' => '28670981',
'end' => '28674773',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-003'
),
'ENST00000433344' => array(
'start' => '27954922',
'end' => '27985295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AJ006995.3-001'
),
'ENST00000433303' => array(
'start' => '28163602',
'end' => '28170143',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-002'
),
'ENST00000437194' => array(
'start' => '28212306',
'end' => '28228480',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-003'
),
'ENST00000453420' => array(
'start' => '28116094',
'end' => '28228667',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-001'
),
'ENSMUST00000158627' => array(
'start' => '86845470',
'end' => '86845594',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25715-201'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0008OF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008OF_0001' => array(
'genes_in_region' => array(
'ENSG00000178457' => array(
[maximum depth reached]
),
'ENSG00000226935' => array(
[maximum depth reached]
),
'ENSG00000232079' => array(
[maximum depth reached]
),
'ENSG00000232855' => array(
[maximum depth reached]
),
'ENSG00000234083' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Placenta',
(int) 36 => 'Testis',
(int) 37 => 'Adipose',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Ovary',
(int) 45 => 'Testis',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Lung',
(int) 58 => 'Placenta',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Adipose',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Testis',
(int) 68 => 'Adipose',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Brain',
(int) 72 => 'Breast',
(int) 73 => 'Colon',
(int) 74 => 'Heart',
(int) 75 => 'Kidney',
(int) 76 => 'Liver',
(int) 77 => 'Lung',
(int) 78 => 'Muscle',
(int) 79 => 'Ovary',
(int) 80 => 'Placenta',
(int) 81 => 'Testis',
(int) 82 => 'Bladder',
(int) 83 => 'Heart',
(int) 84 => 'Adipose',
(int) 85 => 'Adrenal',
(int) 86 => 'Brain',
(int) 87 => 'Breast',
(int) 88 => 'Colon',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Liver',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Testis',
(int) 96 => 'Colon',
(int) 97 => 'Liver',
(int) 98 => 'Placenta',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Bladder',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000178457' => 'long intergenic non-protein coding RNA 314',
'ENSG00000226935' => 'long intergenic non-protein coding RNA 161',
'ENSG00000232079' => null,
'ENSG00000232855' => null,
'ENSG00000234083' => null,
'ENSG00000236532' => null,
'ENSMUSG00000089252' => 'predicted gene, 25715'
)
$gene_name_arr = array(
'ENSG00000178457' => 'LINC00314',
'ENSG00000226935' => 'LINC00161',
'ENSG00000232079' => 'AL035610.1',
'ENSG00000232855' => 'AF131217.1',
'ENSG00000234083' => 'AJ006995.3',
'ENSG00000236532' => 'AL035610.2',
'ENSMUSG00000089252' => 'Gm25715'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008OF_0001',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '27982996',
'seq_end' => '28584445',
'region_length' => '601449',
'region_type' => 'VISTA',
'el_id' => 'hs2400'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008OF_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '86537654',
'seq_end' => '87139343',
'region_length' => '601689',
'region_type' => 'VISTA',
'el_id' => 'hs2400'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 27 => 'Breast',
(int) 36 => 'Colon',
(int) 44 => 'Heart',
(int) 54 => 'Kidney',
(int) 64 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 94 => 'Placenta',
(int) 104 => '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) 17
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000324988' => array(
'start' => '28013363',
'end' => '28023233',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00314-001'
),
'ENST00000412526' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-001'
),
'ENST00000455939' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-002'
),
'ENST00000423808' => array(
'start' => '28090314',
'end' => '28102790',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-003'
),
'ENST00000426534' => array(
'start' => '28048414',
'end' => '28137611',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-001'
),
'ENST00000436878' => array(
'start' => '28090445',
'end' => '28103240',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-002'
),
'ENST00000458316' => array(
'start' => '28048447',
'end' => '28103580',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-004'
),
'ENST00000609782' => array(
'start' => '28130119',
'end' => '28135572',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'AL035610.1-005'
),
'ENST00000616647' => array(
'start' => '28090356',
'end' => '28102639',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-006'
),
'ENST00000430247' => array(
'start' => '28444549',
'end' => '28626604',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-002'
),
'ENST00000433310' => array(
'start' => '28439346',
'end' => '28674848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-001'
),
'ENST00000452028' => array(
'start' => '28670981',
'end' => '28674773',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-003'
),
'ENST00000433344' => array(
'start' => '27954922',
'end' => '27985295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AJ006995.3-001'
),
'ENST00000433303' => array(
'start' => '28163602',
'end' => '28170143',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-002'
),
'ENST00000437194' => array(
'start' => '28212306',
'end' => '28228480',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-003'
),
'ENST00000453420' => array(
'start' => '28116094',
'end' => '28228667',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-001'
),
'ENSMUST00000158627' => array(
'start' => '86845470',
'end' => '86845594',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25715-201'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0008OF_0001' => array(
'genes_in_region' => array(
'ENSG00000178457' => array(
[maximum depth reached]
),
'ENSG00000226935' => array(
[maximum depth reached]
),
'ENSG00000232079' => array(
[maximum depth reached]
),
'ENSG00000232855' => array(
[maximum depth reached]
),
'ENSG00000234083' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Placenta',
(int) 36 => 'Testis',
(int) 37 => 'Adipose',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Ovary',
(int) 45 => 'Testis',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Lung',
(int) 58 => 'Placenta',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Adipose',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Testis',
(int) 68 => 'Adipose',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Brain',
(int) 72 => 'Breast',
(int) 73 => 'Colon',
(int) 74 => 'Heart',
(int) 75 => 'Kidney',
(int) 76 => 'Liver',
(int) 77 => 'Lung',
(int) 78 => 'Muscle',
(int) 79 => 'Ovary',
(int) 80 => 'Placenta',
(int) 81 => 'Testis',
(int) 82 => 'Bladder',
(int) 83 => 'Heart',
(int) 84 => 'Adipose',
(int) 85 => 'Adrenal',
(int) 86 => 'Brain',
(int) 87 => 'Breast',
(int) 88 => 'Colon',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Liver',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Testis',
(int) 96 => 'Colon',
(int) 97 => 'Liver',
(int) 98 => 'Placenta',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Bladder',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008OF_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '86537654',
'seq_end' => '87139343',
'region_length' => '601689',
'region_type' => 'VISTA',
'el_id' => 'hs2400'
)
)
$gene_el = array(
'ENST00000433344' => array(
'Adipose' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.320',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.244',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.149',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.241',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.117',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.075',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000234083'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.320',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.244',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.149',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.241',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.117',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.075',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000433344'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0008OF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000178457' => 'long intergenic non-protein coding RNA 314',
'ENSG00000226935' => 'long intergenic non-protein coding RNA 161',
'ENSG00000232079' => null,
'ENSG00000232855' => null,
'ENSG00000234083' => null,
'ENSG00000236532' => null,
'ENSMUSG00000089252' => 'predicted gene, 25715'
),
'gene_name_arr' => array(
'ENSG00000178457' => 'LINC00314',
'ENSG00000226935' => 'LINC00161',
'ENSG00000232079' => 'AL035610.1',
'ENSG00000232855' => 'AF131217.1',
'ENSG00000234083' => 'AJ006995.3',
'ENSG00000236532' => 'AL035610.2',
'ENSMUSG00000089252' => 'Gm25715'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 27 => 'Breast',
(int) 36 => 'Colon',
(int) 44 => 'Heart',
(int) 54 => 'Kidney',
(int) 64 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 94 => 'Placenta',
(int) 104 => '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) 17,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000324988' => array(
'start' => '28013363',
'end' => '28023233',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00314-001'
),
'ENST00000412526' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-001'
),
'ENST00000455939' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-002'
),
'ENST00000423808' => array(
'start' => '28090314',
'end' => '28102790',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-003'
),
'ENST00000426534' => array(
'start' => '28048414',
'end' => '28137611',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-001'
),
'ENST00000436878' => array(
'start' => '28090445',
'end' => '28103240',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-002'
),
'ENST00000458316' => array(
'start' => '28048447',
'end' => '28103580',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-004'
),
'ENST00000609782' => array(
'start' => '28130119',
'end' => '28135572',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'AL035610.1-005'
),
'ENST00000616647' => array(
'start' => '28090356',
'end' => '28102639',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-006'
),
'ENST00000430247' => array(
'start' => '28444549',
'end' => '28626604',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-002'
),
'ENST00000433310' => array(
'start' => '28439346',
'end' => '28674848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-001'
),
'ENST00000452028' => array(
'start' => '28670981',
'end' => '28674773',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-003'
),
'ENST00000433344' => array(
'start' => '27954922',
'end' => '27985295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AJ006995.3-001'
),
'ENST00000433303' => array(
'start' => '28163602',
'end' => '28170143',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-002'
),
'ENST00000437194' => array(
'start' => '28212306',
'end' => '28228480',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-003'
),
'ENST00000453420' => array(
'start' => '28116094',
'end' => '28228667',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-001'
),
'ENSMUST00000158627' => array(
'start' => '86845470',
'end' => '86845594',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25715-201'
)
),
'accession_map' => array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
),
'sci_name_map' => array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
),
'UCSC_links' => array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
),
'expressed_region_arr' => array(
'CIL_0008OF_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008OF_0001' => array(
'genes_in_region' => array(
'ENSG00000178457' => array(
[maximum depth reached]
),
'ENSG00000226935' => array(
[maximum depth reached]
),
'ENSG00000232079' => array(
[maximum depth reached]
),
'ENSG00000232855' => array(
[maximum depth reached]
),
'ENSG00000234083' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Placenta',
(int) 36 => 'Testis',
(int) 37 => 'Adipose',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Ovary',
(int) 45 => 'Testis',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Lung',
(int) 58 => 'Placenta',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Adipose',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Testis',
(int) 68 => 'Adipose',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Brain',
(int) 72 => 'Breast',
(int) 73 => 'Colon',
(int) 74 => 'Heart',
(int) 75 => 'Kidney',
(int) 76 => 'Liver',
(int) 77 => 'Lung',
(int) 78 => 'Muscle',
(int) 79 => 'Ovary',
(int) 80 => 'Placenta',
(int) 81 => 'Testis',
(int) 82 => 'Bladder',
(int) 83 => 'Heart',
(int) 84 => 'Adipose',
(int) 85 => 'Adrenal',
(int) 86 => 'Brain',
(int) 87 => 'Breast',
(int) 88 => 'Colon',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Liver',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Testis',
(int) 96 => 'Colon',
(int) 97 => 'Liver',
(int) 98 => 'Placenta',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Bladder',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000178457' => 'long intergenic non-protein coding RNA 314',
'ENSG00000226935' => 'long intergenic non-protein coding RNA 161',
'ENSG00000232079' => null,
'ENSG00000232855' => null,
'ENSG00000234083' => null,
'ENSG00000236532' => null,
'ENSMUSG00000089252' => 'predicted gene, 25715'
)
$gene_name_arr = array(
'ENSG00000178457' => 'LINC00314',
'ENSG00000226935' => 'LINC00161',
'ENSG00000232079' => 'AL035610.1',
'ENSG00000232855' => 'AF131217.1',
'ENSG00000234083' => 'AJ006995.3',
'ENSG00000236532' => 'AL035610.2',
'ENSMUSG00000089252' => 'Gm25715'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008OF_0001',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '27982996',
'seq_end' => '28584445',
'region_length' => '601449',
'region_type' => 'VISTA',
'el_id' => 'hs2400'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008OF_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '86537654',
'seq_end' => '87139343',
'region_length' => '601689',
'region_type' => 'VISTA',
'el_id' => 'hs2400'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 18 => 'Brain',
(int) 27 => 'Breast',
(int) 36 => 'Colon',
(int) 44 => 'Heart',
(int) 54 => 'Kidney',
(int) 64 => 'Liver',
(int) 70 => 'Lung',
(int) 78 => 'Muscle',
(int) 84 => 'Ovary',
(int) 94 => 'Placenta',
(int) 104 => '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) 17
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000324988' => array(
'start' => '28013363',
'end' => '28023233',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00314-001'
),
'ENST00000412526' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-001'
),
'ENST00000455939' => array(
'start' => '28539318',
'end' => '28540355',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00161-002'
),
'ENST00000423808' => array(
'start' => '28090314',
'end' => '28102790',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-003'
),
'ENST00000426534' => array(
'start' => '28048414',
'end' => '28137611',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-001'
),
'ENST00000436878' => array(
'start' => '28090445',
'end' => '28103240',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-002'
),
'ENST00000458316' => array(
'start' => '28048447',
'end' => '28103580',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-004'
),
'ENST00000609782' => array(
'start' => '28130119',
'end' => '28135572',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'AL035610.1-005'
),
'ENST00000616647' => array(
'start' => '28090356',
'end' => '28102639',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.1-006'
),
'ENST00000430247' => array(
'start' => '28444549',
'end' => '28626604',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-002'
),
'ENST00000433310' => array(
'start' => '28439346',
'end' => '28674848',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-001'
),
'ENST00000452028' => array(
'start' => '28670981',
'end' => '28674773',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AF131217.1-003'
),
'ENST00000433344' => array(
'start' => '27954922',
'end' => '27985295',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AJ006995.3-001'
),
'ENST00000433303' => array(
'start' => '28163602',
'end' => '28170143',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-002'
),
'ENST00000437194' => array(
'start' => '28212306',
'end' => '28228480',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-003'
),
'ENST00000453420' => array(
'start' => '28116094',
'end' => '28228667',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AL035610.2-001'
),
'ENSMUST00000158627' => array(
'start' => '86845470',
'end' => '86845594',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm25715-201'
)
)
$accession_map = array(
'ENST000' => '9606',
'ENSMUST' => '10090',
'ENSDART' => '7955',
'ENSG000' => '9606',
'ENSMUSG' => '10090',
'ENSDARG' => '7955'
)
$sci_name_map = array(
(int) 9606 => 'Homo_sapiens',
(int) 10090 => 'Mus_musculus',
(int) 7955 => 'Danio_rerio'
)
$UCSC_links = array(
(int) 7955 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=danRer7&position=',
(int) 9606 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=',
(int) 10090 => 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&position='
)
$expressed_region_arr = array(
'CIL_0008OF_0001' => array(
'genes_in_region' => array(
'ENSG00000178457' => array(
[maximum depth reached]
),
'ENSG00000226935' => array(
[maximum depth reached]
),
'ENSG00000232079' => array(
[maximum depth reached]
),
'ENSG00000232855' => array(
[maximum depth reached]
),
'ENSG00000234083' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Muscle',
(int) 21 => 'Ovary',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Heart',
(int) 28 => 'Kidney',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Brain',
(int) 33 => 'Colon',
(int) 34 => 'Kidney',
(int) 35 => 'Placenta',
(int) 36 => 'Testis',
(int) 37 => 'Adipose',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Lung',
(int) 43 => 'Muscle',
(int) 44 => 'Ovary',
(int) 45 => 'Testis',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Colon',
(int) 49 => 'Lung',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Lung',
(int) 58 => 'Placenta',
(int) 59 => 'Ovary',
(int) 60 => 'Placenta',
(int) 61 => 'Adipose',
(int) 62 => 'Breast',
(int) 63 => 'Heart',
(int) 64 => 'Kidney',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Testis',
(int) 68 => 'Adipose',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Brain',
(int) 72 => 'Breast',
(int) 73 => 'Colon',
(int) 74 => 'Heart',
(int) 75 => 'Kidney',
(int) 76 => 'Liver',
(int) 77 => 'Lung',
(int) 78 => 'Muscle',
(int) 79 => 'Ovary',
(int) 80 => 'Placenta',
(int) 81 => 'Testis',
(int) 82 => 'Bladder',
(int) 83 => 'Heart',
(int) 84 => 'Adipose',
(int) 85 => 'Adrenal',
(int) 86 => 'Brain',
(int) 87 => 'Breast',
(int) 88 => 'Colon',
(int) 89 => 'Heart',
(int) 90 => 'Kidney',
(int) 91 => 'Liver',
(int) 92 => 'Lung',
(int) 93 => 'Muscle',
(int) 94 => 'Ovary',
(int) 95 => 'Testis',
(int) 96 => 'Colon',
(int) 97 => 'Liver',
(int) 98 => 'Placenta',
(int) 99 => 'Testis',
(int) 100 => 'Adipose',
(int) 101 => 'Adrenal',
(int) 102 => 'Bladder',
(int) 103 => 'Brain',
(int) 104 => 'Breast',
(int) 105 => 'Colon',
(int) 106 => 'Heart',
(int) 107 => 'Kidney',
(int) 108 => 'Liver',
(int) 109 => 'Lung',
(int) 110 => 'Muscle',
(int) 111 => 'Ovary',
(int) 112 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008OF_0002',
'tax_id' => '10090',
'chromosome' => '16',
'seq_start' => '86537654',
'seq_end' => '87139343',
'region_length' => '601689',
'region_type' => 'VISTA',
'el_id' => 'hs2400'
)
)
$gene_el = array(
'ENST00000433344' => array(
'Adipose' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.320',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.244',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.149',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.241',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.117',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.075',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000234083'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.320',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.244',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.099',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.149',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.047',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.241',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.117',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.075',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.050',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000433344'
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
(LINC00314)