| Source ID |
Type |
Tax ID |
Position |
| ISL1 |
UCNEbase |
10090 |
13:116497700-116633834  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007JG_0004 [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_0007JG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000016082' => 'ISL LIM homeobox 1',
'ENSG00000206606' => 'RNA, U6 small nuclear 1296, pseudogene',
'ENSG00000207060' => 'RNA, U6 small nuclear 480, pseudogene',
'ENSG00000222945' => null,
'ENSG00000240627' => null,
'ENSG00000244621' => 'ribosomal protein S17 pseudogene 11',
'ENSG00000248789' => null,
'ENSG00000248891' => null,
'ENSG00000249270' => 'katanin p80 subunit B-like 1 pseudogene 4',
'ENSG00000249338' => 'high mobility group box 1 pseudogene 47',
'ENSG00000251125' => null,
'ENSG00000251873' => 'RNA, 5S ribosomal pseudogene 182',
'ENSG00000259663' => null,
'ENSG00000278734' => null,
'ENSG00000279470' => null,
'ENSDARG00000004023' => 'islet1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
),
'gene_name_arr' => array(
'ENSG00000016082' => 'ISL1',
'ENSG00000206606' => 'RNU6-1296P',
'ENSG00000207060' => 'RNU6-480P',
'ENSG00000222945' => 'AC091866.1',
'ENSG00000240627' => 'CTD-2312P21.1',
'ENSG00000244621' => 'RPS17P11',
'ENSG00000248789' => 'CTD-2203A3.1',
'ENSG00000248891' => 'CTD-2335O3.2',
'ENSG00000249270' => 'KATNBL1P4',
'ENSG00000249338' => 'HMGB1P47',
'ENSG00000251125' => 'CTD-2335O3.3',
'ENSG00000251873' => 'RNA5SP182',
'ENSG00000259663' => 'CTD-2314G24.2',
'ENSG00000278734' => 'CTD-2054H24.1',
'ENSG00000279470' => 'RP11-182I21.2',
'ENSDARG00000004023' => 'isl1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
),
'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]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 13 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 24 => 'Kidney',
(int) 31 => 'Liver',
(int) 34 => 'Lung',
(int) 38 => 'Muscle',
(int) 40 => 'Ovary',
(int) 44 => 'Placenta',
(int) 48 => '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) 27,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000230658' => array(
'start' => '51383391',
'end' => '51394738',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-001'
),
'ENST00000505475' => array(
'start' => '51386204',
'end' => '51393567',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ISL1-006'
),
'ENST00000511384' => array(
'start' => '51383672',
'end' => '51393610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-003'
),
'ENST00000383879' => array(
'start' => '51167541',
'end' => '51167647',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-1296P-201'
),
'ENST00000384332' => array(
'start' => '51055353',
'end' => '51055459',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-480P-201'
),
'ENST00000411013' => array(
'start' => '51061469',
'end' => '51061557',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC091866.1-201'
),
'ENST00000468490' => array(
'start' => '51275253',
'end' => '51275734',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2312P21.1-001'
),
'ENST00000474297' => array(
'start' => '52282567',
'end' => '52282859',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS17P11-001'
),
'ENST00000505899' => array(
'start' => '52008031',
'end' => '52043909',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-003'
),
'ENST00000510583' => array(
'start' => '52009815',
'end' => '52080987',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-001'
),
'ENST00000505723' => array(
'start' => '51427996',
'end' => '51428427',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2335O3.2-001'
),
'ENST00000503545' => array(
'start' => '51930808',
'end' => '51932036',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'KATNBL1P4-001'
),
'ENST00000511281' => array(
'start' => '51409617',
'end' => '51410205',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P47-001'
),
'ENST00000509423' => array(
'start' => '51451158',
'end' => '51462089',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2335O3.3-001'
),
'ENST00000516064' => array(
'start' => '51886688',
'end' => '51886769',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP182-201'
),
'ENST00000558403' => array(
'start' => '51378575',
'end' => '51379675',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-002'
),
'ENST00000559112' => array(
'start' => '51377068',
'end' => '51383332',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-001'
),
'ENST00000601500' => array(
'start' => '51372736',
'end' => '51379497',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-003'
),
'ENST00000614543' => array(
'start' => '51101172',
'end' => '51101643',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2054H24.1-001'
),
'ENST00000624322' => array(
'start' => '51963992',
'end' => '51964445',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-182I21.2-001'
),
'ENSDART00000010896' => array(
'start' => '42353743',
'end' => '42359175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'isl1-001'
),
'ENSDART00000133613' => array(
'start' => '42324960',
'end' => '42326117',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.3-001'
),
'ENSDART00000132410' => array(
'start' => '42338479',
'end' => '42339732',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.2-001'
),
'ENSDART00000154576' => array(
'start' => '42210507',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-001'
),
'ENSDART00000154891' => array(
'start' => '42182362',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-004'
),
'ENSDART00000155538' => array(
'start' => '42210507',
'end' => '42338896',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-002'
),
'ENSDART00000155814' => array(
'start' => '42225329',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-003'
)
),
'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_0007JG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007JG_0001' => array(
'genes_in_region' => array(
'ENSG00000016082' => array(
[maximum depth reached]
),
'ENSG00000240627' => array(
[maximum depth reached]
),
'ENSG00000248789' => array(
[maximum depth reached]
),
'ENSG00000249270' => array(
[maximum depth reached]
),
'ENSG00000249338' => array(
[maximum depth reached]
),
'ENSG00000251125' => array(
[maximum depth reached]
),
'ENSG00000259663' => array(
[maximum depth reached]
),
'ENSG00000279470' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Ovary',
(int) 4 => 'Placenta',
(int) 5 => 'Testis',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Breast',
(int) 9 => 'Colon',
(int) 10 => 'Lung',
(int) 11 => 'Colon',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Heart',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Ovary',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Liver',
(int) 32 => 'Lung',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Lung',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Testis'
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
'ENSDARG00000004023' => array(
[maximum depth reached]
),
'ENSDARG00000092131' => array(
[maximum depth reached]
),
'ENSDARG00000093270' => array(
[maximum depth reached]
),
'ENSDARG00000097618' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Kidney',
(int) 12 => 'Brain',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Kidney'
)
)
)
$gene_desc_arr = array(
'ENSG00000016082' => 'ISL LIM homeobox 1',
'ENSG00000206606' => 'RNA, U6 small nuclear 1296, pseudogene',
'ENSG00000207060' => 'RNA, U6 small nuclear 480, pseudogene',
'ENSG00000222945' => null,
'ENSG00000240627' => null,
'ENSG00000244621' => 'ribosomal protein S17 pseudogene 11',
'ENSG00000248789' => null,
'ENSG00000248891' => null,
'ENSG00000249270' => 'katanin p80 subunit B-like 1 pseudogene 4',
'ENSG00000249338' => 'high mobility group box 1 pseudogene 47',
'ENSG00000251125' => null,
'ENSG00000251873' => 'RNA, 5S ribosomal pseudogene 182',
'ENSG00000259663' => null,
'ENSG00000278734' => null,
'ENSG00000279470' => null,
'ENSDARG00000004023' => 'islet1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
)
$gene_name_arr = array(
'ENSG00000016082' => 'ISL1',
'ENSG00000206606' => 'RNU6-1296P',
'ENSG00000207060' => 'RNU6-480P',
'ENSG00000222945' => 'AC091866.1',
'ENSG00000240627' => 'CTD-2312P21.1',
'ENSG00000244621' => 'RPS17P11',
'ENSG00000248789' => 'CTD-2203A3.1',
'ENSG00000248891' => 'CTD-2335O3.2',
'ENSG00000249270' => 'KATNBL1P4',
'ENSG00000249338' => 'HMGB1P47',
'ENSG00000251125' => 'CTD-2335O3.3',
'ENSG00000251873' => 'RNA5SP182',
'ENSG00000259663' => 'CTD-2314G24.2',
'ENSG00000278734' => 'CTD-2054H24.1',
'ENSG00000279470' => 'RP11-182I21.2',
'ENSDARG00000004023' => 'isl1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0001',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '51039710',
'seq_end' => '52466387',
'region_length' => '1426677',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0002',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '115379812',
'seq_end' => '115977571',
'region_length' => '597759',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0003',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '42183517',
'seq_end' => '42427797',
'region_length' => '244280',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0004',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '116497700',
'seq_end' => '116633834',
'region_length' => '136134',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 13 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 24 => 'Kidney',
(int) 31 => 'Liver',
(int) 34 => 'Lung',
(int) 38 => 'Muscle',
(int) 40 => 'Ovary',
(int) 44 => 'Placenta',
(int) 48 => '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) 27
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000230658' => array(
'start' => '51383391',
'end' => '51394738',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-001'
),
'ENST00000505475' => array(
'start' => '51386204',
'end' => '51393567',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ISL1-006'
),
'ENST00000511384' => array(
'start' => '51383672',
'end' => '51393610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-003'
),
'ENST00000383879' => array(
'start' => '51167541',
'end' => '51167647',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-1296P-201'
),
'ENST00000384332' => array(
'start' => '51055353',
'end' => '51055459',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-480P-201'
),
'ENST00000411013' => array(
'start' => '51061469',
'end' => '51061557',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC091866.1-201'
),
'ENST00000468490' => array(
'start' => '51275253',
'end' => '51275734',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2312P21.1-001'
),
'ENST00000474297' => array(
'start' => '52282567',
'end' => '52282859',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS17P11-001'
),
'ENST00000505899' => array(
'start' => '52008031',
'end' => '52043909',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-003'
),
'ENST00000510583' => array(
'start' => '52009815',
'end' => '52080987',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-001'
),
'ENST00000505723' => array(
'start' => '51427996',
'end' => '51428427',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2335O3.2-001'
),
'ENST00000503545' => array(
'start' => '51930808',
'end' => '51932036',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'KATNBL1P4-001'
),
'ENST00000511281' => array(
'start' => '51409617',
'end' => '51410205',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P47-001'
),
'ENST00000509423' => array(
'start' => '51451158',
'end' => '51462089',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2335O3.3-001'
),
'ENST00000516064' => array(
'start' => '51886688',
'end' => '51886769',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP182-201'
),
'ENST00000558403' => array(
'start' => '51378575',
'end' => '51379675',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-002'
),
'ENST00000559112' => array(
'start' => '51377068',
'end' => '51383332',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-001'
),
'ENST00000601500' => array(
'start' => '51372736',
'end' => '51379497',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-003'
),
'ENST00000614543' => array(
'start' => '51101172',
'end' => '51101643',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2054H24.1-001'
),
'ENST00000624322' => array(
'start' => '51963992',
'end' => '51964445',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-182I21.2-001'
),
'ENSDART00000010896' => array(
'start' => '42353743',
'end' => '42359175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'isl1-001'
),
'ENSDART00000133613' => array(
'start' => '42324960',
'end' => '42326117',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.3-001'
),
'ENSDART00000132410' => array(
'start' => '42338479',
'end' => '42339732',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.2-001'
),
'ENSDART00000154576' => array(
'start' => '42210507',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-001'
),
'ENSDART00000154891' => array(
'start' => '42182362',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-004'
),
'ENSDART00000155538' => array(
'start' => '42210507',
'end' => '42338896',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-002'
),
'ENSDART00000155814' => array(
'start' => '42225329',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-003'
)
)
$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_0007JG_0001' => array(
'genes_in_region' => array(
'ENSG00000016082' => array(
[maximum depth reached]
),
'ENSG00000240627' => array(
[maximum depth reached]
),
'ENSG00000248789' => array(
[maximum depth reached]
),
'ENSG00000249270' => array(
[maximum depth reached]
),
'ENSG00000249338' => array(
[maximum depth reached]
),
'ENSG00000251125' => array(
[maximum depth reached]
),
'ENSG00000259663' => array(
[maximum depth reached]
),
'ENSG00000279470' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Ovary',
(int) 4 => 'Placenta',
(int) 5 => 'Testis',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Breast',
(int) 9 => 'Colon',
(int) 10 => 'Lung',
(int) 11 => 'Colon',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Heart',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Ovary',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Liver',
(int) 32 => 'Lung',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Lung',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Testis'
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
'ENSDARG00000004023' => array(
[maximum depth reached]
),
'ENSDARG00000092131' => array(
[maximum depth reached]
),
'ENSDARG00000093270' => array(
[maximum depth reached]
),
'ENSDARG00000097618' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Kidney',
(int) 12 => 'Brain',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Kidney'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0004',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '116497700',
'seq_end' => '116633834',
'region_length' => '136134',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
)
$gene_el = array(
'ENSDART00000154576' => array(
'Kidney' => array(
'average_FPKM' => '0.181',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000154891' => array(
'Brain' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000155538' => array(
'Heart' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.712',
'stddev_FPKM' => '0.41'
)
),
'ENSDART00000155814' => array(
'Kidney' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000097618'
$is_first = false
$tran_el = array(
'Kidney' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000155814'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007JG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000016082' => 'ISL LIM homeobox 1',
'ENSG00000206606' => 'RNA, U6 small nuclear 1296, pseudogene',
'ENSG00000207060' => 'RNA, U6 small nuclear 480, pseudogene',
'ENSG00000222945' => null,
'ENSG00000240627' => null,
'ENSG00000244621' => 'ribosomal protein S17 pseudogene 11',
'ENSG00000248789' => null,
'ENSG00000248891' => null,
'ENSG00000249270' => 'katanin p80 subunit B-like 1 pseudogene 4',
'ENSG00000249338' => 'high mobility group box 1 pseudogene 47',
'ENSG00000251125' => null,
'ENSG00000251873' => 'RNA, 5S ribosomal pseudogene 182',
'ENSG00000259663' => null,
'ENSG00000278734' => null,
'ENSG00000279470' => null,
'ENSDARG00000004023' => 'islet1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
),
'gene_name_arr' => array(
'ENSG00000016082' => 'ISL1',
'ENSG00000206606' => 'RNU6-1296P',
'ENSG00000207060' => 'RNU6-480P',
'ENSG00000222945' => 'AC091866.1',
'ENSG00000240627' => 'CTD-2312P21.1',
'ENSG00000244621' => 'RPS17P11',
'ENSG00000248789' => 'CTD-2203A3.1',
'ENSG00000248891' => 'CTD-2335O3.2',
'ENSG00000249270' => 'KATNBL1P4',
'ENSG00000249338' => 'HMGB1P47',
'ENSG00000251125' => 'CTD-2335O3.3',
'ENSG00000251873' => 'RNA5SP182',
'ENSG00000259663' => 'CTD-2314G24.2',
'ENSG00000278734' => 'CTD-2054H24.1',
'ENSG00000279470' => 'RP11-182I21.2',
'ENSDARG00000004023' => 'isl1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
),
'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]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 13 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 24 => 'Kidney',
(int) 31 => 'Liver',
(int) 34 => 'Lung',
(int) 38 => 'Muscle',
(int) 40 => 'Ovary',
(int) 44 => 'Placenta',
(int) 48 => '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) 27,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000230658' => array(
'start' => '51383391',
'end' => '51394738',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-001'
),
'ENST00000505475' => array(
'start' => '51386204',
'end' => '51393567',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ISL1-006'
),
'ENST00000511384' => array(
'start' => '51383672',
'end' => '51393610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-003'
),
'ENST00000383879' => array(
'start' => '51167541',
'end' => '51167647',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-1296P-201'
),
'ENST00000384332' => array(
'start' => '51055353',
'end' => '51055459',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-480P-201'
),
'ENST00000411013' => array(
'start' => '51061469',
'end' => '51061557',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC091866.1-201'
),
'ENST00000468490' => array(
'start' => '51275253',
'end' => '51275734',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2312P21.1-001'
),
'ENST00000474297' => array(
'start' => '52282567',
'end' => '52282859',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS17P11-001'
),
'ENST00000505899' => array(
'start' => '52008031',
'end' => '52043909',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-003'
),
'ENST00000510583' => array(
'start' => '52009815',
'end' => '52080987',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-001'
),
'ENST00000505723' => array(
'start' => '51427996',
'end' => '51428427',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2335O3.2-001'
),
'ENST00000503545' => array(
'start' => '51930808',
'end' => '51932036',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'KATNBL1P4-001'
),
'ENST00000511281' => array(
'start' => '51409617',
'end' => '51410205',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P47-001'
),
'ENST00000509423' => array(
'start' => '51451158',
'end' => '51462089',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2335O3.3-001'
),
'ENST00000516064' => array(
'start' => '51886688',
'end' => '51886769',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP182-201'
),
'ENST00000558403' => array(
'start' => '51378575',
'end' => '51379675',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-002'
),
'ENST00000559112' => array(
'start' => '51377068',
'end' => '51383332',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-001'
),
'ENST00000601500' => array(
'start' => '51372736',
'end' => '51379497',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-003'
),
'ENST00000614543' => array(
'start' => '51101172',
'end' => '51101643',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2054H24.1-001'
),
'ENST00000624322' => array(
'start' => '51963992',
'end' => '51964445',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-182I21.2-001'
),
'ENSDART00000010896' => array(
'start' => '42353743',
'end' => '42359175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'isl1-001'
),
'ENSDART00000133613' => array(
'start' => '42324960',
'end' => '42326117',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.3-001'
),
'ENSDART00000132410' => array(
'start' => '42338479',
'end' => '42339732',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.2-001'
),
'ENSDART00000154576' => array(
'start' => '42210507',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-001'
),
'ENSDART00000154891' => array(
'start' => '42182362',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-004'
),
'ENSDART00000155538' => array(
'start' => '42210507',
'end' => '42338896',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-002'
),
'ENSDART00000155814' => array(
'start' => '42225329',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-003'
)
),
'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_0007JG_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007JG_0001' => array(
'genes_in_region' => array(
'ENSG00000016082' => array(
[maximum depth reached]
),
'ENSG00000240627' => array(
[maximum depth reached]
),
'ENSG00000248789' => array(
[maximum depth reached]
),
'ENSG00000249270' => array(
[maximum depth reached]
),
'ENSG00000249338' => array(
[maximum depth reached]
),
'ENSG00000251125' => array(
[maximum depth reached]
),
'ENSG00000259663' => array(
[maximum depth reached]
),
'ENSG00000279470' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Ovary',
(int) 4 => 'Placenta',
(int) 5 => 'Testis',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Breast',
(int) 9 => 'Colon',
(int) 10 => 'Lung',
(int) 11 => 'Colon',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Heart',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Ovary',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Liver',
(int) 32 => 'Lung',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Lung',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Testis'
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
'ENSDARG00000004023' => array(
[maximum depth reached]
),
'ENSDARG00000092131' => array(
[maximum depth reached]
),
'ENSDARG00000093270' => array(
[maximum depth reached]
),
'ENSDARG00000097618' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Kidney',
(int) 12 => 'Brain',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Kidney'
)
)
)
$gene_desc_arr = array(
'ENSG00000016082' => 'ISL LIM homeobox 1',
'ENSG00000206606' => 'RNA, U6 small nuclear 1296, pseudogene',
'ENSG00000207060' => 'RNA, U6 small nuclear 480, pseudogene',
'ENSG00000222945' => null,
'ENSG00000240627' => null,
'ENSG00000244621' => 'ribosomal protein S17 pseudogene 11',
'ENSG00000248789' => null,
'ENSG00000248891' => null,
'ENSG00000249270' => 'katanin p80 subunit B-like 1 pseudogene 4',
'ENSG00000249338' => 'high mobility group box 1 pseudogene 47',
'ENSG00000251125' => null,
'ENSG00000251873' => 'RNA, 5S ribosomal pseudogene 182',
'ENSG00000259663' => null,
'ENSG00000278734' => null,
'ENSG00000279470' => null,
'ENSDARG00000004023' => 'islet1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
)
$gene_name_arr = array(
'ENSG00000016082' => 'ISL1',
'ENSG00000206606' => 'RNU6-1296P',
'ENSG00000207060' => 'RNU6-480P',
'ENSG00000222945' => 'AC091866.1',
'ENSG00000240627' => 'CTD-2312P21.1',
'ENSG00000244621' => 'RPS17P11',
'ENSG00000248789' => 'CTD-2203A3.1',
'ENSG00000248891' => 'CTD-2335O3.2',
'ENSG00000249270' => 'KATNBL1P4',
'ENSG00000249338' => 'HMGB1P47',
'ENSG00000251125' => 'CTD-2335O3.3',
'ENSG00000251873' => 'RNA5SP182',
'ENSG00000259663' => 'CTD-2314G24.2',
'ENSG00000278734' => 'CTD-2054H24.1',
'ENSG00000279470' => 'RP11-182I21.2',
'ENSDARG00000004023' => 'isl1',
'ENSDARG00000092131' => 'si:ch211-219f7.3',
'ENSDARG00000093270' => 'si:ch211-219f7.2',
'ENSDARG00000097618' => 'si:ch73-365k7.1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0001',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '51039710',
'seq_end' => '52466387',
'region_length' => '1426677',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0002',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '115379812',
'seq_end' => '115977571',
'region_length' => '597759',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0003',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '42183517',
'seq_end' => '42427797',
'region_length' => '244280',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0004',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '116497700',
'seq_end' => '116633834',
'region_length' => '136134',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Brain',
(int) 13 => 'Breast',
(int) 16 => 'Colon',
(int) 20 => 'Heart',
(int) 24 => 'Kidney',
(int) 31 => 'Liver',
(int) 34 => 'Lung',
(int) 38 => 'Muscle',
(int) 40 => 'Ovary',
(int) 44 => 'Placenta',
(int) 48 => '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) 27
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000230658' => array(
'start' => '51383391',
'end' => '51394738',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-001'
),
'ENST00000505475' => array(
'start' => '51386204',
'end' => '51393567',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ISL1-006'
),
'ENST00000511384' => array(
'start' => '51383672',
'end' => '51393610',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ISL1-003'
),
'ENST00000383879' => array(
'start' => '51167541',
'end' => '51167647',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-1296P-201'
),
'ENST00000384332' => array(
'start' => '51055353',
'end' => '51055459',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-480P-201'
),
'ENST00000411013' => array(
'start' => '51061469',
'end' => '51061557',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC091866.1-201'
),
'ENST00000468490' => array(
'start' => '51275253',
'end' => '51275734',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2312P21.1-001'
),
'ENST00000474297' => array(
'start' => '52282567',
'end' => '52282859',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPS17P11-001'
),
'ENST00000505899' => array(
'start' => '52008031',
'end' => '52043909',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-003'
),
'ENST00000510583' => array(
'start' => '52009815',
'end' => '52080987',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2203A3.1-001'
),
'ENST00000505723' => array(
'start' => '51427996',
'end' => '51428427',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2335O3.2-001'
),
'ENST00000503545' => array(
'start' => '51930808',
'end' => '51932036',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'KATNBL1P4-001'
),
'ENST00000511281' => array(
'start' => '51409617',
'end' => '51410205',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P47-001'
),
'ENST00000509423' => array(
'start' => '51451158',
'end' => '51462089',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CTD-2335O3.3-001'
),
'ENST00000516064' => array(
'start' => '51886688',
'end' => '51886769',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP182-201'
),
'ENST00000558403' => array(
'start' => '51378575',
'end' => '51379675',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-002'
),
'ENST00000559112' => array(
'start' => '51377068',
'end' => '51383332',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-001'
),
'ENST00000601500' => array(
'start' => '51372736',
'end' => '51379497',
'transcript_biotype' => 'antisense',
'transcript_name' => 'CTD-2314G24.2-003'
),
'ENST00000614543' => array(
'start' => '51101172',
'end' => '51101643',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'CTD-2054H24.1-001'
),
'ENST00000624322' => array(
'start' => '51963992',
'end' => '51964445',
'transcript_biotype' => 'TEC',
'transcript_name' => 'RP11-182I21.2-001'
),
'ENSDART00000010896' => array(
'start' => '42353743',
'end' => '42359175',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'isl1-001'
),
'ENSDART00000133613' => array(
'start' => '42324960',
'end' => '42326117',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.3-001'
),
'ENSDART00000132410' => array(
'start' => '42338479',
'end' => '42339732',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'si:ch211-219f7.2-001'
),
'ENSDART00000154576' => array(
'start' => '42210507',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-001'
),
'ENSDART00000154891' => array(
'start' => '42182362',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-004'
),
'ENSDART00000155538' => array(
'start' => '42210507',
'end' => '42338896',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-002'
),
'ENSDART00000155814' => array(
'start' => '42225329',
'end' => '42338930',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'si:ch73-365k7.1-003'
)
)
$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_0007JG_0001' => array(
'genes_in_region' => array(
'ENSG00000016082' => array(
[maximum depth reached]
),
'ENSG00000240627' => array(
[maximum depth reached]
),
'ENSG00000248789' => array(
[maximum depth reached]
),
'ENSG00000249270' => array(
[maximum depth reached]
),
'ENSG00000249338' => array(
[maximum depth reached]
),
'ENSG00000251125' => array(
[maximum depth reached]
),
'ENSG00000259663' => array(
[maximum depth reached]
),
'ENSG00000279470' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Brain',
(int) 2 => 'Colon',
(int) 3 => 'Ovary',
(int) 4 => 'Placenta',
(int) 5 => 'Testis',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Breast',
(int) 9 => 'Colon',
(int) 10 => 'Lung',
(int) 11 => 'Colon',
(int) 12 => 'Ovary',
(int) 13 => 'Placenta',
(int) 14 => 'Testis',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Lung',
(int) 21 => 'Testis',
(int) 22 => 'Testis',
(int) 23 => 'Brain',
(int) 24 => 'Heart',
(int) 25 => 'Testis',
(int) 26 => 'Testis',
(int) 27 => 'Adrenal',
(int) 28 => 'Ovary',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Liver',
(int) 32 => 'Lung',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Lung',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Testis'
)
),
'CIL_0007JG_0003' => array(
'genes_in_region' => array(
'ENSDARG00000004023' => array(
[maximum depth reached]
),
'ENSDARG00000092131' => array(
[maximum depth reached]
),
'ENSDARG00000093270' => array(
[maximum depth reached]
),
'ENSDARG00000097618' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Muscle',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Kidney',
(int) 12 => 'Brain',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Kidney'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007JG_0004',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '116497700',
'seq_end' => '116633834',
'region_length' => '136134',
'region_type' => 'UCNEbase',
'el_id' => 'ISL1'
)
)
$gene_el = array(
'ENSDART00000154576' => array(
'Kidney' => array(
'average_FPKM' => '0.181',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000154891' => array(
'Brain' => array(
'average_FPKM' => '0.071',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000155538' => array(
'Heart' => array(
'average_FPKM' => '0.675',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.712',
'stddev_FPKM' => '0.41'
)
),
'ENSDART00000155814' => array(
'Kidney' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000097618'
$is_first = false
$tran_el = array(
'Kidney' => array(
'average_FPKM' => '0.159',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000155814'
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
(ISL1)