| Source ID |
Type |
Tax ID |
Position |
| VPS13B |
UCNEbase |
10090 |
15:35481778-35862316  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007NL_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_0007NL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000206699' => 'Y RNA',
'ENSG00000207804' => 'microRNA 599',
'ENSG00000216069' => 'microRNA 875',
'ENSG00000225017' => null,
'ENSG00000235683' => null,
'ENSG00000236583' => null,
'ENSG00000237704' => null,
'ENSG00000243254' => 'RNA, 7SL, cytoplasmic 350, pseudogene',
'ENSG00000253539' => null,
'ENSMUSG00000076333' => 'microRNA 599',
'ENSMUSG00000077890' => 'microRNA 875',
'ENSMUSG00000089133' => 'predicted gene, 24771'
),
'gene_name_arr' => array(
'ENSG00000206699' => 'Y_RNA',
'ENSG00000207804' => 'MIR599',
'ENSG00000216069' => 'MIR875',
'ENSG00000225017' => 'AP004289.1',
'ENSG00000235683' => 'AC018442.1',
'ENSG00000236583' => 'AP004290.1',
'ENSG00000237704' => 'AP004289.2',
'ENSG00000243254' => 'RN7SL350P',
'ENSG00000253539' => 'RP11-402L5.1',
'ENSMUSG00000076333' => 'Mir599',
'ENSMUSG00000077890' => 'Mir875',
'ENSMUSG00000089133' => 'Gm24771'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 14 => 'Breast',
(int) 20 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 43 => 'Ovary',
(int) 48 => 'Placenta',
(int) 50 => '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) 12,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000383972' => array(
'start' => '99527826',
'end' => '99527927',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Y_RNA.1-604'
),
'ENST00000385069' => array(
'start' => '99536636',
'end' => '99536730',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR599-201'
),
'ENST00000401250' => array(
'start' => '99536786',
'end' => '99536861',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR875-201'
),
'ENST00000436307' => array(
'start' => '99346052',
'end' => '99348256',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.1-001'
),
'ENST00000421439' => array(
'start' => '99695957',
'end' => '99698017',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018442.1-001'
),
'ENST00000440915' => array(
'start' => '99233048',
'end' => '99234459',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004290.1-001'
),
'ENST00000444413' => array(
'start' => '99340305',
'end' => '99341761',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.2-001'
),
'ENST00000492591' => array(
'start' => '99613783',
'end' => '99614081',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL350P-201'
),
'ENST00000523658' => array(
'start' => '99796615',
'end' => '99799187',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-402L5.1-001'
),
'ENSMUST00000102378' => array(
'start' => '35660831',
'end' => '35660918',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir599-201'
),
'ENSMUST00000104698' => array(
'start' => '35660970',
'end' => '35661047',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir875-201'
),
'ENSMUST00000158508' => array(
'start' => '35487400',
'end' => '35487536',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24771-201'
)
),
'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_0007NL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007NL_0001' => array(
'genes_in_region' => array(
'ENSG00000225017' => array(
[maximum depth reached]
),
'ENSG00000235683' => array(
[maximum depth reached]
),
'ENSG00000236583' => array(
[maximum depth reached]
),
'ENSG00000237704' => array(
[maximum depth reached]
),
'ENSG00000243254' => array(
[maximum depth reached]
),
'ENSG00000253539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Testis',
(int) 42 => 'Breast',
(int) 43 => 'Lung',
(int) 44 => 'Adrenal',
(int) 45 => 'Bladder',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000206699' => 'Y RNA',
'ENSG00000207804' => 'microRNA 599',
'ENSG00000216069' => 'microRNA 875',
'ENSG00000225017' => null,
'ENSG00000235683' => null,
'ENSG00000236583' => null,
'ENSG00000237704' => null,
'ENSG00000243254' => 'RNA, 7SL, cytoplasmic 350, pseudogene',
'ENSG00000253539' => null,
'ENSMUSG00000076333' => 'microRNA 599',
'ENSMUSG00000077890' => 'microRNA 875',
'ENSMUSG00000089133' => 'predicted gene, 24771'
)
$gene_name_arr = array(
'ENSG00000206699' => 'Y_RNA',
'ENSG00000207804' => 'MIR599',
'ENSG00000216069' => 'MIR875',
'ENSG00000225017' => 'AP004289.1',
'ENSG00000235683' => 'AC018442.1',
'ENSG00000236583' => 'AP004290.1',
'ENSG00000237704' => 'AP004289.2',
'ENSG00000243254' => 'RN7SL350P',
'ENSG00000253539' => 'RP11-402L5.1',
'ENSMUSG00000076333' => 'Mir599',
'ENSMUSG00000077890' => 'Mir875',
'ENSMUSG00000089133' => 'Gm24771'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NL_0001',
'tax_id' => '9606',
'chromosome' => '8',
'seq_start' => '99206329',
'seq_end' => '99799529',
'region_length' => '593200',
'region_type' => 'UCNEbase',
'el_id' => 'VPS13B'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NL_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '35481778',
'seq_end' => '35862316',
'region_length' => '380538',
'region_type' => 'UCNEbase',
'el_id' => 'VPS13B'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 14 => 'Breast',
(int) 20 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 43 => 'Ovary',
(int) 48 => 'Placenta',
(int) 50 => '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) 12
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000383972' => array(
'start' => '99527826',
'end' => '99527927',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Y_RNA.1-604'
),
'ENST00000385069' => array(
'start' => '99536636',
'end' => '99536730',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR599-201'
),
'ENST00000401250' => array(
'start' => '99536786',
'end' => '99536861',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR875-201'
),
'ENST00000436307' => array(
'start' => '99346052',
'end' => '99348256',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.1-001'
),
'ENST00000421439' => array(
'start' => '99695957',
'end' => '99698017',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018442.1-001'
),
'ENST00000440915' => array(
'start' => '99233048',
'end' => '99234459',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004290.1-001'
),
'ENST00000444413' => array(
'start' => '99340305',
'end' => '99341761',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.2-001'
),
'ENST00000492591' => array(
'start' => '99613783',
'end' => '99614081',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL350P-201'
),
'ENST00000523658' => array(
'start' => '99796615',
'end' => '99799187',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-402L5.1-001'
),
'ENSMUST00000102378' => array(
'start' => '35660831',
'end' => '35660918',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir599-201'
),
'ENSMUST00000104698' => array(
'start' => '35660970',
'end' => '35661047',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir875-201'
),
'ENSMUST00000158508' => array(
'start' => '35487400',
'end' => '35487536',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24771-201'
)
)
$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_0007NL_0001' => array(
'genes_in_region' => array(
'ENSG00000225017' => array(
[maximum depth reached]
),
'ENSG00000235683' => array(
[maximum depth reached]
),
'ENSG00000236583' => array(
[maximum depth reached]
),
'ENSG00000237704' => array(
[maximum depth reached]
),
'ENSG00000243254' => array(
[maximum depth reached]
),
'ENSG00000253539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Testis',
(int) 42 => 'Breast',
(int) 43 => 'Lung',
(int) 44 => 'Adrenal',
(int) 45 => 'Bladder',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NL_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '35481778',
'seq_end' => '35862316',
'region_length' => '380538',
'region_type' => 'UCNEbase',
'el_id' => 'VPS13B'
)
)
$gene_el = array(
'ENST00000523658' => array(
'Adrenal' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '1.329',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.526',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.540',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.324',
'stddev_FPKM' => '1.29'
),
'Ovary' => array(
'average_FPKM' => '0.607',
'stddev_FPKM' => '0.33'
),
'Placenta' => array(
'average_FPKM' => '0.133',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000253539'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '1.329',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.526',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.540',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.324',
'stddev_FPKM' => '1.29'
),
'Ovary' => array(
'average_FPKM' => '0.607',
'stddev_FPKM' => '0.33'
),
'Placenta' => array(
'average_FPKM' => '0.133',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000523658'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007NL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000206699' => 'Y RNA',
'ENSG00000207804' => 'microRNA 599',
'ENSG00000216069' => 'microRNA 875',
'ENSG00000225017' => null,
'ENSG00000235683' => null,
'ENSG00000236583' => null,
'ENSG00000237704' => null,
'ENSG00000243254' => 'RNA, 7SL, cytoplasmic 350, pseudogene',
'ENSG00000253539' => null,
'ENSMUSG00000076333' => 'microRNA 599',
'ENSMUSG00000077890' => 'microRNA 875',
'ENSMUSG00000089133' => 'predicted gene, 24771'
),
'gene_name_arr' => array(
'ENSG00000206699' => 'Y_RNA',
'ENSG00000207804' => 'MIR599',
'ENSG00000216069' => 'MIR875',
'ENSG00000225017' => 'AP004289.1',
'ENSG00000235683' => 'AC018442.1',
'ENSG00000236583' => 'AP004290.1',
'ENSG00000237704' => 'AP004289.2',
'ENSG00000243254' => 'RN7SL350P',
'ENSG00000253539' => 'RP11-402L5.1',
'ENSMUSG00000076333' => 'Mir599',
'ENSMUSG00000077890' => 'Mir875',
'ENSMUSG00000089133' => 'Gm24771'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 14 => 'Breast',
(int) 20 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 43 => 'Ovary',
(int) 48 => 'Placenta',
(int) 50 => '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) 12,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000383972' => array(
'start' => '99527826',
'end' => '99527927',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Y_RNA.1-604'
),
'ENST00000385069' => array(
'start' => '99536636',
'end' => '99536730',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR599-201'
),
'ENST00000401250' => array(
'start' => '99536786',
'end' => '99536861',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR875-201'
),
'ENST00000436307' => array(
'start' => '99346052',
'end' => '99348256',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.1-001'
),
'ENST00000421439' => array(
'start' => '99695957',
'end' => '99698017',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018442.1-001'
),
'ENST00000440915' => array(
'start' => '99233048',
'end' => '99234459',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004290.1-001'
),
'ENST00000444413' => array(
'start' => '99340305',
'end' => '99341761',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.2-001'
),
'ENST00000492591' => array(
'start' => '99613783',
'end' => '99614081',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL350P-201'
),
'ENST00000523658' => array(
'start' => '99796615',
'end' => '99799187',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-402L5.1-001'
),
'ENSMUST00000102378' => array(
'start' => '35660831',
'end' => '35660918',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir599-201'
),
'ENSMUST00000104698' => array(
'start' => '35660970',
'end' => '35661047',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir875-201'
),
'ENSMUST00000158508' => array(
'start' => '35487400',
'end' => '35487536',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24771-201'
)
),
'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_0007NL_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007NL_0001' => array(
'genes_in_region' => array(
'ENSG00000225017' => array(
[maximum depth reached]
),
'ENSG00000235683' => array(
[maximum depth reached]
),
'ENSG00000236583' => array(
[maximum depth reached]
),
'ENSG00000237704' => array(
[maximum depth reached]
),
'ENSG00000243254' => array(
[maximum depth reached]
),
'ENSG00000253539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Testis',
(int) 42 => 'Breast',
(int) 43 => 'Lung',
(int) 44 => 'Adrenal',
(int) 45 => 'Bladder',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000206699' => 'Y RNA',
'ENSG00000207804' => 'microRNA 599',
'ENSG00000216069' => 'microRNA 875',
'ENSG00000225017' => null,
'ENSG00000235683' => null,
'ENSG00000236583' => null,
'ENSG00000237704' => null,
'ENSG00000243254' => 'RNA, 7SL, cytoplasmic 350, pseudogene',
'ENSG00000253539' => null,
'ENSMUSG00000076333' => 'microRNA 599',
'ENSMUSG00000077890' => 'microRNA 875',
'ENSMUSG00000089133' => 'predicted gene, 24771'
)
$gene_name_arr = array(
'ENSG00000206699' => 'Y_RNA',
'ENSG00000207804' => 'MIR599',
'ENSG00000216069' => 'MIR875',
'ENSG00000225017' => 'AP004289.1',
'ENSG00000235683' => 'AC018442.1',
'ENSG00000236583' => 'AP004290.1',
'ENSG00000237704' => 'AP004289.2',
'ENSG00000243254' => 'RN7SL350P',
'ENSG00000253539' => 'RP11-402L5.1',
'ENSMUSG00000076333' => 'Mir599',
'ENSMUSG00000077890' => 'Mir875',
'ENSMUSG00000089133' => 'Gm24771'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NL_0001',
'tax_id' => '9606',
'chromosome' => '8',
'seq_start' => '99206329',
'seq_end' => '99799529',
'region_length' => '593200',
'region_type' => 'UCNEbase',
'el_id' => 'VPS13B'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NL_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '35481778',
'seq_end' => '35862316',
'region_length' => '380538',
'region_type' => 'UCNEbase',
'el_id' => 'VPS13B'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 11 => 'Brain',
(int) 14 => 'Breast',
(int) 20 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 32 => 'Liver',
(int) 37 => 'Lung',
(int) 41 => 'Muscle',
(int) 43 => 'Ovary',
(int) 48 => 'Placenta',
(int) 50 => '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) 12
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000383972' => array(
'start' => '99527826',
'end' => '99527927',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Y_RNA.1-604'
),
'ENST00000385069' => array(
'start' => '99536636',
'end' => '99536730',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR599-201'
),
'ENST00000401250' => array(
'start' => '99536786',
'end' => '99536861',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'MIR875-201'
),
'ENST00000436307' => array(
'start' => '99346052',
'end' => '99348256',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.1-001'
),
'ENST00000421439' => array(
'start' => '99695957',
'end' => '99698017',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018442.1-001'
),
'ENST00000440915' => array(
'start' => '99233048',
'end' => '99234459',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004290.1-001'
),
'ENST00000444413' => array(
'start' => '99340305',
'end' => '99341761',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AP004289.2-001'
),
'ENST00000492591' => array(
'start' => '99613783',
'end' => '99614081',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL350P-201'
),
'ENST00000523658' => array(
'start' => '99796615',
'end' => '99799187',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-402L5.1-001'
),
'ENSMUST00000102378' => array(
'start' => '35660831',
'end' => '35660918',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir599-201'
),
'ENSMUST00000104698' => array(
'start' => '35660970',
'end' => '35661047',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir875-201'
),
'ENSMUST00000158508' => array(
'start' => '35487400',
'end' => '35487536',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24771-201'
)
)
$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_0007NL_0001' => array(
'genes_in_region' => array(
'ENSG00000225017' => array(
[maximum depth reached]
),
'ENSG00000235683' => array(
[maximum depth reached]
),
'ENSG00000236583' => array(
[maximum depth reached]
),
'ENSG00000237704' => array(
[maximum depth reached]
),
'ENSG00000243254' => array(
[maximum depth reached]
),
'ENSG00000253539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Bladder',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 12 => 'Brain',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Heart',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Testis',
(int) 23 => 'Adipose',
(int) 24 => 'Adrenal',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Ovary',
(int) 41 => 'Testis',
(int) 42 => 'Breast',
(int) 43 => 'Lung',
(int) 44 => 'Adrenal',
(int) 45 => 'Bladder',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007NL_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '35481778',
'seq_end' => '35862316',
'region_length' => '380538',
'region_type' => 'UCNEbase',
'el_id' => 'VPS13B'
)
)
$gene_el = array(
'ENST00000523658' => array(
'Adrenal' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '1.329',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.526',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.540',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.324',
'stddev_FPKM' => '1.29'
),
'Ovary' => array(
'average_FPKM' => '0.607',
'stddev_FPKM' => '0.33'
),
'Placenta' => array(
'average_FPKM' => '0.133',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000253539'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.086',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '1.329',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.526',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.540',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.324',
'stddev_FPKM' => '1.29'
),
'Ovary' => array(
'average_FPKM' => '0.607',
'stddev_FPKM' => '0.33'
),
'Placenta' => array(
'average_FPKM' => '0.133',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.039',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000523658'
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
(AP004289.1)