| Source ID |
Type |
Tax ID |
Position |
| CPEB2 |
UCNEbase |
7955 |
23:2184582-2185451  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007L6_0003 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0007L6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000137449' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSG00000202449' => 'Small nucleolar RNA SNORA63',
'ENSG00000247624' => 'CPEB2 antisense RNA 1 (head to head)',
'ENSG00000248360' => 'long intergenic non-protein coding RNA 504',
'ENSG00000249252' => null,
'ENSMUSG00000039782' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSMUSG00000085720' => 'predicted gene 7854'
),
'gene_name_arr' => array(
'ENSG00000137449' => 'CPEB2',
'ENSG00000202449' => 'SNORA63',
'ENSG00000247624' => 'CPEB2-AS1',
'ENSG00000248360' => 'LINC00504',
'ENSG00000249252' => 'RP11-665G4.1',
'ENSMUSG00000039782' => 'Cpeb2',
'ENSMUSG00000085720' => 'Gm7854'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 20 => 'Brain',
(int) 28 => 'Breast',
(int) 37 => 'Colon',
(int) 46 => 'Heart',
(int) 54 => 'Kidney',
(int) 61 => 'Liver',
(int) 69 => 'Lung',
(int) 79 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => '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) 26,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000259997' => array(
'start' => '15003936',
'end' => '15070149',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-007'
),
'ENST00000345451' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-002'
),
'ENST00000382395' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-005'
),
'ENST00000382401' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-006'
),
'ENST00000442003' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-201'
),
'ENST00000503926' => array(
'start' => '15007367',
'end' => '15017434',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPEB2-009'
),
'ENST00000507071' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-001'
),
'ENST00000509684' => array(
'start' => '15054133',
'end' => '15063871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-008'
),
'ENST00000538197' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-202'
),
'ENST00000365579' => array(
'start' => '14690710',
'end' => '14690832',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA63.1-210'
),
'ENST00000500394' => array(
'start' => '14909961',
'end' => '15002045',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-001'
),
'ENST00000501916' => array(
'start' => '14976900',
'end' => '14994505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-002'
),
'ENST00000505089' => array(
'start' => '14470465',
'end' => '14888169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-003'
),
'ENST00000506292' => array(
'start' => '14628756',
'end' => '14716595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-004'
),
'ENST00000509654' => array(
'start' => '14474085',
'end' => '14888167',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-001'
),
'ENST00000515031' => array(
'start' => '14474087',
'end' => '14888168',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-002'
),
'ENST00000502344' => array(
'start' => '15004942',
'end' => '15427914',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-001'
),
'ENST00000513384' => array(
'start' => '15006447',
'end' => '15227960',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-002'
),
'ENSMUST00000114065' => array(
'start' => '43233956',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-001'
),
'ENSMUST00000114066' => array(
'start' => '43233956',
'end' => '43287022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-002'
),
'ENSMUST00000127599' => array(
'start' => '43237316',
'end' => '43246459',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpeb2-003'
),
'ENSMUST00000166713' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-201'
),
'ENSMUST00000169035' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-202'
),
'ENSMUST00000140650' => array(
'start' => '43235002',
'end' => '43235352',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-201'
),
'ENSMUST00000187409' => array(
'start' => '43152047',
'end' => '43235354',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-001'
),
'ENSMUST00000187911' => array(
'start' => '43151689',
'end' => '43234984',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-002'
)
),
'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_0007L6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007L6_0001' => array(
'genes_in_region' => array(
'ENSG00000137449' => array(
[maximum depth reached]
),
'ENSG00000247624' => array(
[maximum depth reached]
),
'ENSG00000248360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Adrenal',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Brain',
(int) 29 => 'Placenta',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Heart',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Lung',
(int) 48 => 'Testis',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Heart',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Adrenal',
(int) 68 => 'Bladder',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Colon',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Liver',
(int) 75 => 'Lung',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis'
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039782' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Breast',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Colon',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000137449' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSG00000202449' => 'Small nucleolar RNA SNORA63',
'ENSG00000247624' => 'CPEB2 antisense RNA 1 (head to head)',
'ENSG00000248360' => 'long intergenic non-protein coding RNA 504',
'ENSG00000249252' => null,
'ENSMUSG00000039782' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSMUSG00000085720' => 'predicted gene 7854'
)
$gene_name_arr = array(
'ENSG00000137449' => 'CPEB2',
'ENSG00000202449' => 'SNORA63',
'ENSG00000247624' => 'CPEB2-AS1',
'ENSG00000248360' => 'LINC00504',
'ENSG00000249252' => 'RP11-665G4.1',
'ENSMUSG00000039782' => 'Cpeb2',
'ENSMUSG00000085720' => 'Gm7854'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0001',
'tax_id' => '9606',
'chromosome' => '4',
'seq_start' => '14574509',
'seq_end' => '15069972',
'region_length' => '495463',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0002',
'tax_id' => '10090',
'chromosome' => '5',
'seq_start' => '42800809',
'seq_end' => '43289546',
'region_length' => '488737',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '2184582',
'seq_end' => '2185451',
'region_length' => '869',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 20 => 'Brain',
(int) 28 => 'Breast',
(int) 37 => 'Colon',
(int) 46 => 'Heart',
(int) 54 => 'Kidney',
(int) 61 => 'Liver',
(int) 69 => 'Lung',
(int) 79 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => '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) 26
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000259997' => array(
'start' => '15003936',
'end' => '15070149',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-007'
),
'ENST00000345451' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-002'
),
'ENST00000382395' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-005'
),
'ENST00000382401' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-006'
),
'ENST00000442003' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-201'
),
'ENST00000503926' => array(
'start' => '15007367',
'end' => '15017434',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPEB2-009'
),
'ENST00000507071' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-001'
),
'ENST00000509684' => array(
'start' => '15054133',
'end' => '15063871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-008'
),
'ENST00000538197' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-202'
),
'ENST00000365579' => array(
'start' => '14690710',
'end' => '14690832',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA63.1-210'
),
'ENST00000500394' => array(
'start' => '14909961',
'end' => '15002045',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-001'
),
'ENST00000501916' => array(
'start' => '14976900',
'end' => '14994505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-002'
),
'ENST00000505089' => array(
'start' => '14470465',
'end' => '14888169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-003'
),
'ENST00000506292' => array(
'start' => '14628756',
'end' => '14716595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-004'
),
'ENST00000509654' => array(
'start' => '14474085',
'end' => '14888167',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-001'
),
'ENST00000515031' => array(
'start' => '14474087',
'end' => '14888168',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-002'
),
'ENST00000502344' => array(
'start' => '15004942',
'end' => '15427914',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-001'
),
'ENST00000513384' => array(
'start' => '15006447',
'end' => '15227960',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-002'
),
'ENSMUST00000114065' => array(
'start' => '43233956',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-001'
),
'ENSMUST00000114066' => array(
'start' => '43233956',
'end' => '43287022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-002'
),
'ENSMUST00000127599' => array(
'start' => '43237316',
'end' => '43246459',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpeb2-003'
),
'ENSMUST00000166713' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-201'
),
'ENSMUST00000169035' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-202'
),
'ENSMUST00000140650' => array(
'start' => '43235002',
'end' => '43235352',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-201'
),
'ENSMUST00000187409' => array(
'start' => '43152047',
'end' => '43235354',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-001'
),
'ENSMUST00000187911' => array(
'start' => '43151689',
'end' => '43234984',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-002'
)
)
$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_0007L6_0001' => array(
'genes_in_region' => array(
'ENSG00000137449' => array(
[maximum depth reached]
),
'ENSG00000247624' => array(
[maximum depth reached]
),
'ENSG00000248360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Adrenal',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Brain',
(int) 29 => 'Placenta',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Heart',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Lung',
(int) 48 => 'Testis',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Heart',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Adrenal',
(int) 68 => 'Bladder',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Colon',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Liver',
(int) 75 => 'Lung',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis'
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039782' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Breast',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Colon',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '2184582',
'seq_end' => '2185451',
'region_length' => '869',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
)
$gene_el = array(
'ENSMUST00000114065' => array(
'Adipose' => array(
'average_FPKM' => '2.481',
'stddev_FPKM' => '0.43'
),
'Adrenal' => array(
'average_FPKM' => '2.858',
'stddev_FPKM' => '0.12'
),
'Bladder' => array(
'average_FPKM' => '4.117',
'stddev_FPKM' => '1.94'
),
'Brain' => array(
'average_FPKM' => '6.665',
'stddev_FPKM' => '2.78'
),
'Breast' => array(
'average_FPKM' => '1.390',
'stddev_FPKM' => '0.96'
),
'Colon' => array(
'average_FPKM' => '1.505',
'stddev_FPKM' => '0.42'
),
'Heart' => array(
'average_FPKM' => '2.561',
'stddev_FPKM' => '0.42'
),
'Kidney' => array(
'average_FPKM' => '2.463',
'stddev_FPKM' => '0.48'
),
'Liver' => array(
'average_FPKM' => '1.826',
'stddev_FPKM' => '1.05'
),
'Lung' => array(
'average_FPKM' => '2.770',
'stddev_FPKM' => '0.81'
),
'Muscle' => array(
'average_FPKM' => '2.179',
'stddev_FPKM' => '0.40'
),
'Ovary' => array(
'average_FPKM' => '1.838',
'stddev_FPKM' => '0.68'
),
'Placenta' => array(
'average_FPKM' => '2.817',
'stddev_FPKM' => '0.87'
),
'Testis' => array(
'average_FPKM' => '9.272',
'stddev_FPKM' => '7.25'
)
),
'ENSMUST00000114066' => array(
'Breast' => array(
'average_FPKM' => '1.251',
'stddev_FPKM' => '0.28'
),
'Testis' => array(
'average_FPKM' => '44.409',
'stddev_FPKM' => '16.71'
)
),
'ENSMUST00000127599' => array(
'Testis' => array(
'average_FPKM' => '46.634',
'stddev_FPKM' => '0.00'
)
),
'ENSMUST00000166713' => array(
'Colon' => array(
'average_FPKM' => '0.483',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.476',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.247',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.430',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '15.577',
'stddev_FPKM' => '8.09'
)
),
'ENSMUST00000169035' => array(
'Adipose' => array(
'average_FPKM' => '0.919',
'stddev_FPKM' => '0.40'
),
'Adrenal' => array(
'average_FPKM' => '1.738',
'stddev_FPKM' => '0.12'
),
'Bladder' => array(
'average_FPKM' => '1.974',
'stddev_FPKM' => '0.49'
),
'Brain' => array(
'average_FPKM' => '3.308',
'stddev_FPKM' => '2.38'
),
'Breast' => array(
'average_FPKM' => '1.208',
'stddev_FPKM' => '0.63'
),
'Colon' => array(
'average_FPKM' => '0.931',
'stddev_FPKM' => '0.50'
),
'Heart' => array(
'average_FPKM' => '0.692',
'stddev_FPKM' => '0.09'
),
'Kidney' => array(
'average_FPKM' => '0.553',
'stddev_FPKM' => '0.08'
),
'Liver' => array(
'average_FPKM' => '0.445',
'stddev_FPKM' => '0.15'
),
'Lung' => array(
'average_FPKM' => '0.470',
'stddev_FPKM' => '0.22'
),
'Muscle' => array(
'average_FPKM' => '0.866',
'stddev_FPKM' => '0.22'
),
'Ovary' => array(
'average_FPKM' => '0.608',
'stddev_FPKM' => '0.35'
),
'Placenta' => array(
'average_FPKM' => '1.023',
'stddev_FPKM' => '0.34'
)
)
)
$gene_key = 'ENSMUSG00000039782'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.919',
'stddev_FPKM' => '0.40'
),
'Adrenal' => array(
'average_FPKM' => '1.738',
'stddev_FPKM' => '0.12'
),
'Bladder' => array(
'average_FPKM' => '1.974',
'stddev_FPKM' => '0.49'
),
'Brain' => array(
'average_FPKM' => '3.308',
'stddev_FPKM' => '2.38'
),
'Breast' => array(
'average_FPKM' => '1.208',
'stddev_FPKM' => '0.63'
),
'Colon' => array(
'average_FPKM' => '0.931',
'stddev_FPKM' => '0.50'
),
'Heart' => array(
'average_FPKM' => '0.692',
'stddev_FPKM' => '0.09'
),
'Kidney' => array(
'average_FPKM' => '0.553',
'stddev_FPKM' => '0.08'
),
'Liver' => array(
'average_FPKM' => '0.445',
'stddev_FPKM' => '0.15'
),
'Lung' => array(
'average_FPKM' => '0.470',
'stddev_FPKM' => '0.22'
),
'Muscle' => array(
'average_FPKM' => '0.866',
'stddev_FPKM' => '0.22'
),
'Ovary' => array(
'average_FPKM' => '0.608',
'stddev_FPKM' => '0.35'
),
'Placenta' => array(
'average_FPKM' => '1.023',
'stddev_FPKM' => '0.34'
)
)
$tran_key = 'ENSMUST00000169035'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007L6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000137449' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSG00000202449' => 'Small nucleolar RNA SNORA63',
'ENSG00000247624' => 'CPEB2 antisense RNA 1 (head to head)',
'ENSG00000248360' => 'long intergenic non-protein coding RNA 504',
'ENSG00000249252' => null,
'ENSMUSG00000039782' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSMUSG00000085720' => 'predicted gene 7854'
),
'gene_name_arr' => array(
'ENSG00000137449' => 'CPEB2',
'ENSG00000202449' => 'SNORA63',
'ENSG00000247624' => 'CPEB2-AS1',
'ENSG00000248360' => 'LINC00504',
'ENSG00000249252' => 'RP11-665G4.1',
'ENSMUSG00000039782' => 'Cpeb2',
'ENSMUSG00000085720' => 'Gm7854'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 20 => 'Brain',
(int) 28 => 'Breast',
(int) 37 => 'Colon',
(int) 46 => 'Heart',
(int) 54 => 'Kidney',
(int) 61 => 'Liver',
(int) 69 => 'Lung',
(int) 79 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => '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) 26,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000259997' => array(
'start' => '15003936',
'end' => '15070149',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-007'
),
'ENST00000345451' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-002'
),
'ENST00000382395' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-005'
),
'ENST00000382401' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-006'
),
'ENST00000442003' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-201'
),
'ENST00000503926' => array(
'start' => '15007367',
'end' => '15017434',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPEB2-009'
),
'ENST00000507071' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-001'
),
'ENST00000509684' => array(
'start' => '15054133',
'end' => '15063871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-008'
),
'ENST00000538197' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-202'
),
'ENST00000365579' => array(
'start' => '14690710',
'end' => '14690832',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA63.1-210'
),
'ENST00000500394' => array(
'start' => '14909961',
'end' => '15002045',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-001'
),
'ENST00000501916' => array(
'start' => '14976900',
'end' => '14994505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-002'
),
'ENST00000505089' => array(
'start' => '14470465',
'end' => '14888169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-003'
),
'ENST00000506292' => array(
'start' => '14628756',
'end' => '14716595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-004'
),
'ENST00000509654' => array(
'start' => '14474085',
'end' => '14888167',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-001'
),
'ENST00000515031' => array(
'start' => '14474087',
'end' => '14888168',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-002'
),
'ENST00000502344' => array(
'start' => '15004942',
'end' => '15427914',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-001'
),
'ENST00000513384' => array(
'start' => '15006447',
'end' => '15227960',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-002'
),
'ENSMUST00000114065' => array(
'start' => '43233956',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-001'
),
'ENSMUST00000114066' => array(
'start' => '43233956',
'end' => '43287022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-002'
),
'ENSMUST00000127599' => array(
'start' => '43237316',
'end' => '43246459',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpeb2-003'
),
'ENSMUST00000166713' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-201'
),
'ENSMUST00000169035' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-202'
),
'ENSMUST00000140650' => array(
'start' => '43235002',
'end' => '43235352',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-201'
),
'ENSMUST00000187409' => array(
'start' => '43152047',
'end' => '43235354',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-001'
),
'ENSMUST00000187911' => array(
'start' => '43151689',
'end' => '43234984',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-002'
)
),
'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_0007L6_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007L6_0001' => array(
'genes_in_region' => array(
'ENSG00000137449' => array(
[maximum depth reached]
),
'ENSG00000247624' => array(
[maximum depth reached]
),
'ENSG00000248360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Adrenal',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Brain',
(int) 29 => 'Placenta',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Heart',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Lung',
(int) 48 => 'Testis',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Heart',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Adrenal',
(int) 68 => 'Bladder',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Colon',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Liver',
(int) 75 => 'Lung',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis'
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039782' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Breast',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Colon',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta'
)
)
)
$gene_desc_arr = array(
'ENSG00000137449' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSG00000202449' => 'Small nucleolar RNA SNORA63',
'ENSG00000247624' => 'CPEB2 antisense RNA 1 (head to head)',
'ENSG00000248360' => 'long intergenic non-protein coding RNA 504',
'ENSG00000249252' => null,
'ENSMUSG00000039782' => 'cytoplasmic polyadenylation element binding protein 2',
'ENSMUSG00000085720' => 'predicted gene 7854'
)
$gene_name_arr = array(
'ENSG00000137449' => 'CPEB2',
'ENSG00000202449' => 'SNORA63',
'ENSG00000247624' => 'CPEB2-AS1',
'ENSG00000248360' => 'LINC00504',
'ENSG00000249252' => 'RP11-665G4.1',
'ENSMUSG00000039782' => 'Cpeb2',
'ENSMUSG00000085720' => 'Gm7854'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0001',
'tax_id' => '9606',
'chromosome' => '4',
'seq_start' => '14574509',
'seq_end' => '15069972',
'region_length' => '495463',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0002',
'tax_id' => '10090',
'chromosome' => '5',
'seq_start' => '42800809',
'seq_end' => '43289546',
'region_length' => '488737',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '2184582',
'seq_end' => '2185451',
'region_length' => '869',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 20 => 'Brain',
(int) 28 => 'Breast',
(int) 37 => 'Colon',
(int) 46 => 'Heart',
(int) 54 => 'Kidney',
(int) 61 => 'Liver',
(int) 69 => 'Lung',
(int) 79 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => '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) 26
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000259997' => array(
'start' => '15003936',
'end' => '15070149',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-007'
),
'ENST00000345451' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-002'
),
'ENST00000382395' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-005'
),
'ENST00000382401' => array(
'start' => '15003936',
'end' => '15070151',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-006'
),
'ENST00000442003' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-201'
),
'ENST00000503926' => array(
'start' => '15007367',
'end' => '15017434',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CPEB2-009'
),
'ENST00000507071' => array(
'start' => '15003898',
'end' => '15066626',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-001'
),
'ENST00000509684' => array(
'start' => '15054133',
'end' => '15063871',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-008'
),
'ENST00000538197' => array(
'start' => '15002674',
'end' => '15070153',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CPEB2-202'
),
'ENST00000365579' => array(
'start' => '14690710',
'end' => '14690832',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'SNORA63.1-210'
),
'ENST00000500394' => array(
'start' => '14909961',
'end' => '15002045',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-001'
),
'ENST00000501916' => array(
'start' => '14976900',
'end' => '14994505',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'CPEB2-AS1-002'
),
'ENST00000505089' => array(
'start' => '14470465',
'end' => '14888169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-003'
),
'ENST00000506292' => array(
'start' => '14628756',
'end' => '14716595',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-004'
),
'ENST00000509654' => array(
'start' => '14474085',
'end' => '14888167',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-001'
),
'ENST00000515031' => array(
'start' => '14474087',
'end' => '14888168',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'LINC00504-002'
),
'ENST00000502344' => array(
'start' => '15004942',
'end' => '15427914',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-001'
),
'ENST00000513384' => array(
'start' => '15006447',
'end' => '15227960',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-665G4.1-002'
),
'ENSMUST00000114065' => array(
'start' => '43233956',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-001'
),
'ENSMUST00000114066' => array(
'start' => '43233956',
'end' => '43287022',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-002'
),
'ENSMUST00000127599' => array(
'start' => '43237316',
'end' => '43246459',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cpeb2-003'
),
'ENSMUST00000166713' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-201'
),
'ENSMUST00000169035' => array(
'start' => '43233463',
'end' => '43289724',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cpeb2-202'
),
'ENSMUST00000140650' => array(
'start' => '43235002',
'end' => '43235352',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-201'
),
'ENSMUST00000187409' => array(
'start' => '43152047',
'end' => '43235354',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-001'
),
'ENSMUST00000187911' => array(
'start' => '43151689',
'end' => '43234984',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'Gm7854-002'
)
)
$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_0007L6_0001' => array(
'genes_in_region' => array(
'ENSG00000137449' => array(
[maximum depth reached]
),
'ENSG00000247624' => array(
[maximum depth reached]
),
'ENSG00000248360' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Bladder',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Liver',
(int) 7 => 'Lung',
(int) 8 => 'Muscle',
(int) 9 => 'Ovary',
(int) 10 => 'Placenta',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Muscle',
(int) 20 => 'Ovary',
(int) 21 => 'Placenta',
(int) 22 => 'Adrenal',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Brain',
(int) 29 => 'Placenta',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Bladder',
(int) 34 => 'Brain',
(int) 35 => 'Heart',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Adipose',
(int) 41 => 'Adrenal',
(int) 42 => 'Bladder',
(int) 43 => 'Breast',
(int) 44 => 'Colon',
(int) 45 => 'Heart',
(int) 46 => 'Kidney',
(int) 47 => 'Lung',
(int) 48 => 'Testis',
(int) 49 => 'Adrenal',
(int) 50 => 'Bladder',
(int) 51 => 'Heart',
(int) 52 => 'Placenta',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain',
(int) 57 => 'Breast',
(int) 58 => 'Colon',
(int) 59 => 'Heart',
(int) 60 => 'Kidney',
(int) 61 => 'Liver',
(int) 62 => 'Lung',
(int) 63 => 'Muscle',
(int) 64 => 'Ovary',
(int) 65 => 'Placenta',
(int) 66 => 'Testis',
(int) 67 => 'Adrenal',
(int) 68 => 'Bladder',
(int) 69 => 'Brain',
(int) 70 => 'Breast',
(int) 71 => 'Colon',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Liver',
(int) 75 => 'Lung',
(int) 76 => 'Ovary',
(int) 77 => 'Placenta',
(int) 78 => 'Testis'
)
),
'CIL_0007L6_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000039782' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Breast',
(int) 15 => 'Testis',
(int) 16 => 'Testis',
(int) 17 => 'Colon',
(int) 18 => 'Liver',
(int) 19 => 'Lung',
(int) 20 => 'Ovary',
(int) 21 => 'Testis',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Kidney',
(int) 30 => 'Liver',
(int) 31 => 'Lung',
(int) 32 => 'Muscle',
(int) 33 => 'Ovary',
(int) 34 => 'Placenta'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007L6_0003',
'tax_id' => '7955',
'chromosome' => '23',
'seq_start' => '2184582',
'seq_end' => '2185451',
'region_length' => '869',
'region_type' => 'UCNEbase',
'el_id' => 'CPEB2'
)
)
$gene_el = array(
'ENSMUST00000114065' => array(
'Adipose' => array(
'average_FPKM' => '2.481',
'stddev_FPKM' => '0.43'
),
'Adrenal' => array(
'average_FPKM' => '2.858',
'stddev_FPKM' => '0.12'
),
'Bladder' => array(
'average_FPKM' => '4.117',
'stddev_FPKM' => '1.94'
),
'Brain' => array(
'average_FPKM' => '6.665',
'stddev_FPKM' => '2.78'
),
'Breast' => array(
'average_FPKM' => '1.390',
'stddev_FPKM' => '0.96'
),
'Colon' => array(
'average_FPKM' => '1.505',
'stddev_FPKM' => '0.42'
),
'Heart' => array(
'average_FPKM' => '2.561',
'stddev_FPKM' => '0.42'
),
'Kidney' => array(
'average_FPKM' => '2.463',
'stddev_FPKM' => '0.48'
),
'Liver' => array(
'average_FPKM' => '1.826',
'stddev_FPKM' => '1.05'
),
'Lung' => array(
'average_FPKM' => '2.770',
'stddev_FPKM' => '0.81'
),
'Muscle' => array(
'average_FPKM' => '2.179',
'stddev_FPKM' => '0.40'
),
'Ovary' => array(
'average_FPKM' => '1.838',
'stddev_FPKM' => '0.68'
),
'Placenta' => array(
'average_FPKM' => '2.817',
'stddev_FPKM' => '0.87'
),
'Testis' => array(
'average_FPKM' => '9.272',
'stddev_FPKM' => '7.25'
)
),
'ENSMUST00000114066' => array(
'Breast' => array(
'average_FPKM' => '1.251',
'stddev_FPKM' => '0.28'
),
'Testis' => array(
'average_FPKM' => '44.409',
'stddev_FPKM' => '16.71'
)
),
'ENSMUST00000127599' => array(
'Testis' => array(
'average_FPKM' => '46.634',
'stddev_FPKM' => '0.00'
)
),
'ENSMUST00000166713' => array(
'Colon' => array(
'average_FPKM' => '0.483',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.476',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.247',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.430',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '15.577',
'stddev_FPKM' => '8.09'
)
),
'ENSMUST00000169035' => array(
'Adipose' => array(
'average_FPKM' => '0.919',
'stddev_FPKM' => '0.40'
),
'Adrenal' => array(
'average_FPKM' => '1.738',
'stddev_FPKM' => '0.12'
),
'Bladder' => array(
'average_FPKM' => '1.974',
'stddev_FPKM' => '0.49'
),
'Brain' => array(
'average_FPKM' => '3.308',
'stddev_FPKM' => '2.38'
),
'Breast' => array(
'average_FPKM' => '1.208',
'stddev_FPKM' => '0.63'
),
'Colon' => array(
'average_FPKM' => '0.931',
'stddev_FPKM' => '0.50'
),
'Heart' => array(
'average_FPKM' => '0.692',
'stddev_FPKM' => '0.09'
),
'Kidney' => array(
'average_FPKM' => '0.553',
'stddev_FPKM' => '0.08'
),
'Liver' => array(
'average_FPKM' => '0.445',
'stddev_FPKM' => '0.15'
),
'Lung' => array(
'average_FPKM' => '0.470',
'stddev_FPKM' => '0.22'
),
'Muscle' => array(
'average_FPKM' => '0.866',
'stddev_FPKM' => '0.22'
),
'Ovary' => array(
'average_FPKM' => '0.608',
'stddev_FPKM' => '0.35'
),
'Placenta' => array(
'average_FPKM' => '1.023',
'stddev_FPKM' => '0.34'
)
)
)
$gene_key = 'ENSMUSG00000039782'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.919',
'stddev_FPKM' => '0.40'
),
'Adrenal' => array(
'average_FPKM' => '1.738',
'stddev_FPKM' => '0.12'
),
'Bladder' => array(
'average_FPKM' => '1.974',
'stddev_FPKM' => '0.49'
),
'Brain' => array(
'average_FPKM' => '3.308',
'stddev_FPKM' => '2.38'
),
'Breast' => array(
'average_FPKM' => '1.208',
'stddev_FPKM' => '0.63'
),
'Colon' => array(
'average_FPKM' => '0.931',
'stddev_FPKM' => '0.50'
),
'Heart' => array(
'average_FPKM' => '0.692',
'stddev_FPKM' => '0.09'
),
'Kidney' => array(
'average_FPKM' => '0.553',
'stddev_FPKM' => '0.08'
),
'Liver' => array(
'average_FPKM' => '0.445',
'stddev_FPKM' => '0.15'
),
'Lung' => array(
'average_FPKM' => '0.470',
'stddev_FPKM' => '0.22'
),
'Muscle' => array(
'average_FPKM' => '0.866',
'stddev_FPKM' => '0.22'
),
'Ovary' => array(
'average_FPKM' => '0.608',
'stddev_FPKM' => '0.35'
),
'Placenta' => array(
'average_FPKM' => '1.023',
'stddev_FPKM' => '0.34'
)
)
$tran_key = 'ENSMUST00000169035'
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
(CPEB2)