| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000006585-ENSMUSG00000006589 |
CGP |
10090 |
8:122568015-122576907  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00057H_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_00057H_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000003519' => 'adenine phosphoribosyl transferase',
'ENSDARG00000051854' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000167513' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000198931' => 'adenine phosphoribosyltransferase',
'ENSMUSG00000006585' => 'chromatin licensing and DNA replication factor 1',
'ENSMUSG00000006589' => 'adenine phosphoribosyl transferase'
),
'gene_name_arr' => array(
'ENSDARG00000003519' => 'aprt',
'ENSDARG00000051854' => 'cdt1',
'ENSG00000167513' => 'CDT1',
'ENSG00000198931' => 'APRT',
'ENSMUSG00000006585' => 'Cdt1',
'ENSMUSG00000006589' => 'Aprt'
),
'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) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 19 => 'Breast',
(int) 25 => 'Colon',
(int) 31 => 'Heart',
(int) 38 => 'Kidney',
(int) 45 => 'Liver',
(int) 56 => 'Lung',
(int) 62 => 'Muscle',
(int) 69 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000013796' => array(
'start' => '56795987',
'end' => '56803001',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-002'
),
'ENSDART00000148514' => array(
'start' => '56793796',
'end' => '56803068',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-001'
),
'ENSDART00000098476' => array(
'start' => '56781782',
'end' => '56793875',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-001'
),
'ENSDART00000149915' => array(
'start' => '56781880',
'end' => '56790942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-002'
),
'ENST00000301019' => array(
'start' => '88803213',
'end' => '88809258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-001'
),
'ENST00000562747' => array(
'start' => '88804611',
'end' => '88806217',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDT1-003'
),
'ENST00000569140' => array(
'start' => '88805768',
'end' => '88807342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-002'
),
'ENST00000378364' => array(
'start' => '88809339',
'end' => '88811944',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-001'
),
'ENST00000426324' => array(
'start' => '88809469',
'end' => '88811925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-002'
),
'ENST00000562464' => array(
'start' => '88809736',
'end' => '88811880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-006'
),
'ENST00000563655' => array(
'start' => '88809472',
'end' => '88811920',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-011'
),
'ENST00000564858' => array(
'start' => '88811174',
'end' => '88811920',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-003'
),
'ENST00000567057' => array(
'start' => '88809469',
'end' => '88810268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-005'
),
'ENST00000567391' => array(
'start' => '88809469',
'end' => '88811928',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-010'
),
'ENST00000567713' => array(
'start' => '88809411',
'end' => '88811923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-007'
),
'ENST00000568319' => array(
'start' => '88809469',
'end' => '88811937',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-009'
),
'ENST00000568575' => array(
'start' => '88809680',
'end' => '88810398',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-004'
),
'ENST00000569616' => array(
'start' => '88809518',
'end' => '88811897',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-008'
),
'ENSMUST00000006760' => array(
'start' => '122568015',
'end' => '122573128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdt1-201'
),
'ENSMUST00000006764' => array(
'start' => '122574637',
'end' => '122576907',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aprt-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_00057H_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00057H_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003519' => array(
[maximum depth reached]
),
'ENSDARG00000051854' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Muscle',
(int) 1 => 'Brain',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Brain',
(int) 7 => 'Heart',
(int) 8 => 'Kidney',
(int) 9 => 'Liver',
(int) 10 => 'Liver'
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
'ENSG00000167513' => array(
[maximum depth reached]
),
'ENSG00000198931' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Placenta',
(int) 16 => 'Brain',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Placenta',
(int) 46 => 'Testis',
(int) 47 => 'Adrenal',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Testis',
(int) 56 => 'Liver',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Brain',
(int) 60 => 'Muscle',
(int) 61 => 'Ovary',
(int) 62 => 'Brain',
(int) 63 => 'Adrenal',
(int) 64 => 'Breast',
(int) 65 => 'Adipose',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000003519' => 'adenine phosphoribosyl transferase',
'ENSDARG00000051854' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000167513' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000198931' => 'adenine phosphoribosyltransferase',
'ENSMUSG00000006585' => 'chromatin licensing and DNA replication factor 1',
'ENSMUSG00000006589' => 'adenine phosphoribosyl transferase'
)
$gene_name_arr = array(
'ENSDARG00000003519' => 'aprt',
'ENSDARG00000051854' => 'cdt1',
'ENSG00000167513' => 'CDT1',
'ENSG00000198931' => 'APRT',
'ENSMUSG00000006585' => 'Cdt1',
'ENSMUSG00000006589' => 'Aprt'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '56781782',
'seq_end' => '56803068',
'region_length' => '21286',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000051854-ENSDARG00000003519'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '88803213',
'seq_end' => '88811944',
'region_length' => '8731',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167513-ENSG00000198931'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122568015',
'seq_end' => '122576907',
'region_length' => '8892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006585-ENSMUSG00000006589'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 19 => 'Breast',
(int) 25 => 'Colon',
(int) 31 => 'Heart',
(int) 38 => 'Kidney',
(int) 45 => 'Liver',
(int) 56 => 'Lung',
(int) 62 => 'Muscle',
(int) 69 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000013796' => array(
'start' => '56795987',
'end' => '56803001',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-002'
),
'ENSDART00000148514' => array(
'start' => '56793796',
'end' => '56803068',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-001'
),
'ENSDART00000098476' => array(
'start' => '56781782',
'end' => '56793875',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-001'
),
'ENSDART00000149915' => array(
'start' => '56781880',
'end' => '56790942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-002'
),
'ENST00000301019' => array(
'start' => '88803213',
'end' => '88809258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-001'
),
'ENST00000562747' => array(
'start' => '88804611',
'end' => '88806217',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDT1-003'
),
'ENST00000569140' => array(
'start' => '88805768',
'end' => '88807342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-002'
),
'ENST00000378364' => array(
'start' => '88809339',
'end' => '88811944',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-001'
),
'ENST00000426324' => array(
'start' => '88809469',
'end' => '88811925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-002'
),
'ENST00000562464' => array(
'start' => '88809736',
'end' => '88811880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-006'
),
'ENST00000563655' => array(
'start' => '88809472',
'end' => '88811920',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-011'
),
'ENST00000564858' => array(
'start' => '88811174',
'end' => '88811920',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-003'
),
'ENST00000567057' => array(
'start' => '88809469',
'end' => '88810268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-005'
),
'ENST00000567391' => array(
'start' => '88809469',
'end' => '88811928',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-010'
),
'ENST00000567713' => array(
'start' => '88809411',
'end' => '88811923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-007'
),
'ENST00000568319' => array(
'start' => '88809469',
'end' => '88811937',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-009'
),
'ENST00000568575' => array(
'start' => '88809680',
'end' => '88810398',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-004'
),
'ENST00000569616' => array(
'start' => '88809518',
'end' => '88811897',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-008'
),
'ENSMUST00000006760' => array(
'start' => '122568015',
'end' => '122573128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdt1-201'
),
'ENSMUST00000006764' => array(
'start' => '122574637',
'end' => '122576907',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aprt-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_00057H_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003519' => array(
[maximum depth reached]
),
'ENSDARG00000051854' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Muscle',
(int) 1 => 'Brain',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Brain',
(int) 7 => 'Heart',
(int) 8 => 'Kidney',
(int) 9 => 'Liver',
(int) 10 => 'Liver'
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
'ENSG00000167513' => array(
[maximum depth reached]
),
'ENSG00000198931' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Placenta',
(int) 16 => 'Brain',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Placenta',
(int) 46 => 'Testis',
(int) 47 => 'Adrenal',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Testis',
(int) 56 => 'Liver',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Brain',
(int) 60 => 'Muscle',
(int) 61 => 'Ovary',
(int) 62 => 'Brain',
(int) 63 => 'Adrenal',
(int) 64 => 'Breast',
(int) 65 => 'Adipose',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122568015',
'seq_end' => '122576907',
'region_length' => '8892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006585-ENSMUSG00000006589'
)
)
$gene_el = array(
'ENST00000378364' => array(
'Bladder' => array(
'average_FPKM' => '0.935',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.997',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '4.792',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '1.543',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '8.509',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.569',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '2.531',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.909',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '20.156',
'stddev_FPKM' => '11.44'
),
'Placenta' => array(
'average_FPKM' => '51.315',
'stddev_FPKM' => '27.82'
),
'Testis' => array(
'average_FPKM' => '3.480',
'stddev_FPKM' => '0.00'
)
),
'ENST00000426324' => array(
'Adipose' => array(
'average_FPKM' => '23.364',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '52.577',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '8.886',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '11.335',
'stddev_FPKM' => '9.51'
),
'Colon' => array(
'average_FPKM' => '17.599',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '7.651',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '34.749',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '34.061',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '35.815',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '15.253',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '29.761',
'stddev_FPKM' => '13.30'
),
'Placenta' => array(
'average_FPKM' => '46.663',
'stddev_FPKM' => '27.74'
),
'Testis' => array(
'average_FPKM' => '14.426',
'stddev_FPKM' => '7.37'
)
),
'ENST00000562464' => array(
'Liver' => array(
'average_FPKM' => '0.236',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '27.465',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '10.886',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '3.118',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563655' => array(
'Adrenal' => array(
'average_FPKM' => '31.571',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '8.726',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '9.914',
'stddev_FPKM' => '9.39'
),
'Colon' => array(
'average_FPKM' => '21.710',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '5.254',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '37.304',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '31.477',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '37.565',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '23.067',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564858' => array(
'Liver' => array(
'average_FPKM' => '0.449',
'stddev_FPKM' => '0.00'
)
),
'ENST00000567057' => array(),
'ENST00000567391' => array(
'Adipose' => array(
'average_FPKM' => '18.578',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '17.329',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '1.056',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '11.988',
'stddev_FPKM' => '7.95'
),
'Ovary' => array(
'average_FPKM' => '18.261',
'stddev_FPKM' => '0.00'
)
),
'ENST00000567713' => array(),
'ENST00000568319' => array(
'Brain' => array(
'average_FPKM' => '2.098',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568575' => array(
'Adrenal' => array(
'average_FPKM' => '18.081',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.499',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569616' => array(
'Adipose' => array(
'average_FPKM' => '15.962',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '20.574',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '18.429',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '7.046',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '15.442',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '19.438',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '11.517',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '9.752',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '6.832',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '8.811',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000198931'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '15.962',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '20.574',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '18.429',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '7.046',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '15.442',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '19.438',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '11.517',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '9.752',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '6.832',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '8.811',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000569616'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00057H_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000003519' => 'adenine phosphoribosyl transferase',
'ENSDARG00000051854' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000167513' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000198931' => 'adenine phosphoribosyltransferase',
'ENSMUSG00000006585' => 'chromatin licensing and DNA replication factor 1',
'ENSMUSG00000006589' => 'adenine phosphoribosyl transferase'
),
'gene_name_arr' => array(
'ENSDARG00000003519' => 'aprt',
'ENSDARG00000051854' => 'cdt1',
'ENSG00000167513' => 'CDT1',
'ENSG00000198931' => 'APRT',
'ENSMUSG00000006585' => 'Cdt1',
'ENSMUSG00000006589' => 'Aprt'
),
'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) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 19 => 'Breast',
(int) 25 => 'Colon',
(int) 31 => 'Heart',
(int) 38 => 'Kidney',
(int) 45 => 'Liver',
(int) 56 => 'Lung',
(int) 62 => 'Muscle',
(int) 69 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 20,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000013796' => array(
'start' => '56795987',
'end' => '56803001',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-002'
),
'ENSDART00000148514' => array(
'start' => '56793796',
'end' => '56803068',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-001'
),
'ENSDART00000098476' => array(
'start' => '56781782',
'end' => '56793875',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-001'
),
'ENSDART00000149915' => array(
'start' => '56781880',
'end' => '56790942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-002'
),
'ENST00000301019' => array(
'start' => '88803213',
'end' => '88809258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-001'
),
'ENST00000562747' => array(
'start' => '88804611',
'end' => '88806217',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDT1-003'
),
'ENST00000569140' => array(
'start' => '88805768',
'end' => '88807342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-002'
),
'ENST00000378364' => array(
'start' => '88809339',
'end' => '88811944',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-001'
),
'ENST00000426324' => array(
'start' => '88809469',
'end' => '88811925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-002'
),
'ENST00000562464' => array(
'start' => '88809736',
'end' => '88811880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-006'
),
'ENST00000563655' => array(
'start' => '88809472',
'end' => '88811920',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-011'
),
'ENST00000564858' => array(
'start' => '88811174',
'end' => '88811920',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-003'
),
'ENST00000567057' => array(
'start' => '88809469',
'end' => '88810268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-005'
),
'ENST00000567391' => array(
'start' => '88809469',
'end' => '88811928',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-010'
),
'ENST00000567713' => array(
'start' => '88809411',
'end' => '88811923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-007'
),
'ENST00000568319' => array(
'start' => '88809469',
'end' => '88811937',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-009'
),
'ENST00000568575' => array(
'start' => '88809680',
'end' => '88810398',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-004'
),
'ENST00000569616' => array(
'start' => '88809518',
'end' => '88811897',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-008'
),
'ENSMUST00000006760' => array(
'start' => '122568015',
'end' => '122573128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdt1-201'
),
'ENSMUST00000006764' => array(
'start' => '122574637',
'end' => '122576907',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aprt-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_00057H_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00057H_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003519' => array(
[maximum depth reached]
),
'ENSDARG00000051854' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Muscle',
(int) 1 => 'Brain',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Brain',
(int) 7 => 'Heart',
(int) 8 => 'Kidney',
(int) 9 => 'Liver',
(int) 10 => 'Liver'
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
'ENSG00000167513' => array(
[maximum depth reached]
),
'ENSG00000198931' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Placenta',
(int) 16 => 'Brain',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Placenta',
(int) 46 => 'Testis',
(int) 47 => 'Adrenal',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Testis',
(int) 56 => 'Liver',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Brain',
(int) 60 => 'Muscle',
(int) 61 => 'Ovary',
(int) 62 => 'Brain',
(int) 63 => 'Adrenal',
(int) 64 => 'Breast',
(int) 65 => 'Adipose',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000003519' => 'adenine phosphoribosyl transferase',
'ENSDARG00000051854' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000167513' => 'chromatin licensing and DNA replication factor 1',
'ENSG00000198931' => 'adenine phosphoribosyltransferase',
'ENSMUSG00000006585' => 'chromatin licensing and DNA replication factor 1',
'ENSMUSG00000006589' => 'adenine phosphoribosyl transferase'
)
$gene_name_arr = array(
'ENSDARG00000003519' => 'aprt',
'ENSDARG00000051854' => 'cdt1',
'ENSG00000167513' => 'CDT1',
'ENSG00000198931' => 'APRT',
'ENSMUSG00000006585' => 'Cdt1',
'ENSMUSG00000006589' => 'Aprt'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0001',
'tax_id' => '7955',
'chromosome' => '7',
'seq_start' => '56781782',
'seq_end' => '56803068',
'region_length' => '21286',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000051854-ENSDARG00000003519'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0002',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '88803213',
'seq_end' => '88811944',
'region_length' => '8731',
'region_type' => 'CGP',
'el_id' => 'ENSG00000167513-ENSG00000198931'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122568015',
'seq_end' => '122576907',
'region_length' => '8892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006585-ENSMUSG00000006589'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 9 => 'Bladder',
(int) 10 => 'Brain',
(int) 19 => 'Breast',
(int) 25 => 'Colon',
(int) 31 => 'Heart',
(int) 38 => 'Kidney',
(int) 45 => 'Liver',
(int) 56 => 'Lung',
(int) 62 => 'Muscle',
(int) 69 => 'Ovary',
(int) 74 => 'Placenta',
(int) 80 => '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) 20
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000013796' => array(
'start' => '56795987',
'end' => '56803001',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-002'
),
'ENSDART00000148514' => array(
'start' => '56793796',
'end' => '56803068',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'aprt-001'
),
'ENSDART00000098476' => array(
'start' => '56781782',
'end' => '56793875',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-001'
),
'ENSDART00000149915' => array(
'start' => '56781880',
'end' => '56790942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cdt1-002'
),
'ENST00000301019' => array(
'start' => '88803213',
'end' => '88809258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-001'
),
'ENST00000562747' => array(
'start' => '88804611',
'end' => '88806217',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CDT1-003'
),
'ENST00000569140' => array(
'start' => '88805768',
'end' => '88807342',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CDT1-002'
),
'ENST00000378364' => array(
'start' => '88809339',
'end' => '88811944',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-001'
),
'ENST00000426324' => array(
'start' => '88809469',
'end' => '88811925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-002'
),
'ENST00000562464' => array(
'start' => '88809736',
'end' => '88811880',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-006'
),
'ENST00000563655' => array(
'start' => '88809472',
'end' => '88811920',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-011'
),
'ENST00000564858' => array(
'start' => '88811174',
'end' => '88811920',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-003'
),
'ENST00000567057' => array(
'start' => '88809469',
'end' => '88810268',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-005'
),
'ENST00000567391' => array(
'start' => '88809469',
'end' => '88811928',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-010'
),
'ENST00000567713' => array(
'start' => '88809411',
'end' => '88811923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-007'
),
'ENST00000568319' => array(
'start' => '88809469',
'end' => '88811937',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'APRT-009'
),
'ENST00000568575' => array(
'start' => '88809680',
'end' => '88810398',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'APRT-004'
),
'ENST00000569616' => array(
'start' => '88809518',
'end' => '88811897',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'APRT-008'
),
'ENSMUST00000006760' => array(
'start' => '122568015',
'end' => '122573128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cdt1-201'
),
'ENSMUST00000006764' => array(
'start' => '122574637',
'end' => '122576907',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Aprt-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_00057H_0001' => array(
'genes_in_region' => array(
'ENSDARG00000003519' => array(
[maximum depth reached]
),
'ENSDARG00000051854' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Muscle',
(int) 1 => 'Brain',
(int) 2 => 'Heart',
(int) 3 => 'Kidney',
(int) 4 => 'Liver',
(int) 5 => 'Muscle',
(int) 6 => 'Brain',
(int) 7 => 'Heart',
(int) 8 => 'Kidney',
(int) 9 => 'Liver',
(int) 10 => 'Liver'
)
),
'CIL_00057H_0002' => array(
'genes_in_region' => array(
'ENSG00000167513' => array(
[maximum depth reached]
),
'ENSG00000198931' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Breast',
(int) 14 => 'Colon',
(int) 15 => 'Placenta',
(int) 16 => 'Brain',
(int) 17 => 'Liver',
(int) 18 => 'Lung',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Colon',
(int) 22 => 'Heart',
(int) 23 => 'Kidney',
(int) 24 => 'Liver',
(int) 25 => 'Lung',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Liver',
(int) 44 => 'Ovary',
(int) 45 => 'Placenta',
(int) 46 => 'Testis',
(int) 47 => 'Adrenal',
(int) 48 => 'Brain',
(int) 49 => 'Breast',
(int) 50 => 'Colon',
(int) 51 => 'Heart',
(int) 52 => 'Kidney',
(int) 53 => 'Liver',
(int) 54 => 'Lung',
(int) 55 => 'Testis',
(int) 56 => 'Liver',
(int) 57 => 'Adipose',
(int) 58 => 'Adrenal',
(int) 59 => 'Brain',
(int) 60 => 'Muscle',
(int) 61 => 'Ovary',
(int) 62 => 'Brain',
(int) 63 => 'Adrenal',
(int) 64 => 'Breast',
(int) 65 => 'Adipose',
(int) 66 => 'Breast',
(int) 67 => 'Colon',
(int) 68 => 'Heart',
(int) 69 => 'Kidney',
(int) 70 => 'Liver',
(int) 71 => 'Lung',
(int) 72 => 'Muscle',
(int) 73 => 'Placenta',
(int) 74 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00057H_0003',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '122568015',
'seq_end' => '122576907',
'region_length' => '8892',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000006585-ENSMUSG00000006589'
)
)
$gene_el = array(
'ENST00000378364' => array(
'Bladder' => array(
'average_FPKM' => '0.935',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.997',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '4.792',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '1.543',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '8.509',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.569',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '2.531',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.909',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '20.156',
'stddev_FPKM' => '11.44'
),
'Placenta' => array(
'average_FPKM' => '51.315',
'stddev_FPKM' => '27.82'
),
'Testis' => array(
'average_FPKM' => '3.480',
'stddev_FPKM' => '0.00'
)
),
'ENST00000426324' => array(
'Adipose' => array(
'average_FPKM' => '23.364',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '52.577',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '8.886',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '11.335',
'stddev_FPKM' => '9.51'
),
'Colon' => array(
'average_FPKM' => '17.599',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '7.651',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '34.749',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '34.061',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '35.815',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '15.253',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '29.761',
'stddev_FPKM' => '13.30'
),
'Placenta' => array(
'average_FPKM' => '46.663',
'stddev_FPKM' => '27.74'
),
'Testis' => array(
'average_FPKM' => '14.426',
'stddev_FPKM' => '7.37'
)
),
'ENST00000562464' => array(
'Liver' => array(
'average_FPKM' => '0.236',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '27.465',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '10.886',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '3.118',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563655' => array(
'Adrenal' => array(
'average_FPKM' => '31.571',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '8.726',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '9.914',
'stddev_FPKM' => '9.39'
),
'Colon' => array(
'average_FPKM' => '21.710',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '5.254',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '37.304',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '31.477',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '37.565',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '23.067',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564858' => array(
'Liver' => array(
'average_FPKM' => '0.449',
'stddev_FPKM' => '0.00'
)
),
'ENST00000567057' => array(),
'ENST00000567391' => array(
'Adipose' => array(
'average_FPKM' => '18.578',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '17.329',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '1.056',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '11.988',
'stddev_FPKM' => '7.95'
),
'Ovary' => array(
'average_FPKM' => '18.261',
'stddev_FPKM' => '0.00'
)
),
'ENST00000567713' => array(),
'ENST00000568319' => array(
'Brain' => array(
'average_FPKM' => '2.098',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568575' => array(
'Adrenal' => array(
'average_FPKM' => '18.081',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.499',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569616' => array(
'Adipose' => array(
'average_FPKM' => '15.962',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '20.574',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '18.429',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '7.046',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '15.442',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '19.438',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '11.517',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '9.752',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '6.832',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '8.811',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000198931'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '15.962',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '20.574',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '18.429',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '7.046',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '15.442',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '19.438',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '11.517',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '9.752',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '6.832',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '8.811',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000569616'
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
(aprt)