Notice (8): Undefined index: CIL_0007OT_0004 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0007OT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000125484' => 'general transcription factor IIIC, polypeptide 4, 90kDa',
'ENSG00000125485' => 'DEAD (Asp-Glu-Ala-Asp) box polypeptide 31',
'ENSG00000165695' => 'adenylate kinase 8',
'ENSG00000224992' => null,
'ENSG00000276629' => null,
'ENSMUSG00000026806' => 'DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31',
'ENSMUSG00000026807' => 'adenylate kinase 8',
'ENSMUSG00000035666' => 'general transcription factor IIIC, polypeptide 4',
'ENSMUSG00000082796' => 'predicted gene 13385',
'ENSMUSG00000083115' => 'predicted gene 13386',
'ENSMUSG00000092832' => 'microRNA 3088'
),
'gene_name_arr' => array(
'ENSG00000125484' => 'GTF3C4',
'ENSG00000125485' => 'DDX31',
'ENSG00000165695' => 'AK8',
'ENSG00000224992' => 'RP11-295G24.5',
'ENSG00000276629' => 'AL160165.1',
'ENSMUSG00000026806' => 'Ddx31',
'ENSMUSG00000026807' => 'Ak8',
'ENSMUSG00000035666' => 'Gtf3c4',
'ENSMUSG00000082796' => 'Gm13385',
'ENSMUSG00000083115' => 'Gm13386',
'ENSMUSG00000092832' => 'Mir3088'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 34 => 'Breast',
(int) 43 => 'Colon',
(int) 52 => 'Heart',
(int) 59 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 89 => 'Ovary',
(int) 101 => 'Placenta',
(int) 110 => '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) 30,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000372146' => array(
'start' => '132670035',
'end' => '132694955',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-001'
),
'ENST00000483873' => array(
'start' => '132670035',
'end' => '132679310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-002'
),
'ENST00000310532' => array(
'start' => '132637863',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-003'
),
'ENST00000372153' => array(
'start' => '132594289',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-201'
),
'ENST00000372155' => array(
'start' => '132592997',
'end' => '132612313',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-002'
),
'ENST00000372159' => array(
'start' => '132592997',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-001'
),
'ENST00000438527' => array(
'start' => '132594386',
'end' => '132670027',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-006'
),
'ENST00000480876' => array(
'start' => '132658081',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-004'
),
'ENST00000482620' => array(
'start' => '132661076',
'end' => '132670401',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-005'
),
'ENST00000298545' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'AK8-001'
),
'ENST00000467161' => array(
'start' => '132725583',
'end' => '132727598',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-005'
),
'ENST00000476719' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-003'
),
'ENST00000477396' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-002'
),
'ENST00000482422' => array(
'start' => '132861396',
'end' => '132863712',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-004'
),
'ENST00000451318' => array(
'start' => '132769453',
'end' => '132770212',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-295G24.5-001'
),
'ENST00000620273' => array(
'start' => '132623250',
'end' => '132623333',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL160165.1-201'
),
'ENSMUST00000113853' => array(
'start' => '28840459',
'end' => '28905571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ddx31-001'
),
'ENSMUST00000147071' => array(
'start' => '28844902',
'end' => '28856231',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-003'
),
'ENSMUST00000147779' => array(
'start' => '28840406',
'end' => '28847511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-002'
),
'ENSMUST00000152685' => array(
'start' => '28857141',
'end' => '28860077',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-004'
),
'ENSMUST00000074156' => array(
'start' => '28700164',
'end' => '28813165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ak8-001'
),
'ENSMUST00000123794' => array(
'start' => '28700207',
'end' => '28734444',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-002'
),
'ENSMUST00000137588' => array(
'start' => '28742250',
'end' => '28760136',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-003'
),
'ENSMUST00000037117' => array(
'start' => '28822305',
'end' => '28840286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-001'
),
'ENSMUST00000124390' => array(
'start' => '28835304',
'end' => '28840352',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-002'
),
'ENSMUST00000156468' => array(
'start' => '28835204',
'end' => '28840286',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-003'
),
'ENSMUST00000171404' => array(
'start' => '28822299',
'end' => '28840360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-201'
),
'ENSMUST00000121089' => array(
'start' => '28793350',
'end' => '28793569',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13385-001'
),
'ENSMUST00000117677' => array(
'start' => '28807708',
'end' => '28807831',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13386-001'
),
'ENSMUST00000175091' => array(
'start' => '28733278',
'end' => '28733351',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3088-201'
)
),
'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_0007OT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007OT_0001' => array(
'genes_in_region' => array(
'ENSG00000125484' => array(
[maximum depth reached]
),
'ENSG00000165695' => array(
[maximum depth reached]
),
'ENSG00000224992' => array(
[maximum depth reached]
),
'ENSG00000276629' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Kidney',
(int) 29 => 'Lung',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Heart',
(int) 35 => 'Adipose',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Placenta',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain'
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000026806' => array(
[maximum depth reached]
),
'ENSMUSG00000026807' => array(
[maximum depth reached]
),
'ENSMUSG00000035666' => array(
[maximum depth reached]
),
'ENSMUSG00000082796' => array(
[maximum depth reached]
),
'ENSMUSG00000083115' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Ovary',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Breast',
(int) 34 => 'Muscle',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Ovary',
(int) 53 => 'Adrenal',
(int) 54 => 'Bladder',
(int) 55 => 'Brain',
(int) 56 => 'Breast',
(int) 57 => 'Colon',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Liver',
(int) 61 => 'Lung',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Brain',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000125484' => 'general transcription factor IIIC, polypeptide 4, 90kDa',
'ENSG00000125485' => 'DEAD (Asp-Glu-Ala-Asp) box polypeptide 31',
'ENSG00000165695' => 'adenylate kinase 8',
'ENSG00000224992' => null,
'ENSG00000276629' => null,
'ENSMUSG00000026806' => 'DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31',
'ENSMUSG00000026807' => 'adenylate kinase 8',
'ENSMUSG00000035666' => 'general transcription factor IIIC, polypeptide 4',
'ENSMUSG00000082796' => 'predicted gene 13385',
'ENSMUSG00000083115' => 'predicted gene 13386',
'ENSMUSG00000092832' => 'microRNA 3088'
)
$gene_name_arr = array(
'ENSG00000125484' => 'GTF3C4',
'ENSG00000125485' => 'DDX31',
'ENSG00000165695' => 'AK8',
'ENSG00000224992' => 'RP11-295G24.5',
'ENSG00000276629' => 'AL160165.1',
'ENSMUSG00000026806' => 'Ddx31',
'ENSMUSG00000026807' => 'Ak8',
'ENSMUSG00000035666' => 'Gtf3c4',
'ENSMUSG00000082796' => 'Gm13385',
'ENSMUSG00000083115' => 'Gm13386',
'ENSMUSG00000092832' => 'Mir3088'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0001',
'tax_id' => '9606',
'chromosome' => '9',
'seq_start' => '132620132',
'seq_end' => '132870600',
'region_length' => '250468',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '28706607',
'seq_end' => '28885151',
'region_length' => '178544',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0003',
'tax_id' => '7955',
'chromosome' => '21',
'seq_start' => '15893617',
'seq_end' => '15893787',
'region_length' => '170',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0004',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '31334650',
'seq_end' => '31346149',
'region_length' => '11499',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 34 => 'Breast',
(int) 43 => 'Colon',
(int) 52 => 'Heart',
(int) 59 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 89 => 'Ovary',
(int) 101 => 'Placenta',
(int) 110 => '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) 30
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000372146' => array(
'start' => '132670035',
'end' => '132694955',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-001'
),
'ENST00000483873' => array(
'start' => '132670035',
'end' => '132679310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-002'
),
'ENST00000310532' => array(
'start' => '132637863',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-003'
),
'ENST00000372153' => array(
'start' => '132594289',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-201'
),
'ENST00000372155' => array(
'start' => '132592997',
'end' => '132612313',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-002'
),
'ENST00000372159' => array(
'start' => '132592997',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-001'
),
'ENST00000438527' => array(
'start' => '132594386',
'end' => '132670027',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-006'
),
'ENST00000480876' => array(
'start' => '132658081',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-004'
),
'ENST00000482620' => array(
'start' => '132661076',
'end' => '132670401',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-005'
),
'ENST00000298545' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'AK8-001'
),
'ENST00000467161' => array(
'start' => '132725583',
'end' => '132727598',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-005'
),
'ENST00000476719' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-003'
),
'ENST00000477396' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-002'
),
'ENST00000482422' => array(
'start' => '132861396',
'end' => '132863712',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-004'
),
'ENST00000451318' => array(
'start' => '132769453',
'end' => '132770212',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-295G24.5-001'
),
'ENST00000620273' => array(
'start' => '132623250',
'end' => '132623333',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL160165.1-201'
),
'ENSMUST00000113853' => array(
'start' => '28840459',
'end' => '28905571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ddx31-001'
),
'ENSMUST00000147071' => array(
'start' => '28844902',
'end' => '28856231',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-003'
),
'ENSMUST00000147779' => array(
'start' => '28840406',
'end' => '28847511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-002'
),
'ENSMUST00000152685' => array(
'start' => '28857141',
'end' => '28860077',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-004'
),
'ENSMUST00000074156' => array(
'start' => '28700164',
'end' => '28813165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ak8-001'
),
'ENSMUST00000123794' => array(
'start' => '28700207',
'end' => '28734444',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-002'
),
'ENSMUST00000137588' => array(
'start' => '28742250',
'end' => '28760136',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-003'
),
'ENSMUST00000037117' => array(
'start' => '28822305',
'end' => '28840286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-001'
),
'ENSMUST00000124390' => array(
'start' => '28835304',
'end' => '28840352',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-002'
),
'ENSMUST00000156468' => array(
'start' => '28835204',
'end' => '28840286',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-003'
),
'ENSMUST00000171404' => array(
'start' => '28822299',
'end' => '28840360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-201'
),
'ENSMUST00000121089' => array(
'start' => '28793350',
'end' => '28793569',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13385-001'
),
'ENSMUST00000117677' => array(
'start' => '28807708',
'end' => '28807831',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13386-001'
),
'ENSMUST00000175091' => array(
'start' => '28733278',
'end' => '28733351',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3088-201'
)
)
$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_0007OT_0001' => array(
'genes_in_region' => array(
'ENSG00000125484' => array(
[maximum depth reached]
),
'ENSG00000165695' => array(
[maximum depth reached]
),
'ENSG00000224992' => array(
[maximum depth reached]
),
'ENSG00000276629' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Kidney',
(int) 29 => 'Lung',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Heart',
(int) 35 => 'Adipose',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Placenta',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain'
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000026806' => array(
[maximum depth reached]
),
'ENSMUSG00000026807' => array(
[maximum depth reached]
),
'ENSMUSG00000035666' => array(
[maximum depth reached]
),
'ENSMUSG00000082796' => array(
[maximum depth reached]
),
'ENSMUSG00000083115' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Ovary',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Breast',
(int) 34 => 'Muscle',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Ovary',
(int) 53 => 'Adrenal',
(int) 54 => 'Bladder',
(int) 55 => 'Brain',
(int) 56 => 'Breast',
(int) 57 => 'Colon',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Liver',
(int) 61 => 'Lung',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Brain',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0004',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '31334650',
'seq_end' => '31346149',
'region_length' => '11499',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
)
$gene_el = array(
'ENSMUST00000117677' => array(
'Ovary' => array(
'average_FPKM' => '56.146',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '30.451',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '6.284',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000083115'
$is_first = false
$tran_el = array(
'Ovary' => array(
'average_FPKM' => '56.146',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '30.451',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '6.284',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000117677'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007OT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000125484' => 'general transcription factor IIIC, polypeptide 4, 90kDa',
'ENSG00000125485' => 'DEAD (Asp-Glu-Ala-Asp) box polypeptide 31',
'ENSG00000165695' => 'adenylate kinase 8',
'ENSG00000224992' => null,
'ENSG00000276629' => null,
'ENSMUSG00000026806' => 'DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31',
'ENSMUSG00000026807' => 'adenylate kinase 8',
'ENSMUSG00000035666' => 'general transcription factor IIIC, polypeptide 4',
'ENSMUSG00000082796' => 'predicted gene 13385',
'ENSMUSG00000083115' => 'predicted gene 13386',
'ENSMUSG00000092832' => 'microRNA 3088'
),
'gene_name_arr' => array(
'ENSG00000125484' => 'GTF3C4',
'ENSG00000125485' => 'DDX31',
'ENSG00000165695' => 'AK8',
'ENSG00000224992' => 'RP11-295G24.5',
'ENSG00000276629' => 'AL160165.1',
'ENSMUSG00000026806' => 'Ddx31',
'ENSMUSG00000026807' => 'Ak8',
'ENSMUSG00000035666' => 'Gtf3c4',
'ENSMUSG00000082796' => 'Gm13385',
'ENSMUSG00000083115' => 'Gm13386',
'ENSMUSG00000092832' => 'Mir3088'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 34 => 'Breast',
(int) 43 => 'Colon',
(int) 52 => 'Heart',
(int) 59 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 89 => 'Ovary',
(int) 101 => 'Placenta',
(int) 110 => '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) 30,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000372146' => array(
'start' => '132670035',
'end' => '132694955',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-001'
),
'ENST00000483873' => array(
'start' => '132670035',
'end' => '132679310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-002'
),
'ENST00000310532' => array(
'start' => '132637863',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-003'
),
'ENST00000372153' => array(
'start' => '132594289',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-201'
),
'ENST00000372155' => array(
'start' => '132592997',
'end' => '132612313',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-002'
),
'ENST00000372159' => array(
'start' => '132592997',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-001'
),
'ENST00000438527' => array(
'start' => '132594386',
'end' => '132670027',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-006'
),
'ENST00000480876' => array(
'start' => '132658081',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-004'
),
'ENST00000482620' => array(
'start' => '132661076',
'end' => '132670401',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-005'
),
'ENST00000298545' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'AK8-001'
),
'ENST00000467161' => array(
'start' => '132725583',
'end' => '132727598',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-005'
),
'ENST00000476719' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-003'
),
'ENST00000477396' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-002'
),
'ENST00000482422' => array(
'start' => '132861396',
'end' => '132863712',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-004'
),
'ENST00000451318' => array(
'start' => '132769453',
'end' => '132770212',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-295G24.5-001'
),
'ENST00000620273' => array(
'start' => '132623250',
'end' => '132623333',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL160165.1-201'
),
'ENSMUST00000113853' => array(
'start' => '28840459',
'end' => '28905571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ddx31-001'
),
'ENSMUST00000147071' => array(
'start' => '28844902',
'end' => '28856231',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-003'
),
'ENSMUST00000147779' => array(
'start' => '28840406',
'end' => '28847511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-002'
),
'ENSMUST00000152685' => array(
'start' => '28857141',
'end' => '28860077',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-004'
),
'ENSMUST00000074156' => array(
'start' => '28700164',
'end' => '28813165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ak8-001'
),
'ENSMUST00000123794' => array(
'start' => '28700207',
'end' => '28734444',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-002'
),
'ENSMUST00000137588' => array(
'start' => '28742250',
'end' => '28760136',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-003'
),
'ENSMUST00000037117' => array(
'start' => '28822305',
'end' => '28840286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-001'
),
'ENSMUST00000124390' => array(
'start' => '28835304',
'end' => '28840352',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-002'
),
'ENSMUST00000156468' => array(
'start' => '28835204',
'end' => '28840286',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-003'
),
'ENSMUST00000171404' => array(
'start' => '28822299',
'end' => '28840360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-201'
),
'ENSMUST00000121089' => array(
'start' => '28793350',
'end' => '28793569',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13385-001'
),
'ENSMUST00000117677' => array(
'start' => '28807708',
'end' => '28807831',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13386-001'
),
'ENSMUST00000175091' => array(
'start' => '28733278',
'end' => '28733351',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3088-201'
)
),
'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_0007OT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007OT_0001' => array(
'genes_in_region' => array(
'ENSG00000125484' => array(
[maximum depth reached]
),
'ENSG00000165695' => array(
[maximum depth reached]
),
'ENSG00000224992' => array(
[maximum depth reached]
),
'ENSG00000276629' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Kidney',
(int) 29 => 'Lung',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Heart',
(int) 35 => 'Adipose',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Placenta',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain'
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000026806' => array(
[maximum depth reached]
),
'ENSMUSG00000026807' => array(
[maximum depth reached]
),
'ENSMUSG00000035666' => array(
[maximum depth reached]
),
'ENSMUSG00000082796' => array(
[maximum depth reached]
),
'ENSMUSG00000083115' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Ovary',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Breast',
(int) 34 => 'Muscle',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Ovary',
(int) 53 => 'Adrenal',
(int) 54 => 'Bladder',
(int) 55 => 'Brain',
(int) 56 => 'Breast',
(int) 57 => 'Colon',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Liver',
(int) 61 => 'Lung',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Brain',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000125484' => 'general transcription factor IIIC, polypeptide 4, 90kDa',
'ENSG00000125485' => 'DEAD (Asp-Glu-Ala-Asp) box polypeptide 31',
'ENSG00000165695' => 'adenylate kinase 8',
'ENSG00000224992' => null,
'ENSG00000276629' => null,
'ENSMUSG00000026806' => 'DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31',
'ENSMUSG00000026807' => 'adenylate kinase 8',
'ENSMUSG00000035666' => 'general transcription factor IIIC, polypeptide 4',
'ENSMUSG00000082796' => 'predicted gene 13385',
'ENSMUSG00000083115' => 'predicted gene 13386',
'ENSMUSG00000092832' => 'microRNA 3088'
)
$gene_name_arr = array(
'ENSG00000125484' => 'GTF3C4',
'ENSG00000125485' => 'DDX31',
'ENSG00000165695' => 'AK8',
'ENSG00000224992' => 'RP11-295G24.5',
'ENSG00000276629' => 'AL160165.1',
'ENSMUSG00000026806' => 'Ddx31',
'ENSMUSG00000026807' => 'Ak8',
'ENSMUSG00000035666' => 'Gtf3c4',
'ENSMUSG00000082796' => 'Gm13385',
'ENSMUSG00000083115' => 'Gm13386',
'ENSMUSG00000092832' => 'Mir3088'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0001',
'tax_id' => '9606',
'chromosome' => '9',
'seq_start' => '132620132',
'seq_end' => '132870600',
'region_length' => '250468',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0002',
'tax_id' => '10090',
'chromosome' => '2',
'seq_start' => '28706607',
'seq_end' => '28885151',
'region_length' => '178544',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0003',
'tax_id' => '7955',
'chromosome' => '21',
'seq_start' => '15893617',
'seq_end' => '15893787',
'region_length' => '170',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0004',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '31334650',
'seq_end' => '31346149',
'region_length' => '11499',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 34 => 'Breast',
(int) 43 => 'Colon',
(int) 52 => 'Heart',
(int) 59 => 'Kidney',
(int) 67 => 'Liver',
(int) 75 => 'Lung',
(int) 83 => 'Muscle',
(int) 89 => 'Ovary',
(int) 101 => 'Placenta',
(int) 110 => '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) 30
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000372146' => array(
'start' => '132670035',
'end' => '132694955',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-001'
),
'ENST00000483873' => array(
'start' => '132670035',
'end' => '132679310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GTF3C4-002'
),
'ENST00000310532' => array(
'start' => '132637863',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-003'
),
'ENST00000372153' => array(
'start' => '132594289',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-201'
),
'ENST00000372155' => array(
'start' => '132592997',
'end' => '132612313',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-002'
),
'ENST00000372159' => array(
'start' => '132592997',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-001'
),
'ENST00000438527' => array(
'start' => '132594386',
'end' => '132670027',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-006'
),
'ENST00000480876' => array(
'start' => '132658081',
'end' => '132670401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DDX31-004'
),
'ENST00000482620' => array(
'start' => '132661076',
'end' => '132670401',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DDX31-005'
),
'ENST00000298545' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'AK8-001'
),
'ENST00000467161' => array(
'start' => '132725583',
'end' => '132727598',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-005'
),
'ENST00000476719' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-003'
),
'ENST00000477396' => array(
'start' => '132725578',
'end' => '132878777',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-002'
),
'ENST00000482422' => array(
'start' => '132861396',
'end' => '132863712',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'AK8-004'
),
'ENST00000451318' => array(
'start' => '132769453',
'end' => '132770212',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-295G24.5-001'
),
'ENST00000620273' => array(
'start' => '132623250',
'end' => '132623333',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AL160165.1-201'
),
'ENSMUST00000113853' => array(
'start' => '28840459',
'end' => '28905571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ddx31-001'
),
'ENSMUST00000147071' => array(
'start' => '28844902',
'end' => '28856231',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-003'
),
'ENSMUST00000147779' => array(
'start' => '28840406',
'end' => '28847511',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-002'
),
'ENSMUST00000152685' => array(
'start' => '28857141',
'end' => '28860077',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ddx31-004'
),
'ENSMUST00000074156' => array(
'start' => '28700164',
'end' => '28813165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ak8-001'
),
'ENSMUST00000123794' => array(
'start' => '28700207',
'end' => '28734444',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-002'
),
'ENSMUST00000137588' => array(
'start' => '28742250',
'end' => '28760136',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Ak8-003'
),
'ENSMUST00000037117' => array(
'start' => '28822305',
'end' => '28840286',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-001'
),
'ENSMUST00000124390' => array(
'start' => '28835304',
'end' => '28840352',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-002'
),
'ENSMUST00000156468' => array(
'start' => '28835204',
'end' => '28840286',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Gtf3c4-003'
),
'ENSMUST00000171404' => array(
'start' => '28822299',
'end' => '28840360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gtf3c4-201'
),
'ENSMUST00000121089' => array(
'start' => '28793350',
'end' => '28793569',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13385-001'
),
'ENSMUST00000117677' => array(
'start' => '28807708',
'end' => '28807831',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm13386-001'
),
'ENSMUST00000175091' => array(
'start' => '28733278',
'end' => '28733351',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Mir3088-201'
)
)
$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_0007OT_0001' => array(
'genes_in_region' => array(
'ENSG00000125484' => array(
[maximum depth reached]
),
'ENSG00000165695' => array(
[maximum depth reached]
),
'ENSG00000224992' => array(
[maximum depth reached]
),
'ENSG00000276629' => 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 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Brain',
(int) 28 => 'Kidney',
(int) 29 => 'Lung',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Adipose',
(int) 33 => 'Bladder',
(int) 34 => 'Heart',
(int) 35 => 'Adipose',
(int) 36 => 'Brain',
(int) 37 => 'Breast',
(int) 38 => 'Colon',
(int) 39 => 'Heart',
(int) 40 => 'Kidney',
(int) 41 => 'Liver',
(int) 42 => 'Lung',
(int) 43 => 'Ovary',
(int) 44 => 'Placenta',
(int) 45 => 'Testis',
(int) 46 => 'Adrenal',
(int) 47 => 'Brain'
)
),
'CIL_0007OT_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000026806' => array(
[maximum depth reached]
),
'ENSMUSG00000026807' => array(
[maximum depth reached]
),
'ENSMUSG00000035666' => array(
[maximum depth reached]
),
'ENSMUSG00000082796' => array(
[maximum depth reached]
),
'ENSMUSG00000083115' => 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 => 'Adrenal',
(int) 15 => 'Brain',
(int) 16 => 'Breast',
(int) 17 => 'Colon',
(int) 18 => 'Ovary',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Breast',
(int) 34 => 'Muscle',
(int) 35 => 'Placenta',
(int) 36 => 'Adipose',
(int) 37 => 'Adrenal',
(int) 38 => 'Bladder',
(int) 39 => 'Brain',
(int) 40 => 'Breast',
(int) 41 => 'Colon',
(int) 42 => 'Heart',
(int) 43 => 'Kidney',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adrenal',
(int) 51 => 'Colon',
(int) 52 => 'Ovary',
(int) 53 => 'Adrenal',
(int) 54 => 'Bladder',
(int) 55 => 'Brain',
(int) 56 => 'Breast',
(int) 57 => 'Colon',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Liver',
(int) 61 => 'Lung',
(int) 62 => 'Ovary',
(int) 63 => 'Testis',
(int) 64 => 'Brain',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Placenta',
(int) 68 => 'Testis',
(int) 69 => 'Ovary',
(int) 70 => 'Placenta',
(int) 71 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OT_0004',
'tax_id' => '7955',
'chromosome' => '5',
'seq_start' => '31334650',
'seq_end' => '31346149',
'region_length' => '11499',
'region_type' => 'UCNEbase',
'el_id' => 'BARHL1'
)
)
$gene_el = array(
'ENSMUST00000117677' => array(
'Ovary' => array(
'average_FPKM' => '56.146',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '30.451',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '6.284',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000083115'
$is_first = false
$tran_el = array(
'Ovary' => array(
'average_FPKM' => '56.146',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '30.451',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '6.284',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000117677'
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
| Source ID |
Type |
Tax ID |
Position |
| BARHL1 |
UCNEbase |
7955 |
5:31334650-31346149  |
| Gene | Transcript | Position | Biotype |
|---|
(GTF3C4)