| Source ID |
Type |
Tax ID |
Position |
| ENSG00000222046-ENSG00000160055 |
CGP |
9606 |
1:32209094-32222359  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0004JM_0002 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0004JM_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000053744' => 'doublecortin domain containing 2B',
'ENSDARG00000078333' => 'transmembrane protein 234',
'ENSG00000084623' => 'eukaryotic translation initiation factor 3, subunit I',
'ENSG00000160055' => 'transmembrane protein 234',
'ENSG00000222046' => 'doublecortin domain containing 2B'
),
'gene_name_arr' => array(
'ENSDARG00000053744' => 'dcdc2b',
'ENSDARG00000078333' => 'tmem234',
'ENSG00000084623' => 'EIF3I',
'ENSG00000160055' => 'TMEM234',
'ENSG00000222046' => 'DCDC2B'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 18 => 'Kidney',
(int) 21 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 32 => 'Ovary',
(int) 35 => 'Placenta',
(int) 38 => '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) 25,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000075826' => array(
'start' => '33527789',
'end' => '33538360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-001'
),
'ENSDART00000145295' => array(
'start' => '33527795',
'end' => '33531916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-002'
),
'ENSDART00000110295' => array(
'start' => '33538277',
'end' => '33540925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-001'
),
'ENSDART00000136701' => array(
'start' => '33538275',
'end' => '33541000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-002'
),
'ENSDART00000144848' => array(
'start' => '33538449',
'end' => '33540928',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-003'
),
'ENST00000355082' => array(
'start' => '32221928',
'end' => '32226295',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-005'
),
'ENST00000373586' => array(
'start' => '32222370',
'end' => '32231604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-001'
),
'ENST00000471486' => array(
'start' => '32222437',
'end' => '32228814',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-003'
),
'ENST00000474371' => array(
'start' => '32222545',
'end' => '32231054',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-004'
),
'ENST00000483517' => array(
'start' => '32222440',
'end' => '32229208',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-002'
),
'ENST00000489353' => array(
'start' => '32222407',
'end' => '32226472',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-006'
),
'ENST00000309777' => array(
'start' => '32216197',
'end' => '32222325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-001'
),
'ENST00000344461' => array(
'start' => '32216200',
'end' => '32222338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-009'
),
'ENST00000373593' => array(
'start' => '32216197',
'end' => '32222343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-005'
),
'ENST00000461402' => array(
'start' => '32214478',
'end' => '32222347',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-002'
),
'ENST00000466796' => array(
'start' => '32214472',
'end' => '32221196',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-006'
),
'ENST00000483001' => array(
'start' => '32215847',
'end' => '32222335',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-010'
),
'ENST00000484490' => array(
'start' => '32216357',
'end' => '32222359',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-011'
),
'ENST00000485689' => array(
'start' => '32216589',
'end' => '32217427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-008'
),
'ENST00000487174' => array(
'start' => '32216730',
'end' => '32222319',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-007'
),
'ENST00000489170' => array(
'start' => '32214477',
'end' => '32222348',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-003'
),
'ENST00000491434' => array(
'start' => '32214477',
'end' => '32222333',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-004'
),
'ENST00000495091' => array(
'start' => '32214477',
'end' => '32215795',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-012'
),
'ENST00000409358' => array(
'start' => '32209094',
'end' => '32216196',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCDC2B-002'
),
'ENST00000487056' => array(
'start' => '32209096',
'end' => '32216192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCDC2B-001'
)
),
'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_0004JM_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004JM_0001' => array(
'genes_in_region' => array(
'ENSDARG00000053744' => array(
[maximum depth reached]
),
'ENSDARG00000078333' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Muscle',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000053744' => 'doublecortin domain containing 2B',
'ENSDARG00000078333' => 'transmembrane protein 234',
'ENSG00000084623' => 'eukaryotic translation initiation factor 3, subunit I',
'ENSG00000160055' => 'transmembrane protein 234',
'ENSG00000222046' => 'doublecortin domain containing 2B'
)
$gene_name_arr = array(
'ENSDARG00000053744' => 'dcdc2b',
'ENSDARG00000078333' => 'tmem234',
'ENSG00000084623' => 'EIF3I',
'ENSG00000160055' => 'TMEM234',
'ENSG00000222046' => 'DCDC2B'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JM_0001',
'tax_id' => '7955',
'chromosome' => '13',
'seq_start' => '33527789',
'seq_end' => '33541000',
'region_length' => '13211',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000053744-ENSDARG00000078333'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JM_0002',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '32209094',
'seq_end' => '32222359',
'region_length' => '13265',
'region_type' => 'CGP',
'el_id' => 'ENSG00000222046-ENSG00000160055'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 18 => 'Kidney',
(int) 21 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 32 => 'Ovary',
(int) 35 => 'Placenta',
(int) 38 => '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) 25
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000075826' => array(
'start' => '33527789',
'end' => '33538360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-001'
),
'ENSDART00000145295' => array(
'start' => '33527795',
'end' => '33531916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-002'
),
'ENSDART00000110295' => array(
'start' => '33538277',
'end' => '33540925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-001'
),
'ENSDART00000136701' => array(
'start' => '33538275',
'end' => '33541000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-002'
),
'ENSDART00000144848' => array(
'start' => '33538449',
'end' => '33540928',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-003'
),
'ENST00000355082' => array(
'start' => '32221928',
'end' => '32226295',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-005'
),
'ENST00000373586' => array(
'start' => '32222370',
'end' => '32231604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-001'
),
'ENST00000471486' => array(
'start' => '32222437',
'end' => '32228814',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-003'
),
'ENST00000474371' => array(
'start' => '32222545',
'end' => '32231054',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-004'
),
'ENST00000483517' => array(
'start' => '32222440',
'end' => '32229208',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-002'
),
'ENST00000489353' => array(
'start' => '32222407',
'end' => '32226472',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-006'
),
'ENST00000309777' => array(
'start' => '32216197',
'end' => '32222325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-001'
),
'ENST00000344461' => array(
'start' => '32216200',
'end' => '32222338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-009'
),
'ENST00000373593' => array(
'start' => '32216197',
'end' => '32222343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-005'
),
'ENST00000461402' => array(
'start' => '32214478',
'end' => '32222347',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-002'
),
'ENST00000466796' => array(
'start' => '32214472',
'end' => '32221196',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-006'
),
'ENST00000483001' => array(
'start' => '32215847',
'end' => '32222335',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-010'
),
'ENST00000484490' => array(
'start' => '32216357',
'end' => '32222359',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-011'
),
'ENST00000485689' => array(
'start' => '32216589',
'end' => '32217427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-008'
),
'ENST00000487174' => array(
'start' => '32216730',
'end' => '32222319',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-007'
),
'ENST00000489170' => array(
'start' => '32214477',
'end' => '32222348',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-003'
),
'ENST00000491434' => array(
'start' => '32214477',
'end' => '32222333',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-004'
),
'ENST00000495091' => array(
'start' => '32214477',
'end' => '32215795',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-012'
),
'ENST00000409358' => array(
'start' => '32209094',
'end' => '32216196',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCDC2B-002'
),
'ENST00000487056' => array(
'start' => '32209096',
'end' => '32216192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCDC2B-001'
)
)
$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_0004JM_0001' => array(
'genes_in_region' => array(
'ENSDARG00000053744' => array(
[maximum depth reached]
),
'ENSDARG00000078333' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Muscle',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JM_0002',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '32209094',
'seq_end' => '32222359',
'region_length' => '13265',
'region_type' => 'CGP',
'el_id' => 'ENSG00000222046-ENSG00000160055'
)
)
$gene_el = array(
'ENSDART00000110295' => array(
'Brain' => array(
'average_FPKM' => '1.324',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '2.474',
'stddev_FPKM' => '1.59'
),
'Kidney' => array(
'average_FPKM' => '13.823',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.658',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.696',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000136701' => array(
'Brain' => array(
'average_FPKM' => '2.997',
'stddev_FPKM' => '1.24'
),
'Heart' => array(
'average_FPKM' => '4.350',
'stddev_FPKM' => '1.89'
),
'Kidney' => array(
'average_FPKM' => '8.236',
'stddev_FPKM' => '3.16'
),
'Liver' => array(
'average_FPKM' => '0.251',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000144848' => array(
'Brain' => array(
'average_FPKM' => '1.206',
'stddev_FPKM' => '0.03'
)
)
)
$gene_key = 'ENSDARG00000078333'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '1.206',
'stddev_FPKM' => '0.03'
)
)
$tran_key = 'ENSDART00000144848'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0004JM_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000053744' => 'doublecortin domain containing 2B',
'ENSDARG00000078333' => 'transmembrane protein 234',
'ENSG00000084623' => 'eukaryotic translation initiation factor 3, subunit I',
'ENSG00000160055' => 'transmembrane protein 234',
'ENSG00000222046' => 'doublecortin domain containing 2B'
),
'gene_name_arr' => array(
'ENSDARG00000053744' => 'dcdc2b',
'ENSDARG00000078333' => 'tmem234',
'ENSG00000084623' => 'EIF3I',
'ENSG00000160055' => 'TMEM234',
'ENSG00000222046' => 'DCDC2B'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 18 => 'Kidney',
(int) 21 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 32 => 'Ovary',
(int) 35 => 'Placenta',
(int) 38 => '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) 25,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000075826' => array(
'start' => '33527789',
'end' => '33538360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-001'
),
'ENSDART00000145295' => array(
'start' => '33527795',
'end' => '33531916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-002'
),
'ENSDART00000110295' => array(
'start' => '33538277',
'end' => '33540925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-001'
),
'ENSDART00000136701' => array(
'start' => '33538275',
'end' => '33541000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-002'
),
'ENSDART00000144848' => array(
'start' => '33538449',
'end' => '33540928',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-003'
),
'ENST00000355082' => array(
'start' => '32221928',
'end' => '32226295',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-005'
),
'ENST00000373586' => array(
'start' => '32222370',
'end' => '32231604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-001'
),
'ENST00000471486' => array(
'start' => '32222437',
'end' => '32228814',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-003'
),
'ENST00000474371' => array(
'start' => '32222545',
'end' => '32231054',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-004'
),
'ENST00000483517' => array(
'start' => '32222440',
'end' => '32229208',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-002'
),
'ENST00000489353' => array(
'start' => '32222407',
'end' => '32226472',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-006'
),
'ENST00000309777' => array(
'start' => '32216197',
'end' => '32222325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-001'
),
'ENST00000344461' => array(
'start' => '32216200',
'end' => '32222338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-009'
),
'ENST00000373593' => array(
'start' => '32216197',
'end' => '32222343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-005'
),
'ENST00000461402' => array(
'start' => '32214478',
'end' => '32222347',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-002'
),
'ENST00000466796' => array(
'start' => '32214472',
'end' => '32221196',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-006'
),
'ENST00000483001' => array(
'start' => '32215847',
'end' => '32222335',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-010'
),
'ENST00000484490' => array(
'start' => '32216357',
'end' => '32222359',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-011'
),
'ENST00000485689' => array(
'start' => '32216589',
'end' => '32217427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-008'
),
'ENST00000487174' => array(
'start' => '32216730',
'end' => '32222319',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-007'
),
'ENST00000489170' => array(
'start' => '32214477',
'end' => '32222348',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-003'
),
'ENST00000491434' => array(
'start' => '32214477',
'end' => '32222333',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-004'
),
'ENST00000495091' => array(
'start' => '32214477',
'end' => '32215795',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-012'
),
'ENST00000409358' => array(
'start' => '32209094',
'end' => '32216196',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCDC2B-002'
),
'ENST00000487056' => array(
'start' => '32209096',
'end' => '32216192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCDC2B-001'
)
),
'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_0004JM_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004JM_0001' => array(
'genes_in_region' => array(
'ENSDARG00000053744' => array(
[maximum depth reached]
),
'ENSDARG00000078333' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Muscle',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000053744' => 'doublecortin domain containing 2B',
'ENSDARG00000078333' => 'transmembrane protein 234',
'ENSG00000084623' => 'eukaryotic translation initiation factor 3, subunit I',
'ENSG00000160055' => 'transmembrane protein 234',
'ENSG00000222046' => 'doublecortin domain containing 2B'
)
$gene_name_arr = array(
'ENSDARG00000053744' => 'dcdc2b',
'ENSDARG00000078333' => 'tmem234',
'ENSG00000084623' => 'EIF3I',
'ENSG00000160055' => 'TMEM234',
'ENSG00000222046' => 'DCDC2B'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JM_0001',
'tax_id' => '7955',
'chromosome' => '13',
'seq_start' => '33527789',
'seq_end' => '33541000',
'region_length' => '13211',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000053744-ENSDARG00000078333'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JM_0002',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '32209094',
'seq_end' => '32222359',
'region_length' => '13265',
'region_type' => 'CGP',
'el_id' => 'ENSG00000222046-ENSG00000160055'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 3 => 'Bladder',
(int) 4 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 18 => 'Kidney',
(int) 21 => 'Liver',
(int) 25 => 'Lung',
(int) 27 => 'Muscle',
(int) 32 => 'Ovary',
(int) 35 => 'Placenta',
(int) 38 => '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) 25
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000075826' => array(
'start' => '33527789',
'end' => '33538360',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-001'
),
'ENSDART00000145295' => array(
'start' => '33527795',
'end' => '33531916',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'dcdc2b-002'
),
'ENSDART00000110295' => array(
'start' => '33538277',
'end' => '33540925',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-001'
),
'ENSDART00000136701' => array(
'start' => '33538275',
'end' => '33541000',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-002'
),
'ENSDART00000144848' => array(
'start' => '33538449',
'end' => '33540928',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'tmem234-003'
),
'ENST00000355082' => array(
'start' => '32221928',
'end' => '32226295',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-005'
),
'ENST00000373586' => array(
'start' => '32222370',
'end' => '32231604',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'EIF3I-001'
),
'ENST00000471486' => array(
'start' => '32222437',
'end' => '32228814',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-003'
),
'ENST00000474371' => array(
'start' => '32222545',
'end' => '32231054',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-004'
),
'ENST00000483517' => array(
'start' => '32222440',
'end' => '32229208',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-002'
),
'ENST00000489353' => array(
'start' => '32222407',
'end' => '32226472',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'EIF3I-006'
),
'ENST00000309777' => array(
'start' => '32216197',
'end' => '32222325',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-001'
),
'ENST00000344461' => array(
'start' => '32216200',
'end' => '32222338',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-009'
),
'ENST00000373593' => array(
'start' => '32216197',
'end' => '32222343',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TMEM234-005'
),
'ENST00000461402' => array(
'start' => '32214478',
'end' => '32222347',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-002'
),
'ENST00000466796' => array(
'start' => '32214472',
'end' => '32221196',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-006'
),
'ENST00000483001' => array(
'start' => '32215847',
'end' => '32222335',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-010'
),
'ENST00000484490' => array(
'start' => '32216357',
'end' => '32222359',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-011'
),
'ENST00000485689' => array(
'start' => '32216589',
'end' => '32217427',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-008'
),
'ENST00000487174' => array(
'start' => '32216730',
'end' => '32222319',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TMEM234-007'
),
'ENST00000489170' => array(
'start' => '32214477',
'end' => '32222348',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-003'
),
'ENST00000491434' => array(
'start' => '32214477',
'end' => '32222333',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TMEM234-004'
),
'ENST00000495091' => array(
'start' => '32214477',
'end' => '32215795',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TMEM234-012'
),
'ENST00000409358' => array(
'start' => '32209094',
'end' => '32216196',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DCDC2B-002'
),
'ENST00000487056' => array(
'start' => '32209096',
'end' => '32216192',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DCDC2B-001'
)
)
$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_0004JM_0001' => array(
'genes_in_region' => array(
'ENSDARG00000053744' => array(
[maximum depth reached]
),
'ENSDARG00000078333' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Muscle',
(int) 3 => 'Muscle',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Muscle',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Liver',
(int) 13 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JM_0002',
'tax_id' => '9606',
'chromosome' => '1',
'seq_start' => '32209094',
'seq_end' => '32222359',
'region_length' => '13265',
'region_type' => 'CGP',
'el_id' => 'ENSG00000222046-ENSG00000160055'
)
)
$gene_el = array(
'ENSDART00000110295' => array(
'Brain' => array(
'average_FPKM' => '1.324',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '2.474',
'stddev_FPKM' => '1.59'
),
'Kidney' => array(
'average_FPKM' => '13.823',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.658',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.696',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000136701' => array(
'Brain' => array(
'average_FPKM' => '2.997',
'stddev_FPKM' => '1.24'
),
'Heart' => array(
'average_FPKM' => '4.350',
'stddev_FPKM' => '1.89'
),
'Kidney' => array(
'average_FPKM' => '8.236',
'stddev_FPKM' => '3.16'
),
'Liver' => array(
'average_FPKM' => '0.251',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000144848' => array(
'Brain' => array(
'average_FPKM' => '1.206',
'stddev_FPKM' => '0.03'
)
)
)
$gene_key = 'ENSDARG00000078333'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '1.206',
'stddev_FPKM' => '0.03'
)
)
$tran_key = 'ENSDART00000144848'
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
(dcdc2b)