| Source ID |
Type |
Tax ID |
Position |
| NRXN3 |
UCNEbase |
10090 |
12:90199235-90551630  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007OJ_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_0007OJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000258416' => null,
'ENSG00000258637' => null,
'ENSDARG00000043746' => 'neurexin 3a',
'ENSMUSG00000066392' => 'neurexin III'
),
'gene_name_arr' => array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000258416' => 'RP11-526N18.1',
'ENSG00000258637' => 'RP11-242P2.1',
'ENSDARG00000043746' => 'nrxn3a',
'ENSMUSG00000066392' => 'Nrxn3'
),
'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]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 40 => 'Heart',
(int) 53 => 'Kidney',
(int) 68 => 'Liver',
(int) 82 => 'Lung',
(int) 93 => 'Muscle',
(int) 100 => 'Ovary',
(int) 112 => 'Placenta',
(int) 121 => '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) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000281127' => array(
'start' => '79279413',
'end' => '79868290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-005'
),
'ENST00000335750' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-201'
),
'ENST00000428277' => array(
'start' => '79279906',
'end' => '79864417',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-006'
),
'ENST00000553363' => array(
'start' => '78278643',
'end' => '78651311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-010'
),
'ENST00000553631' => array(
'start' => '78403731',
'end' => '78709507',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-009'
),
'ENST00000553803' => array(
'start' => '79298795',
'end' => '79573011',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-014'
),
'ENST00000554719' => array(
'start' => '78403750',
'end' => '79862443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-001'
),
'ENST00000554738' => array(
'start' => '78242391',
'end' => '79862033',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-002'
),
'ENST00000555073' => array(
'start' => '79280502',
'end' => '79663892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-012'
),
'ENST00000555387' => array(
'start' => '79280263',
'end' => '79862454',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-007'
),
'ENST00000556003' => array(
'start' => '79314051',
'end' => '79861959',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-013'
),
'ENST00000556088' => array(
'start' => '78243602',
'end' => '78645427',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-008'
),
'ENST00000556496' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-003'
),
'ENST00000557081' => array(
'start' => '78698220',
'end' => '78709641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-011'
),
'ENST00000557594' => array(
'start' => '79279339',
'end' => '79862478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-004'
),
'ENST00000554307' => array(
'start' => '79893080',
'end' => '79974169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-526N18.1-001'
),
'ENST00000553322' => array(
'start' => '79661666',
'end' => '79791263',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-242P2.1-001'
),
'ENSDART00000064241' => array(
'start' => '16748762',
'end' => '16960491',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-201'
),
'ENSDART00000088179' => array(
'start' => '16748762',
'end' => '17271594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-202'
),
'ENSDART00000109034' => array(
'start' => '17270168',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-203'
),
'ENSDART00000153697' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-003'
),
'ENSDART00000154519' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'nrxn3a-002'
),
'ENSDART00000155007' => array(
'start' => '17087463',
'end' => '17096032',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-006'
),
'ENSDART00000155341' => array(
'start' => '17274528',
'end' => '17278055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'nrxn3a-005'
),
'ENSDART00000156391' => array(
'start' => '17098775',
'end' => '17100853',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-004'
),
'ENSDART00000156928' => array(
'start' => '17087594',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-001'
),
'ENSMUST00000057634' => array(
'start' => '88953399',
'end' => '90333060',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-002'
),
'ENSMUST00000110130' => array(
'start' => '89812483',
'end' => '90333443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-006'
),
'ENSMUST00000110133' => array(
'start' => '89812483',
'end' => '90332899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-010'
),
'ENSMUST00000110138' => array(
'start' => '88722888',
'end' => '88850849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-005'
),
'ENSMUST00000163134' => array(
'start' => '88794504',
'end' => '90334935',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-001'
),
'ENSMUST00000163944' => array(
'start' => '88725009',
'end' => '88795115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-007'
),
'ENSMUST00000164072' => array(
'start' => '88795439',
'end' => '88853243',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-008'
),
'ENSMUST00000167103' => array(
'start' => '88723109',
'end' => '90332897',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-003'
),
'ENSMUST00000167734' => array(
'start' => '88722876',
'end' => '89261571',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-004'
),
'ENSMUST00000167887' => array(
'start' => '89193106',
'end' => '90332410',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-201'
),
'ENSMUST00000170533' => array(
'start' => '88953390',
'end' => '89187319',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-009'
),
'ENSMUST00000190030' => array(
'start' => '88725681',
'end' => '88794981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-013'
),
'ENSMUST00000190626' => array(
'start' => '88722986',
'end' => '90332878',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-012'
)
),
'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_0007OJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007OJ_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258416' => array(
[maximum depth reached]
),
'ENSG00000258637' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Liver',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Bladder',
(int) 21 => 'Heart',
(int) 22 => 'Lung',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Testis'
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
'ENSDARG00000043746' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Heart',
(int) 13 => 'Kidney',
(int) 14 => 'Kidney',
(int) 15 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000258416' => null,
'ENSG00000258637' => null,
'ENSDARG00000043746' => 'neurexin 3a',
'ENSMUSG00000066392' => 'neurexin III'
)
$gene_name_arr = array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000258416' => 'RP11-526N18.1',
'ENSG00000258637' => 'RP11-242P2.1',
'ENSDARG00000043746' => 'nrxn3a',
'ENSMUSG00000066392' => 'Nrxn3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0001',
'tax_id' => '9606',
'chromosome' => '14',
'seq_start' => '79692123',
'seq_end' => '80016148',
'region_length' => '324025',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '89190998',
'seq_end' => '89191254',
'region_length' => '256',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0003',
'tax_id' => '7955',
'chromosome' => '17',
'seq_start' => '16743749',
'seq_end' => '16749642',
'region_length' => '5893',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0004',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '90199235',
'seq_end' => '90551630',
'region_length' => '352395',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0005',
'tax_id' => '7955',
'chromosome' => '20',
'seq_start' => '5996517',
'seq_end' => '5996940',
'region_length' => '423',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 40 => 'Heart',
(int) 53 => 'Kidney',
(int) 68 => 'Liver',
(int) 82 => 'Lung',
(int) 93 => 'Muscle',
(int) 100 => 'Ovary',
(int) 112 => 'Placenta',
(int) 121 => '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) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000281127' => array(
'start' => '79279413',
'end' => '79868290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-005'
),
'ENST00000335750' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-201'
),
'ENST00000428277' => array(
'start' => '79279906',
'end' => '79864417',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-006'
),
'ENST00000553363' => array(
'start' => '78278643',
'end' => '78651311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-010'
),
'ENST00000553631' => array(
'start' => '78403731',
'end' => '78709507',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-009'
),
'ENST00000553803' => array(
'start' => '79298795',
'end' => '79573011',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-014'
),
'ENST00000554719' => array(
'start' => '78403750',
'end' => '79862443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-001'
),
'ENST00000554738' => array(
'start' => '78242391',
'end' => '79862033',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-002'
),
'ENST00000555073' => array(
'start' => '79280502',
'end' => '79663892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-012'
),
'ENST00000555387' => array(
'start' => '79280263',
'end' => '79862454',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-007'
),
'ENST00000556003' => array(
'start' => '79314051',
'end' => '79861959',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-013'
),
'ENST00000556088' => array(
'start' => '78243602',
'end' => '78645427',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-008'
),
'ENST00000556496' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-003'
),
'ENST00000557081' => array(
'start' => '78698220',
'end' => '78709641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-011'
),
'ENST00000557594' => array(
'start' => '79279339',
'end' => '79862478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-004'
),
'ENST00000554307' => array(
'start' => '79893080',
'end' => '79974169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-526N18.1-001'
),
'ENST00000553322' => array(
'start' => '79661666',
'end' => '79791263',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-242P2.1-001'
),
'ENSDART00000064241' => array(
'start' => '16748762',
'end' => '16960491',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-201'
),
'ENSDART00000088179' => array(
'start' => '16748762',
'end' => '17271594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-202'
),
'ENSDART00000109034' => array(
'start' => '17270168',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-203'
),
'ENSDART00000153697' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-003'
),
'ENSDART00000154519' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'nrxn3a-002'
),
'ENSDART00000155007' => array(
'start' => '17087463',
'end' => '17096032',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-006'
),
'ENSDART00000155341' => array(
'start' => '17274528',
'end' => '17278055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'nrxn3a-005'
),
'ENSDART00000156391' => array(
'start' => '17098775',
'end' => '17100853',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-004'
),
'ENSDART00000156928' => array(
'start' => '17087594',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-001'
),
'ENSMUST00000057634' => array(
'start' => '88953399',
'end' => '90333060',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-002'
),
'ENSMUST00000110130' => array(
'start' => '89812483',
'end' => '90333443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-006'
),
'ENSMUST00000110133' => array(
'start' => '89812483',
'end' => '90332899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-010'
),
'ENSMUST00000110138' => array(
'start' => '88722888',
'end' => '88850849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-005'
),
'ENSMUST00000163134' => array(
'start' => '88794504',
'end' => '90334935',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-001'
),
'ENSMUST00000163944' => array(
'start' => '88725009',
'end' => '88795115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-007'
),
'ENSMUST00000164072' => array(
'start' => '88795439',
'end' => '88853243',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-008'
),
'ENSMUST00000167103' => array(
'start' => '88723109',
'end' => '90332897',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-003'
),
'ENSMUST00000167734' => array(
'start' => '88722876',
'end' => '89261571',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-004'
),
'ENSMUST00000167887' => array(
'start' => '89193106',
'end' => '90332410',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-201'
),
'ENSMUST00000170533' => array(
'start' => '88953390',
'end' => '89187319',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-009'
),
'ENSMUST00000190030' => array(
'start' => '88725681',
'end' => '88794981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-013'
),
'ENSMUST00000190626' => array(
'start' => '88722986',
'end' => '90332878',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-012'
)
)
$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_0007OJ_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258416' => array(
[maximum depth reached]
),
'ENSG00000258637' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Liver',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Bladder',
(int) 21 => 'Heart',
(int) 22 => 'Lung',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Testis'
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
'ENSDARG00000043746' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Heart',
(int) 13 => 'Kidney',
(int) 14 => 'Kidney',
(int) 15 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0004',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '90199235',
'seq_end' => '90551630',
'region_length' => '352395',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
)
$gene_el = array(
'ENSDART00000064241' => array(
'Heart' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000088179' => array(
'Liver' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.294',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000109034' => array(
'Heart' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000153697' => array(
'Heart' => array(
'average_FPKM' => '0.046',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.129',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.021',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000154519' => array(
'Brain' => array(
'average_FPKM' => '14.099',
'stddev_FPKM' => '0.01'
),
'Heart' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.05'
),
'Muscle' => array(
'average_FPKM' => '1.161',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000155007' => array(),
'ENSDART00000155341' => array(),
'ENSDART00000156391' => array(
'Heart' => array(
'average_FPKM' => '0.217',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '2.096',
'stddev_FPKM' => '1.05'
)
),
'ENSDART00000156928' => array(
'Kidney' => array(
'average_FPKM' => '0.018',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.784',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000043746'
$is_first = false
$tran_el = array(
'Kidney' => array(
'average_FPKM' => '0.018',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.784',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000156928'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007OJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000258416' => null,
'ENSG00000258637' => null,
'ENSDARG00000043746' => 'neurexin 3a',
'ENSMUSG00000066392' => 'neurexin III'
),
'gene_name_arr' => array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000258416' => 'RP11-526N18.1',
'ENSG00000258637' => 'RP11-242P2.1',
'ENSDARG00000043746' => 'nrxn3a',
'ENSMUSG00000066392' => 'Nrxn3'
),
'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]
)
),
(int) 4 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 40 => 'Heart',
(int) 53 => 'Kidney',
(int) 68 => 'Liver',
(int) 82 => 'Lung',
(int) 93 => 'Muscle',
(int) 100 => 'Ovary',
(int) 112 => 'Placenta',
(int) 121 => '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) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000281127' => array(
'start' => '79279413',
'end' => '79868290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-005'
),
'ENST00000335750' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-201'
),
'ENST00000428277' => array(
'start' => '79279906',
'end' => '79864417',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-006'
),
'ENST00000553363' => array(
'start' => '78278643',
'end' => '78651311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-010'
),
'ENST00000553631' => array(
'start' => '78403731',
'end' => '78709507',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-009'
),
'ENST00000553803' => array(
'start' => '79298795',
'end' => '79573011',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-014'
),
'ENST00000554719' => array(
'start' => '78403750',
'end' => '79862443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-001'
),
'ENST00000554738' => array(
'start' => '78242391',
'end' => '79862033',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-002'
),
'ENST00000555073' => array(
'start' => '79280502',
'end' => '79663892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-012'
),
'ENST00000555387' => array(
'start' => '79280263',
'end' => '79862454',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-007'
),
'ENST00000556003' => array(
'start' => '79314051',
'end' => '79861959',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-013'
),
'ENST00000556088' => array(
'start' => '78243602',
'end' => '78645427',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-008'
),
'ENST00000556496' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-003'
),
'ENST00000557081' => array(
'start' => '78698220',
'end' => '78709641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-011'
),
'ENST00000557594' => array(
'start' => '79279339',
'end' => '79862478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-004'
),
'ENST00000554307' => array(
'start' => '79893080',
'end' => '79974169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-526N18.1-001'
),
'ENST00000553322' => array(
'start' => '79661666',
'end' => '79791263',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-242P2.1-001'
),
'ENSDART00000064241' => array(
'start' => '16748762',
'end' => '16960491',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-201'
),
'ENSDART00000088179' => array(
'start' => '16748762',
'end' => '17271594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-202'
),
'ENSDART00000109034' => array(
'start' => '17270168',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-203'
),
'ENSDART00000153697' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-003'
),
'ENSDART00000154519' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'nrxn3a-002'
),
'ENSDART00000155007' => array(
'start' => '17087463',
'end' => '17096032',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-006'
),
'ENSDART00000155341' => array(
'start' => '17274528',
'end' => '17278055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'nrxn3a-005'
),
'ENSDART00000156391' => array(
'start' => '17098775',
'end' => '17100853',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-004'
),
'ENSDART00000156928' => array(
'start' => '17087594',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-001'
),
'ENSMUST00000057634' => array(
'start' => '88953399',
'end' => '90333060',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-002'
),
'ENSMUST00000110130' => array(
'start' => '89812483',
'end' => '90333443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-006'
),
'ENSMUST00000110133' => array(
'start' => '89812483',
'end' => '90332899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-010'
),
'ENSMUST00000110138' => array(
'start' => '88722888',
'end' => '88850849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-005'
),
'ENSMUST00000163134' => array(
'start' => '88794504',
'end' => '90334935',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-001'
),
'ENSMUST00000163944' => array(
'start' => '88725009',
'end' => '88795115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-007'
),
'ENSMUST00000164072' => array(
'start' => '88795439',
'end' => '88853243',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-008'
),
'ENSMUST00000167103' => array(
'start' => '88723109',
'end' => '90332897',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-003'
),
'ENSMUST00000167734' => array(
'start' => '88722876',
'end' => '89261571',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-004'
),
'ENSMUST00000167887' => array(
'start' => '89193106',
'end' => '90332410',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-201'
),
'ENSMUST00000170533' => array(
'start' => '88953390',
'end' => '89187319',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-009'
),
'ENSMUST00000190030' => array(
'start' => '88725681',
'end' => '88794981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-013'
),
'ENSMUST00000190626' => array(
'start' => '88722986',
'end' => '90332878',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-012'
)
),
'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_0007OJ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007OJ_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258416' => array(
[maximum depth reached]
),
'ENSG00000258637' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Liver',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Bladder',
(int) 21 => 'Heart',
(int) 22 => 'Lung',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Testis'
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
'ENSDARG00000043746' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Heart',
(int) 13 => 'Kidney',
(int) 14 => 'Kidney',
(int) 15 => 'Muscle'
)
)
)
$gene_desc_arr = array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000258416' => null,
'ENSG00000258637' => null,
'ENSDARG00000043746' => 'neurexin 3a',
'ENSMUSG00000066392' => 'neurexin III'
)
$gene_name_arr = array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000258416' => 'RP11-526N18.1',
'ENSG00000258637' => 'RP11-242P2.1',
'ENSDARG00000043746' => 'nrxn3a',
'ENSMUSG00000066392' => 'Nrxn3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0001',
'tax_id' => '9606',
'chromosome' => '14',
'seq_start' => '79692123',
'seq_end' => '80016148',
'region_length' => '324025',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '89190998',
'seq_end' => '89191254',
'region_length' => '256',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0003',
'tax_id' => '7955',
'chromosome' => '17',
'seq_start' => '16743749',
'seq_end' => '16749642',
'region_length' => '5893',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0004',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '90199235',
'seq_end' => '90551630',
'region_length' => '352395',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
),
(int) 4 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0005',
'tax_id' => '7955',
'chromosome' => '20',
'seq_start' => '5996517',
'seq_end' => '5996940',
'region_length' => '423',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 24 => 'Breast',
(int) 31 => 'Colon',
(int) 40 => 'Heart',
(int) 53 => 'Kidney',
(int) 68 => 'Liver',
(int) 82 => 'Lung',
(int) 93 => 'Muscle',
(int) 100 => 'Ovary',
(int) 112 => 'Placenta',
(int) 121 => '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) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000281127' => array(
'start' => '79279413',
'end' => '79868290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-005'
),
'ENST00000335750' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-201'
),
'ENST00000428277' => array(
'start' => '79279906',
'end' => '79864417',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-006'
),
'ENST00000553363' => array(
'start' => '78278643',
'end' => '78651311',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-010'
),
'ENST00000553631' => array(
'start' => '78403731',
'end' => '78709507',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-009'
),
'ENST00000553803' => array(
'start' => '79298795',
'end' => '79573011',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-014'
),
'ENST00000554719' => array(
'start' => '78403750',
'end' => '79862443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-001'
),
'ENST00000554738' => array(
'start' => '78242391',
'end' => '79862033',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-002'
),
'ENST00000555073' => array(
'start' => '79280502',
'end' => '79663892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-012'
),
'ENST00000555387' => array(
'start' => '79280263',
'end' => '79862454',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'NRXN3-007'
),
'ENST00000556003' => array(
'start' => '79314051',
'end' => '79861959',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'NRXN3-013'
),
'ENST00000556088' => array(
'start' => '78243602',
'end' => '78645427',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-008'
),
'ENST00000556496' => array(
'start' => '78614932',
'end' => '78988299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'NRXN3-003'
),
'ENST00000557081' => array(
'start' => '78698220',
'end' => '78709641',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-011'
),
'ENST00000557594' => array(
'start' => '79279339',
'end' => '79862478',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NRXN3-004'
),
'ENST00000554307' => array(
'start' => '79893080',
'end' => '79974169',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP11-526N18.1-001'
),
'ENST00000553322' => array(
'start' => '79661666',
'end' => '79791263',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-242P2.1-001'
),
'ENSDART00000064241' => array(
'start' => '16748762',
'end' => '16960491',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-201'
),
'ENSDART00000088179' => array(
'start' => '16748762',
'end' => '17271594',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-202'
),
'ENSDART00000109034' => array(
'start' => '17270168',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-203'
),
'ENSDART00000153697' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-003'
),
'ENSDART00000154519' => array(
'start' => '16747762',
'end' => '16807048',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'nrxn3a-002'
),
'ENSDART00000155007' => array(
'start' => '17087463',
'end' => '17096032',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-006'
),
'ENSDART00000155341' => array(
'start' => '17274528',
'end' => '17278055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'nrxn3a-005'
),
'ENSDART00000156391' => array(
'start' => '17098775',
'end' => '17100853',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'nrxn3a-004'
),
'ENSDART00000156928' => array(
'start' => '17087594',
'end' => '17278052',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'nrxn3a-001'
),
'ENSMUST00000057634' => array(
'start' => '88953399',
'end' => '90333060',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-002'
),
'ENSMUST00000110130' => array(
'start' => '89812483',
'end' => '90333443',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-006'
),
'ENSMUST00000110133' => array(
'start' => '89812483',
'end' => '90332899',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-010'
),
'ENSMUST00000110138' => array(
'start' => '88722888',
'end' => '88850849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-005'
),
'ENSMUST00000163134' => array(
'start' => '88794504',
'end' => '90334935',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-001'
),
'ENSMUST00000163944' => array(
'start' => '88725009',
'end' => '88795115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-007'
),
'ENSMUST00000164072' => array(
'start' => '88795439',
'end' => '88853243',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-008'
),
'ENSMUST00000167103' => array(
'start' => '88723109',
'end' => '90332897',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-003'
),
'ENSMUST00000167734' => array(
'start' => '88722876',
'end' => '89261571',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Nrxn3-004'
),
'ENSMUST00000167887' => array(
'start' => '89193106',
'end' => '90332410',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nrxn3-201'
),
'ENSMUST00000170533' => array(
'start' => '88953390',
'end' => '89187319',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-009'
),
'ENSMUST00000190030' => array(
'start' => '88725681',
'end' => '88794981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nrxn3-013'
),
'ENSMUST00000190626' => array(
'start' => '88722986',
'end' => '90332878',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Nrxn3-012'
)
)
$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_0007OJ_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258416' => array(
[maximum depth reached]
),
'ENSG00000258637' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Liver',
(int) 3 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 5 => 'Bladder',
(int) 6 => 'Brain',
(int) 7 => 'Breast',
(int) 8 => 'Colon',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Lung',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Ovary',
(int) 20 => 'Bladder',
(int) 21 => 'Heart',
(int) 22 => 'Lung',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Placenta',
(int) 35 => 'Testis',
(int) 36 => 'Brain',
(int) 37 => 'Colon',
(int) 38 => 'Testis'
)
),
'CIL_0007OJ_0003' => array(
'genes_in_region' => array(
'ENSDARG00000043746' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Liver',
(int) 2 => 'Liver',
(int) 3 => 'Muscle',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Brain',
(int) 10 => 'Heart',
(int) 11 => 'Muscle',
(int) 12 => 'Heart',
(int) 13 => 'Kidney',
(int) 14 => 'Kidney',
(int) 15 => 'Muscle'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007OJ_0004',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '90199235',
'seq_end' => '90551630',
'region_length' => '352395',
'region_type' => 'UCNEbase',
'el_id' => 'NRXN3'
)
)
$gene_el = array(
'ENSDART00000064241' => array(
'Heart' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.025',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000088179' => array(
'Liver' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.294',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000109034' => array(
'Heart' => array(
'average_FPKM' => '0.026',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000153697' => array(
'Heart' => array(
'average_FPKM' => '0.046',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.129',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.021',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000154519' => array(
'Brain' => array(
'average_FPKM' => '14.099',
'stddev_FPKM' => '0.01'
),
'Heart' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.05'
),
'Muscle' => array(
'average_FPKM' => '1.161',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000155007' => array(),
'ENSDART00000155341' => array(),
'ENSDART00000156391' => array(
'Heart' => array(
'average_FPKM' => '0.217',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '2.096',
'stddev_FPKM' => '1.05'
)
),
'ENSDART00000156928' => array(
'Kidney' => array(
'average_FPKM' => '0.018',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.784',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000043746'
$is_first = false
$tran_el = array(
'Kidney' => array(
'average_FPKM' => '0.018',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.784',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000156928'
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
(NRXN3)