| Source ID |
Type |
Tax ID |
Position |
| mm296 |
VISTA |
10090 |
12:88683898-89284926  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0008FT_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_0008FT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000199454' => 'RNA, 5S ribosomal pseudogene 388',
'ENSG00000221178' => null,
'ENSG00000239163' => null,
'ENSG00000239438' => null,
'ENSG00000258719' => null,
'ENSG00000258723' => null,
'ENSG00000258874' => null,
'ENSMUSG00000066392' => 'neurexin III'
),
'gene_name_arr' => array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000199454' => 'RNA5SP388',
'ENSG00000221178' => 'AC008045.1',
'ENSG00000239163' => 'AC007056.1',
'ENSG00000239438' => 'RP11-332E19.1',
'ENSG00000258719' => 'RP11-232C2.3',
'ENSG00000258723' => 'RP11-332E19.2',
'ENSG00000258874' => 'RP11-232C2.2',
'ENSMUSG00000066392' => 'Nrxn3'
),
'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) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 27 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 54 => 'Liver',
(int) 65 => 'Lung',
(int) 77 => 'Muscle',
(int) 81 => 'Ovary',
(int) 93 => 'Placenta',
(int) 101 => '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) 35,
'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'
),
'ENST00000362584' => array(
'start' => '78177803',
'end' => '78177921',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP388-201'
),
'ENST00000408251' => array(
'start' => '78617866',
'end' => '78617975',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC008045.1-201'
),
'ENST00000459199' => array(
'start' => '78397878',
'end' => '78397959',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007056.1-201'
),
'ENST00000491713' => array(
'start' => '78231281',
'end' => '78231619',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-332E19.1-001'
),
'ENST00000555954' => array(
'start' => '78695321',
'end' => '78698122',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.3-001'
),
'ENST00000554219' => array(
'start' => '78279572',
'end' => '78283376',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-332E19.2-001'
),
'ENST00000555680' => array(
'start' => '78703615',
'end' => '78709934',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.2-001'
),
'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_0008FT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008FT_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258723' => array(
[maximum depth reached]
),
'ENSG00000258874' => 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 => 'Lung',
(int) 33 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000199454' => 'RNA, 5S ribosomal pseudogene 388',
'ENSG00000221178' => null,
'ENSG00000239163' => null,
'ENSG00000239438' => null,
'ENSG00000258719' => null,
'ENSG00000258723' => null,
'ENSG00000258874' => null,
'ENSMUSG00000066392' => 'neurexin III'
)
$gene_name_arr = array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000199454' => 'RNA5SP388',
'ENSG00000221178' => 'AC008045.1',
'ENSG00000239163' => 'AC007056.1',
'ENSG00000239438' => 'RP11-332E19.1',
'ENSG00000258719' => 'RP11-232C2.3',
'ENSG00000258723' => 'RP11-332E19.2',
'ENSG00000258874' => 'RP11-232C2.2',
'ENSMUSG00000066392' => 'Nrxn3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008FT_0001',
'tax_id' => '9606',
'chromosome' => '14',
'seq_start' => '78139980',
'seq_end' => '78740994',
'region_length' => '601014',
'region_type' => 'VISTA',
'el_id' => 'mm296'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008FT_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '88683898',
'seq_end' => '89284926',
'region_length' => '601028',
'region_type' => 'VISTA',
'el_id' => 'mm296'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 27 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 54 => 'Liver',
(int) 65 => 'Lung',
(int) 77 => 'Muscle',
(int) 81 => 'Ovary',
(int) 93 => 'Placenta',
(int) 101 => '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) 35
$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'
),
'ENST00000362584' => array(
'start' => '78177803',
'end' => '78177921',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP388-201'
),
'ENST00000408251' => array(
'start' => '78617866',
'end' => '78617975',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC008045.1-201'
),
'ENST00000459199' => array(
'start' => '78397878',
'end' => '78397959',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007056.1-201'
),
'ENST00000491713' => array(
'start' => '78231281',
'end' => '78231619',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-332E19.1-001'
),
'ENST00000555954' => array(
'start' => '78695321',
'end' => '78698122',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.3-001'
),
'ENST00000554219' => array(
'start' => '78279572',
'end' => '78283376',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-332E19.2-001'
),
'ENST00000555680' => array(
'start' => '78703615',
'end' => '78709934',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.2-001'
),
'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_0008FT_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258723' => array(
[maximum depth reached]
),
'ENSG00000258874' => 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 => 'Lung',
(int) 33 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008FT_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '88683898',
'seq_end' => '89284926',
'region_length' => '601028',
'region_type' => 'VISTA',
'el_id' => 'mm296'
)
)
$gene_el = array(
'ENST00000555680' => array(
'Testis' => array(
'average_FPKM' => '17.117',
'stddev_FPKM' => '14.57'
)
)
)
$gene_key = 'ENSG00000258874'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '17.117',
'stddev_FPKM' => '14.57'
)
)
$tran_key = 'ENST00000555680'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0008FT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000199454' => 'RNA, 5S ribosomal pseudogene 388',
'ENSG00000221178' => null,
'ENSG00000239163' => null,
'ENSG00000239438' => null,
'ENSG00000258719' => null,
'ENSG00000258723' => null,
'ENSG00000258874' => null,
'ENSMUSG00000066392' => 'neurexin III'
),
'gene_name_arr' => array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000199454' => 'RNA5SP388',
'ENSG00000221178' => 'AC008045.1',
'ENSG00000239163' => 'AC007056.1',
'ENSG00000239438' => 'RP11-332E19.1',
'ENSG00000258719' => 'RP11-232C2.3',
'ENSG00000258723' => 'RP11-332E19.2',
'ENSG00000258874' => 'RP11-232C2.2',
'ENSMUSG00000066392' => 'Nrxn3'
),
'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) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 27 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 54 => 'Liver',
(int) 65 => 'Lung',
(int) 77 => 'Muscle',
(int) 81 => 'Ovary',
(int) 93 => 'Placenta',
(int) 101 => '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) 35,
'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'
),
'ENST00000362584' => array(
'start' => '78177803',
'end' => '78177921',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP388-201'
),
'ENST00000408251' => array(
'start' => '78617866',
'end' => '78617975',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC008045.1-201'
),
'ENST00000459199' => array(
'start' => '78397878',
'end' => '78397959',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007056.1-201'
),
'ENST00000491713' => array(
'start' => '78231281',
'end' => '78231619',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-332E19.1-001'
),
'ENST00000555954' => array(
'start' => '78695321',
'end' => '78698122',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.3-001'
),
'ENST00000554219' => array(
'start' => '78279572',
'end' => '78283376',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-332E19.2-001'
),
'ENST00000555680' => array(
'start' => '78703615',
'end' => '78709934',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.2-001'
),
'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_0008FT_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0008FT_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258723' => array(
[maximum depth reached]
),
'ENSG00000258874' => 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 => 'Lung',
(int) 33 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000021645' => 'neurexin 3',
'ENSG00000199454' => 'RNA, 5S ribosomal pseudogene 388',
'ENSG00000221178' => null,
'ENSG00000239163' => null,
'ENSG00000239438' => null,
'ENSG00000258719' => null,
'ENSG00000258723' => null,
'ENSG00000258874' => null,
'ENSMUSG00000066392' => 'neurexin III'
)
$gene_name_arr = array(
'ENSG00000021645' => 'NRXN3',
'ENSG00000199454' => 'RNA5SP388',
'ENSG00000221178' => 'AC008045.1',
'ENSG00000239163' => 'AC007056.1',
'ENSG00000239438' => 'RP11-332E19.1',
'ENSG00000258719' => 'RP11-232C2.3',
'ENSG00000258723' => 'RP11-332E19.2',
'ENSG00000258874' => 'RP11-232C2.2',
'ENSMUSG00000066392' => 'Nrxn3'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008FT_0001',
'tax_id' => '9606',
'chromosome' => '14',
'seq_start' => '78139980',
'seq_end' => '78740994',
'region_length' => '601014',
'region_type' => 'VISTA',
'el_id' => 'mm296'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0008FT_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '88683898',
'seq_end' => '89284926',
'region_length' => '601028',
'region_type' => 'VISTA',
'el_id' => 'mm296'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 14 => 'Brain',
(int) 21 => 'Breast',
(int) 27 => 'Colon',
(int) 35 => 'Heart',
(int) 43 => 'Kidney',
(int) 54 => 'Liver',
(int) 65 => 'Lung',
(int) 77 => 'Muscle',
(int) 81 => 'Ovary',
(int) 93 => 'Placenta',
(int) 101 => '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) 35
$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'
),
'ENST00000362584' => array(
'start' => '78177803',
'end' => '78177921',
'transcript_biotype' => 'rRNA',
'transcript_name' => 'RNA5SP388-201'
),
'ENST00000408251' => array(
'start' => '78617866',
'end' => '78617975',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC008045.1-201'
),
'ENST00000459199' => array(
'start' => '78397878',
'end' => '78397959',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC007056.1-201'
),
'ENST00000491713' => array(
'start' => '78231281',
'end' => '78231619',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-332E19.1-001'
),
'ENST00000555954' => array(
'start' => '78695321',
'end' => '78698122',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.3-001'
),
'ENST00000554219' => array(
'start' => '78279572',
'end' => '78283376',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-332E19.2-001'
),
'ENST00000555680' => array(
'start' => '78703615',
'end' => '78709934',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-232C2.2-001'
),
'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_0008FT_0001' => array(
'genes_in_region' => array(
'ENSG00000021645' => array(
[maximum depth reached]
),
'ENSG00000258723' => array(
[maximum depth reached]
),
'ENSG00000258874' => 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 => 'Lung',
(int) 33 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0008FT_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '88683898',
'seq_end' => '89284926',
'region_length' => '601028',
'region_type' => 'VISTA',
'el_id' => 'mm296'
)
)
$gene_el = array(
'ENST00000555680' => array(
'Testis' => array(
'average_FPKM' => '17.117',
'stddev_FPKM' => '14.57'
)
)
)
$gene_key = 'ENSG00000258874'
$is_first = false
$tran_el = array(
'Testis' => array(
'average_FPKM' => '17.117',
'stddev_FPKM' => '14.57'
)
)
$tran_key = 'ENST00000555680'
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)