| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000023805-ENSMUSG00000015659 |
CGP |
10090 |
17:5941280-6079741  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00055M_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_00055M_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000078269' => 'synaptojanin 2',
'ENSG00000122335' => 'serine active site containing 1',
'ENSG00000233496' => 'SYNJ2 intronic transcript 1 (non-protein coding)',
'ENSMUSG00000015659' => 'serine active site containing 1',
'ENSMUSG00000023805' => 'synaptojanin 2'
),
'gene_name_arr' => array(
'ENSG00000078269' => 'SYNJ2',
'ENSG00000122335' => 'SERAC1',
'ENSG00000233496' => 'SYNJ2-IT1',
'ENSMUSG00000015659' => 'Serac1',
'ENSMUSG00000023805' => 'Synj2'
),
'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) 8 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 26 => 'Brain',
(int) 32 => 'Breast',
(int) 39 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 62 => 'Liver',
(int) 72 => 'Lung',
(int) 80 => 'Muscle',
(int) 89 => 'Ovary',
(int) 99 => 'Placenta',
(int) 107 => '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(
'ENST00000355585' => array(
'start' => '157981887',
'end' => '158099176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-002'
),
'ENST00000367112' => array(
'start' => '158077680',
'end' => '158097854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-003'
),
'ENST00000367113' => array(
'start' => '157982038',
'end' => '158030497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-004'
),
'ENST00000367122' => array(
'start' => '158070128',
'end' => '158096463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-201'
),
'ENST00000449320' => array(
'start' => '158017465',
'end' => '158028971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-005'
),
'ENST00000485863' => array(
'start' => '158033490',
'end' => '158063872',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SYNJ2-001'
),
'ENST00000367101' => array(
'start' => '158114731',
'end' => '158168259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-002'
),
'ENST00000367104' => array(
'start' => '158109515',
'end' => '158168270',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-001'
),
'ENST00000435180' => array(
'start' => '158114691',
'end' => '158119061',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-003'
),
'ENST00000606965' => array(
'start' => '158114471',
'end' => '158168171',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-004'
),
'ENST00000607000' => array(
'start' => '158145920',
'end' => '158159298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-007'
),
'ENST00000607071' => array(
'start' => '158110627',
'end' => '158166159',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-008'
),
'ENST00000607742' => array(
'start' => '158109691',
'end' => '158168246',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-005'
),
'ENST00000442328' => array(
'start' => '158001107',
'end' => '158002383',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'SYNJ2-IT1-001'
),
'ENSMUST00000024570' => array(
'start' => '6044066',
'end' => '6079727',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-002'
),
'ENSMUST00000097432' => array(
'start' => '6042196',
'end' => '6079741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-001'
),
'ENSMUST00000139542' => array(
'start' => '6064949',
'end' => '6079733',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-004'
),
'ENSMUST00000144284' => array(
'start' => '6050027',
'end' => '6051388',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Serac1-005'
),
'ENSMUST00000153325' => array(
'start' => '6043904',
'end' => '6050055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-006'
),
'ENSMUST00000061091' => array(
'start' => '5975641',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-004'
),
'ENSMUST00000080283' => array(
'start' => '5941403',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-001'
),
'ENSMUST00000115784' => array(
'start' => '6007580',
'end' => '6032929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-010'
),
'ENSMUST00000115785' => array(
'start' => '6007597',
'end' => '6038406',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-011'
),
'ENSMUST00000115786' => array(
'start' => '5996846',
'end' => '6020555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-009'
),
'ENSMUST00000115787' => array(
'start' => '5996016',
'end' => '6038328',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-008'
),
'ENSMUST00000115788' => array(
'start' => '5990063',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-015'
),
'ENSMUST00000115789' => array(
'start' => '5987986',
'end' => '6039341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-007'
),
'ENSMUST00000115790' => array(
'start' => '5975740',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-006'
),
'ENSMUST00000115791' => array(
'start' => '5941280',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-201'
),
'ENSMUST00000126881' => array(
'start' => '6025076',
'end' => '6037462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-014'
),
'ENSMUST00000130661' => array(
'start' => '6007612',
'end' => '6010490',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Synj2-012'
),
'ENSMUST00000134767' => array(
'start' => '5941378',
'end' => '6039390',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Synj2-002'
),
'ENSMUST00000142409' => array(
'start' => '5975586',
'end' => '6026290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-005'
),
'ENSMUST00000146009' => array(
'start' => '5941280',
'end' => '6032793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-003'
),
'ENSMUST00000154114' => array(
'start' => '6013549',
'end' => '6038373',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-013'
)
),
'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_00055M_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00055M_0001' => array(
'genes_in_region' => array(
'ENSG00000078269' => array(
[maximum depth reached]
),
'ENSG00000122335' => array(
[maximum depth reached]
),
'ENSG00000233496' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Colon',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Bladder',
(int) 33 => 'Bladder',
(int) 34 => 'Muscle',
(int) 35 => 'Testis',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Ovary',
(int) 42 => 'Adipose',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000078269' => 'synaptojanin 2',
'ENSG00000122335' => 'serine active site containing 1',
'ENSG00000233496' => 'SYNJ2 intronic transcript 1 (non-protein coding)',
'ENSMUSG00000015659' => 'serine active site containing 1',
'ENSMUSG00000023805' => 'synaptojanin 2'
)
$gene_name_arr = array(
'ENSG00000078269' => 'SYNJ2',
'ENSG00000122335' => 'SERAC1',
'ENSG00000233496' => 'SYNJ2-IT1',
'ENSMUSG00000015659' => 'Serac1',
'ENSMUSG00000023805' => 'Synj2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00055M_0001',
'tax_id' => '9606',
'chromosome' => '6',
'seq_start' => '157981887',
'seq_end' => '158168270',
'region_length' => '186383',
'region_type' => 'CGP',
'el_id' => 'ENSG00000078269-ENSG00000122335'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00055M_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '5941280',
'seq_end' => '6079741',
'region_length' => '138461',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000023805-ENSMUSG00000015659'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 26 => 'Brain',
(int) 32 => 'Breast',
(int) 39 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 62 => 'Liver',
(int) 72 => 'Lung',
(int) 80 => 'Muscle',
(int) 89 => 'Ovary',
(int) 99 => 'Placenta',
(int) 107 => '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(
'ENST00000355585' => array(
'start' => '157981887',
'end' => '158099176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-002'
),
'ENST00000367112' => array(
'start' => '158077680',
'end' => '158097854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-003'
),
'ENST00000367113' => array(
'start' => '157982038',
'end' => '158030497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-004'
),
'ENST00000367122' => array(
'start' => '158070128',
'end' => '158096463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-201'
),
'ENST00000449320' => array(
'start' => '158017465',
'end' => '158028971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-005'
),
'ENST00000485863' => array(
'start' => '158033490',
'end' => '158063872',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SYNJ2-001'
),
'ENST00000367101' => array(
'start' => '158114731',
'end' => '158168259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-002'
),
'ENST00000367104' => array(
'start' => '158109515',
'end' => '158168270',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-001'
),
'ENST00000435180' => array(
'start' => '158114691',
'end' => '158119061',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-003'
),
'ENST00000606965' => array(
'start' => '158114471',
'end' => '158168171',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-004'
),
'ENST00000607000' => array(
'start' => '158145920',
'end' => '158159298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-007'
),
'ENST00000607071' => array(
'start' => '158110627',
'end' => '158166159',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-008'
),
'ENST00000607742' => array(
'start' => '158109691',
'end' => '158168246',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-005'
),
'ENST00000442328' => array(
'start' => '158001107',
'end' => '158002383',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'SYNJ2-IT1-001'
),
'ENSMUST00000024570' => array(
'start' => '6044066',
'end' => '6079727',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-002'
),
'ENSMUST00000097432' => array(
'start' => '6042196',
'end' => '6079741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-001'
),
'ENSMUST00000139542' => array(
'start' => '6064949',
'end' => '6079733',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-004'
),
'ENSMUST00000144284' => array(
'start' => '6050027',
'end' => '6051388',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Serac1-005'
),
'ENSMUST00000153325' => array(
'start' => '6043904',
'end' => '6050055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-006'
),
'ENSMUST00000061091' => array(
'start' => '5975641',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-004'
),
'ENSMUST00000080283' => array(
'start' => '5941403',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-001'
),
'ENSMUST00000115784' => array(
'start' => '6007580',
'end' => '6032929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-010'
),
'ENSMUST00000115785' => array(
'start' => '6007597',
'end' => '6038406',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-011'
),
'ENSMUST00000115786' => array(
'start' => '5996846',
'end' => '6020555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-009'
),
'ENSMUST00000115787' => array(
'start' => '5996016',
'end' => '6038328',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-008'
),
'ENSMUST00000115788' => array(
'start' => '5990063',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-015'
),
'ENSMUST00000115789' => array(
'start' => '5987986',
'end' => '6039341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-007'
),
'ENSMUST00000115790' => array(
'start' => '5975740',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-006'
),
'ENSMUST00000115791' => array(
'start' => '5941280',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-201'
),
'ENSMUST00000126881' => array(
'start' => '6025076',
'end' => '6037462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-014'
),
'ENSMUST00000130661' => array(
'start' => '6007612',
'end' => '6010490',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Synj2-012'
),
'ENSMUST00000134767' => array(
'start' => '5941378',
'end' => '6039390',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Synj2-002'
),
'ENSMUST00000142409' => array(
'start' => '5975586',
'end' => '6026290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-005'
),
'ENSMUST00000146009' => array(
'start' => '5941280',
'end' => '6032793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-003'
),
'ENSMUST00000154114' => array(
'start' => '6013549',
'end' => '6038373',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-013'
)
)
$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_00055M_0001' => array(
'genes_in_region' => array(
'ENSG00000078269' => array(
[maximum depth reached]
),
'ENSG00000122335' => array(
[maximum depth reached]
),
'ENSG00000233496' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Colon',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Bladder',
(int) 33 => 'Bladder',
(int) 34 => 'Muscle',
(int) 35 => 'Testis',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Ovary',
(int) 42 => 'Adipose',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00055M_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '5941280',
'seq_end' => '6079741',
'region_length' => '138461',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000023805-ENSMUSG00000015659'
)
)
$gene_el = array(
'ENST00000442328' => array(
'Adipose' => array(
'average_FPKM' => '0.031',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.160',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.152',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.109',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.169',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.16'
),
'Kidney' => array(
'average_FPKM' => '0.065',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.298',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.057',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.190',
'stddev_FPKM' => '0.06'
),
'Testis' => array(
'average_FPKM' => '0.481',
'stddev_FPKM' => '0.39'
)
)
)
$gene_key = 'ENSG00000233496'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.031',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.160',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.152',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.109',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.169',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.16'
),
'Kidney' => array(
'average_FPKM' => '0.065',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.298',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.057',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.190',
'stddev_FPKM' => '0.06'
),
'Testis' => array(
'average_FPKM' => '0.481',
'stddev_FPKM' => '0.39'
)
)
$tran_key = 'ENST00000442328'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00055M_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000078269' => 'synaptojanin 2',
'ENSG00000122335' => 'serine active site containing 1',
'ENSG00000233496' => 'SYNJ2 intronic transcript 1 (non-protein coding)',
'ENSMUSG00000015659' => 'serine active site containing 1',
'ENSMUSG00000023805' => 'synaptojanin 2'
),
'gene_name_arr' => array(
'ENSG00000078269' => 'SYNJ2',
'ENSG00000122335' => 'SERAC1',
'ENSG00000233496' => 'SYNJ2-IT1',
'ENSMUSG00000015659' => 'Serac1',
'ENSMUSG00000023805' => 'Synj2'
),
'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) 8 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 26 => 'Brain',
(int) 32 => 'Breast',
(int) 39 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 62 => 'Liver',
(int) 72 => 'Lung',
(int) 80 => 'Muscle',
(int) 89 => 'Ovary',
(int) 99 => 'Placenta',
(int) 107 => '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(
'ENST00000355585' => array(
'start' => '157981887',
'end' => '158099176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-002'
),
'ENST00000367112' => array(
'start' => '158077680',
'end' => '158097854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-003'
),
'ENST00000367113' => array(
'start' => '157982038',
'end' => '158030497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-004'
),
'ENST00000367122' => array(
'start' => '158070128',
'end' => '158096463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-201'
),
'ENST00000449320' => array(
'start' => '158017465',
'end' => '158028971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-005'
),
'ENST00000485863' => array(
'start' => '158033490',
'end' => '158063872',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SYNJ2-001'
),
'ENST00000367101' => array(
'start' => '158114731',
'end' => '158168259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-002'
),
'ENST00000367104' => array(
'start' => '158109515',
'end' => '158168270',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-001'
),
'ENST00000435180' => array(
'start' => '158114691',
'end' => '158119061',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-003'
),
'ENST00000606965' => array(
'start' => '158114471',
'end' => '158168171',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-004'
),
'ENST00000607000' => array(
'start' => '158145920',
'end' => '158159298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-007'
),
'ENST00000607071' => array(
'start' => '158110627',
'end' => '158166159',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-008'
),
'ENST00000607742' => array(
'start' => '158109691',
'end' => '158168246',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-005'
),
'ENST00000442328' => array(
'start' => '158001107',
'end' => '158002383',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'SYNJ2-IT1-001'
),
'ENSMUST00000024570' => array(
'start' => '6044066',
'end' => '6079727',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-002'
),
'ENSMUST00000097432' => array(
'start' => '6042196',
'end' => '6079741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-001'
),
'ENSMUST00000139542' => array(
'start' => '6064949',
'end' => '6079733',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-004'
),
'ENSMUST00000144284' => array(
'start' => '6050027',
'end' => '6051388',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Serac1-005'
),
'ENSMUST00000153325' => array(
'start' => '6043904',
'end' => '6050055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-006'
),
'ENSMUST00000061091' => array(
'start' => '5975641',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-004'
),
'ENSMUST00000080283' => array(
'start' => '5941403',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-001'
),
'ENSMUST00000115784' => array(
'start' => '6007580',
'end' => '6032929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-010'
),
'ENSMUST00000115785' => array(
'start' => '6007597',
'end' => '6038406',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-011'
),
'ENSMUST00000115786' => array(
'start' => '5996846',
'end' => '6020555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-009'
),
'ENSMUST00000115787' => array(
'start' => '5996016',
'end' => '6038328',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-008'
),
'ENSMUST00000115788' => array(
'start' => '5990063',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-015'
),
'ENSMUST00000115789' => array(
'start' => '5987986',
'end' => '6039341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-007'
),
'ENSMUST00000115790' => array(
'start' => '5975740',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-006'
),
'ENSMUST00000115791' => array(
'start' => '5941280',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-201'
),
'ENSMUST00000126881' => array(
'start' => '6025076',
'end' => '6037462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-014'
),
'ENSMUST00000130661' => array(
'start' => '6007612',
'end' => '6010490',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Synj2-012'
),
'ENSMUST00000134767' => array(
'start' => '5941378',
'end' => '6039390',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Synj2-002'
),
'ENSMUST00000142409' => array(
'start' => '5975586',
'end' => '6026290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-005'
),
'ENSMUST00000146009' => array(
'start' => '5941280',
'end' => '6032793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-003'
),
'ENSMUST00000154114' => array(
'start' => '6013549',
'end' => '6038373',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-013'
)
),
'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_00055M_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00055M_0001' => array(
'genes_in_region' => array(
'ENSG00000078269' => array(
[maximum depth reached]
),
'ENSG00000122335' => array(
[maximum depth reached]
),
'ENSG00000233496' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Colon',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Bladder',
(int) 33 => 'Bladder',
(int) 34 => 'Muscle',
(int) 35 => 'Testis',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Ovary',
(int) 42 => 'Adipose',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000078269' => 'synaptojanin 2',
'ENSG00000122335' => 'serine active site containing 1',
'ENSG00000233496' => 'SYNJ2 intronic transcript 1 (non-protein coding)',
'ENSMUSG00000015659' => 'serine active site containing 1',
'ENSMUSG00000023805' => 'synaptojanin 2'
)
$gene_name_arr = array(
'ENSG00000078269' => 'SYNJ2',
'ENSG00000122335' => 'SERAC1',
'ENSG00000233496' => 'SYNJ2-IT1',
'ENSMUSG00000015659' => 'Serac1',
'ENSMUSG00000023805' => 'Synj2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00055M_0001',
'tax_id' => '9606',
'chromosome' => '6',
'seq_start' => '157981887',
'seq_end' => '158168270',
'region_length' => '186383',
'region_type' => 'CGP',
'el_id' => 'ENSG00000078269-ENSG00000122335'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00055M_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '5941280',
'seq_end' => '6079741',
'region_length' => '138461',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000023805-ENSMUSG00000015659'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 8 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 26 => 'Brain',
(int) 32 => 'Breast',
(int) 39 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 62 => 'Liver',
(int) 72 => 'Lung',
(int) 80 => 'Muscle',
(int) 89 => 'Ovary',
(int) 99 => 'Placenta',
(int) 107 => '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(
'ENST00000355585' => array(
'start' => '157981887',
'end' => '158099176',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-002'
),
'ENST00000367112' => array(
'start' => '158077680',
'end' => '158097854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-003'
),
'ENST00000367113' => array(
'start' => '157982038',
'end' => '158030497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-004'
),
'ENST00000367122' => array(
'start' => '158070128',
'end' => '158096463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-201'
),
'ENST00000449320' => array(
'start' => '158017465',
'end' => '158028971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SYNJ2-005'
),
'ENST00000485863' => array(
'start' => '158033490',
'end' => '158063872',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SYNJ2-001'
),
'ENST00000367101' => array(
'start' => '158114731',
'end' => '158168259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-002'
),
'ENST00000367104' => array(
'start' => '158109515',
'end' => '158168270',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-001'
),
'ENST00000435180' => array(
'start' => '158114691',
'end' => '158119061',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-003'
),
'ENST00000606965' => array(
'start' => '158114471',
'end' => '158168171',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-004'
),
'ENST00000607000' => array(
'start' => '158145920',
'end' => '158159298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERAC1-007'
),
'ENST00000607071' => array(
'start' => '158110627',
'end' => '158166159',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-008'
),
'ENST00000607742' => array(
'start' => '158109691',
'end' => '158168246',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SERAC1-005'
),
'ENST00000442328' => array(
'start' => '158001107',
'end' => '158002383',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'SYNJ2-IT1-001'
),
'ENSMUST00000024570' => array(
'start' => '6044066',
'end' => '6079727',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-002'
),
'ENSMUST00000097432' => array(
'start' => '6042196',
'end' => '6079741',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serac1-001'
),
'ENSMUST00000139542' => array(
'start' => '6064949',
'end' => '6079733',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-004'
),
'ENSMUST00000144284' => array(
'start' => '6050027',
'end' => '6051388',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Serac1-005'
),
'ENSMUST00000153325' => array(
'start' => '6043904',
'end' => '6050055',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Serac1-006'
),
'ENSMUST00000061091' => array(
'start' => '5975641',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-004'
),
'ENSMUST00000080283' => array(
'start' => '5941403',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-001'
),
'ENSMUST00000115784' => array(
'start' => '6007580',
'end' => '6032929',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-010'
),
'ENSMUST00000115785' => array(
'start' => '6007597',
'end' => '6038406',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-011'
),
'ENSMUST00000115786' => array(
'start' => '5996846',
'end' => '6020555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-009'
),
'ENSMUST00000115787' => array(
'start' => '5996016',
'end' => '6038328',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-008'
),
'ENSMUST00000115788' => array(
'start' => '5990063',
'end' => '6044290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-015'
),
'ENSMUST00000115789' => array(
'start' => '5987986',
'end' => '6039341',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-007'
),
'ENSMUST00000115790' => array(
'start' => '5975740',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-006'
),
'ENSMUST00000115791' => array(
'start' => '5941280',
'end' => '6038555',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-201'
),
'ENSMUST00000126881' => array(
'start' => '6025076',
'end' => '6037462',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-014'
),
'ENSMUST00000130661' => array(
'start' => '6007612',
'end' => '6010490',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Synj2-012'
),
'ENSMUST00000134767' => array(
'start' => '5941378',
'end' => '6039390',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Synj2-002'
),
'ENSMUST00000142409' => array(
'start' => '5975586',
'end' => '6026290',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-005'
),
'ENSMUST00000146009' => array(
'start' => '5941280',
'end' => '6032793',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-003'
),
'ENSMUST00000154114' => array(
'start' => '6013549',
'end' => '6038373',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Synj2-013'
)
)
$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_00055M_0001' => array(
'genes_in_region' => array(
'ENSG00000078269' => array(
[maximum depth reached]
),
'ENSG00000122335' => array(
[maximum depth reached]
),
'ENSG00000233496' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Colon',
(int) 17 => 'Muscle',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Heart',
(int) 25 => 'Kidney',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Bladder',
(int) 33 => 'Bladder',
(int) 34 => 'Muscle',
(int) 35 => 'Testis',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Heart',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Ovary',
(int) 42 => 'Adipose',
(int) 43 => 'Adrenal',
(int) 44 => 'Bladder',
(int) 45 => 'Brain',
(int) 46 => 'Breast',
(int) 47 => 'Colon',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Liver',
(int) 51 => 'Lung',
(int) 52 => 'Muscle',
(int) 53 => 'Ovary',
(int) 54 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00055M_0002',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '5941280',
'seq_end' => '6079741',
'region_length' => '138461',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000023805-ENSMUSG00000015659'
)
)
$gene_el = array(
'ENST00000442328' => array(
'Adipose' => array(
'average_FPKM' => '0.031',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.160',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.152',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.109',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.169',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.16'
),
'Kidney' => array(
'average_FPKM' => '0.065',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.298',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.057',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.190',
'stddev_FPKM' => '0.06'
),
'Testis' => array(
'average_FPKM' => '0.481',
'stddev_FPKM' => '0.39'
)
)
)
$gene_key = 'ENSG00000233496'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.031',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.160',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.152',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.109',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.169',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.16'
),
'Kidney' => array(
'average_FPKM' => '0.065',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.298',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.057',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.190',
'stddev_FPKM' => '0.06'
),
'Testis' => array(
'average_FPKM' => '0.481',
'stddev_FPKM' => '0.39'
)
)
$tran_key = 'ENST00000442328'
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
(SYNJ2)