| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000001240-ENSMUSG00000078656 |
CGP |
10090 |
11:101246028-101259549  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0004JZ_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_0004JZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000131475' => 'vacuolar protein sorting 25 homolog (S. cerevisiae)',
'ENSG00000131477' => 'receptor (G protein-coupled) activity modifying protein 2',
'ENSG00000197291' => 'RAMP2 antisense RNA 1',
'ENSMUSG00000001240' => 'receptor (calcitonin) activity modifying protein 2',
'ENSMUSG00000078656' => 'vacuolar protein sorting 25 (yeast)'
),
'gene_name_arr' => array(
'ENSG00000131475' => 'VPS25',
'ENSG00000131477' => 'RAMP2',
'ENSG00000197291' => 'RAMP2-AS1',
'ENSMUSG00000001240' => 'Ramp2',
'ENSMUSG00000078656' => 'Vps25'
),
'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) 5 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 31 => 'Breast',
(int) 40 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 64 => 'Liver',
(int) 73 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => 'Placenta',
(int) 104 => '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) 32,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000253794' => array(
'start' => '42773436',
'end' => '42779599',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-001'
),
'ENST00000589219' => array(
'start' => '42773464',
'end' => '42775348',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-006'
),
'ENST00000589520' => array(
'start' => '42773508',
'end' => '42779374',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-005'
),
'ENST00000589577' => array(
'start' => '42773469',
'end' => '42776320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS25-004'
),
'ENST00000590339' => array(
'start' => '42773480',
'end' => '42779006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-002'
),
'ENST00000591584' => array(
'start' => '42773458',
'end' => '42774328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-003'
),
'ENST00000253796' => array(
'start' => '42761194',
'end' => '42763036',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-001'
),
'ENST00000587142' => array(
'start' => '42761258',
'end' => '42762854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-002'
),
'ENST00000588576' => array(
'start' => '42761258',
'end' => '42763002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-003'
),
'ENST00000588928' => array(
'start' => '42760805',
'end' => '42762698',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-005'
),
'ENST00000589683' => array(
'start' => '42760775',
'end' => '42763041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-004'
),
'ENST00000591972' => array(
'start' => '42758447',
'end' => '42761899',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RAMP2-006'
),
'ENST00000587694' => array(
'start' => '42753931',
'end' => '42761117',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-003'
),
'ENST00000589716' => array(
'start' => '42753914',
'end' => '42761257',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-004'
),
'ENST00000591082' => array(
'start' => '42756199',
'end' => '42761119',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-005'
),
'ENST00000592195' => array(
'start' => '42758295',
'end' => '42761011',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-002'
),
'ENST00000592670' => array(
'start' => '42753914',
'end' => '42761103',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-001'
),
'ENSMUST00000107282' => array(
'start' => '101247093',
'end' => '101248064',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-003'
),
'ENSMUST00000122006' => array(
'start' => '101246429',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-002'
),
'ENSMUST00000128260' => array(
'start' => '101246391',
'end' => '101259546',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-008'
),
'ENSMUST00000129680' => array(
'start' => '101246028',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-001'
),
'ENSMUST00000138229' => array(
'start' => '101246933',
'end' => '101248250',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-007'
),
'ENSMUST00000149006' => array(
'start' => '101246312',
'end' => '101247684',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-004'
),
'ENSMUST00000149585' => array(
'start' => '101246432',
'end' => '101248250',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-005'
),
'ENSMUST00000151830' => array(
'start' => '101246567',
'end' => '101247636',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-006'
),
'ENSMUST00000007533' => array(
'start' => '101253707',
'end' => '101258049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-002'
),
'ENSMUST00000042477' => array(
'start' => '101253707',
'end' => '101259549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-001'
),
'ENSMUST00000100414' => array(
'start' => '101253729',
'end' => '101259545',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-003'
),
'ENSMUST00000107280' => array(
'start' => '101253735',
'end' => '101259323',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-007'
),
'ENSMUST00000121331' => array(
'start' => '101253753',
'end' => '101259056',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-004'
),
'ENSMUST00000123529' => array(
'start' => '101253764',
'end' => '101259210',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps25-005'
),
'ENSMUST00000144306' => array(
'start' => '101253730',
'end' => '101258916',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps25-006'
)
),
'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_0004JZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004JZ_0001' => array(
'genes_in_region' => array(
'ENSG00000131475' => array(
[maximum depth reached]
),
'ENSG00000131477' => array(
[maximum depth reached]
),
'ENSG00000197291' => 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 => 'Bladder',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Placenta',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(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 => 'Adrenal',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Kidney',
(int) 36 => 'Testis',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Bladder',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Breast',
(int) 51 => 'Liver',
(int) 52 => 'Brain',
(int) 53 => 'Colon',
(int) 54 => 'Kidney',
(int) 55 => 'Muscle',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Lung',
(int) 61 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000131475' => 'vacuolar protein sorting 25 homolog (S. cerevisiae)',
'ENSG00000131477' => 'receptor (G protein-coupled) activity modifying protein 2',
'ENSG00000197291' => 'RAMP2 antisense RNA 1',
'ENSMUSG00000001240' => 'receptor (calcitonin) activity modifying protein 2',
'ENSMUSG00000078656' => 'vacuolar protein sorting 25 (yeast)'
)
$gene_name_arr = array(
'ENSG00000131475' => 'VPS25',
'ENSG00000131477' => 'RAMP2',
'ENSG00000197291' => 'RAMP2-AS1',
'ENSMUSG00000001240' => 'Ramp2',
'ENSMUSG00000078656' => 'Vps25'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JZ_0001',
'tax_id' => '9606',
'chromosome' => '17',
'seq_start' => '42758447',
'seq_end' => '42779599',
'region_length' => '21152',
'region_type' => 'CGP',
'el_id' => 'ENSG00000131477-ENSG00000131475'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JZ_0002',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '101246028',
'seq_end' => '101259549',
'region_length' => '13521',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001240-ENSMUSG00000078656'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 31 => 'Breast',
(int) 40 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 64 => 'Liver',
(int) 73 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => 'Placenta',
(int) 104 => '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) 32
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000253794' => array(
'start' => '42773436',
'end' => '42779599',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-001'
),
'ENST00000589219' => array(
'start' => '42773464',
'end' => '42775348',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-006'
),
'ENST00000589520' => array(
'start' => '42773508',
'end' => '42779374',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-005'
),
'ENST00000589577' => array(
'start' => '42773469',
'end' => '42776320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS25-004'
),
'ENST00000590339' => array(
'start' => '42773480',
'end' => '42779006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-002'
),
'ENST00000591584' => array(
'start' => '42773458',
'end' => '42774328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-003'
),
'ENST00000253796' => array(
'start' => '42761194',
'end' => '42763036',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-001'
),
'ENST00000587142' => array(
'start' => '42761258',
'end' => '42762854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-002'
),
'ENST00000588576' => array(
'start' => '42761258',
'end' => '42763002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-003'
),
'ENST00000588928' => array(
'start' => '42760805',
'end' => '42762698',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-005'
),
'ENST00000589683' => array(
'start' => '42760775',
'end' => '42763041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-004'
),
'ENST00000591972' => array(
'start' => '42758447',
'end' => '42761899',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RAMP2-006'
),
'ENST00000587694' => array(
'start' => '42753931',
'end' => '42761117',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-003'
),
'ENST00000589716' => array(
'start' => '42753914',
'end' => '42761257',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-004'
),
'ENST00000591082' => array(
'start' => '42756199',
'end' => '42761119',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-005'
),
'ENST00000592195' => array(
'start' => '42758295',
'end' => '42761011',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-002'
),
'ENST00000592670' => array(
'start' => '42753914',
'end' => '42761103',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-001'
),
'ENSMUST00000107282' => array(
'start' => '101247093',
'end' => '101248064',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-003'
),
'ENSMUST00000122006' => array(
'start' => '101246429',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-002'
),
'ENSMUST00000128260' => array(
'start' => '101246391',
'end' => '101259546',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-008'
),
'ENSMUST00000129680' => array(
'start' => '101246028',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-001'
),
'ENSMUST00000138229' => array(
'start' => '101246933',
'end' => '101248250',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-007'
),
'ENSMUST00000149006' => array(
'start' => '101246312',
'end' => '101247684',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-004'
),
'ENSMUST00000149585' => array(
'start' => '101246432',
'end' => '101248250',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-005'
),
'ENSMUST00000151830' => array(
'start' => '101246567',
'end' => '101247636',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-006'
),
'ENSMUST00000007533' => array(
'start' => '101253707',
'end' => '101258049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-002'
),
'ENSMUST00000042477' => array(
'start' => '101253707',
'end' => '101259549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-001'
),
'ENSMUST00000100414' => array(
'start' => '101253729',
'end' => '101259545',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-003'
),
'ENSMUST00000107280' => array(
'start' => '101253735',
'end' => '101259323',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-007'
),
'ENSMUST00000121331' => array(
'start' => '101253753',
'end' => '101259056',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-004'
),
'ENSMUST00000123529' => array(
'start' => '101253764',
'end' => '101259210',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps25-005'
),
'ENSMUST00000144306' => array(
'start' => '101253730',
'end' => '101258916',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps25-006'
)
)
$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_0004JZ_0001' => array(
'genes_in_region' => array(
'ENSG00000131475' => array(
[maximum depth reached]
),
'ENSG00000131477' => array(
[maximum depth reached]
),
'ENSG00000197291' => 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 => 'Bladder',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Placenta',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(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 => 'Adrenal',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Kidney',
(int) 36 => 'Testis',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Bladder',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Breast',
(int) 51 => 'Liver',
(int) 52 => 'Brain',
(int) 53 => 'Colon',
(int) 54 => 'Kidney',
(int) 55 => 'Muscle',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Lung',
(int) 61 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JZ_0002',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '101246028',
'seq_end' => '101259549',
'region_length' => '13521',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001240-ENSMUSG00000078656'
)
)
$gene_el = array(
'ENST00000587694' => array(
'Breast' => array(
'average_FPKM' => '0.539',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.290',
'stddev_FPKM' => '0.00'
)
),
'ENST00000589716' => array(
'Brain' => array(
'average_FPKM' => '0.405',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.211',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
)
),
'ENST00000591082' => array(
'Muscle' => array(
'average_FPKM' => '0.963',
'stddev_FPKM' => '0.00'
)
),
'ENST00000592195' => array(),
'ENST00000592670' => array(
'Bladder' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.132',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.156',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.381',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.655',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000197291'
$is_first = false
$tran_el = array(
'Bladder' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.132',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.156',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.381',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.655',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000592670'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0004JZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000131475' => 'vacuolar protein sorting 25 homolog (S. cerevisiae)',
'ENSG00000131477' => 'receptor (G protein-coupled) activity modifying protein 2',
'ENSG00000197291' => 'RAMP2 antisense RNA 1',
'ENSMUSG00000001240' => 'receptor (calcitonin) activity modifying protein 2',
'ENSMUSG00000078656' => 'vacuolar protein sorting 25 (yeast)'
),
'gene_name_arr' => array(
'ENSG00000131475' => 'VPS25',
'ENSG00000131477' => 'RAMP2',
'ENSG00000197291' => 'RAMP2-AS1',
'ENSMUSG00000001240' => 'Ramp2',
'ENSMUSG00000078656' => 'Vps25'
),
'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) 5 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 31 => 'Breast',
(int) 40 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 64 => 'Liver',
(int) 73 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => 'Placenta',
(int) 104 => '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) 32,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000253794' => array(
'start' => '42773436',
'end' => '42779599',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-001'
),
'ENST00000589219' => array(
'start' => '42773464',
'end' => '42775348',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-006'
),
'ENST00000589520' => array(
'start' => '42773508',
'end' => '42779374',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-005'
),
'ENST00000589577' => array(
'start' => '42773469',
'end' => '42776320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS25-004'
),
'ENST00000590339' => array(
'start' => '42773480',
'end' => '42779006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-002'
),
'ENST00000591584' => array(
'start' => '42773458',
'end' => '42774328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-003'
),
'ENST00000253796' => array(
'start' => '42761194',
'end' => '42763036',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-001'
),
'ENST00000587142' => array(
'start' => '42761258',
'end' => '42762854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-002'
),
'ENST00000588576' => array(
'start' => '42761258',
'end' => '42763002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-003'
),
'ENST00000588928' => array(
'start' => '42760805',
'end' => '42762698',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-005'
),
'ENST00000589683' => array(
'start' => '42760775',
'end' => '42763041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-004'
),
'ENST00000591972' => array(
'start' => '42758447',
'end' => '42761899',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RAMP2-006'
),
'ENST00000587694' => array(
'start' => '42753931',
'end' => '42761117',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-003'
),
'ENST00000589716' => array(
'start' => '42753914',
'end' => '42761257',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-004'
),
'ENST00000591082' => array(
'start' => '42756199',
'end' => '42761119',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-005'
),
'ENST00000592195' => array(
'start' => '42758295',
'end' => '42761011',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-002'
),
'ENST00000592670' => array(
'start' => '42753914',
'end' => '42761103',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-001'
),
'ENSMUST00000107282' => array(
'start' => '101247093',
'end' => '101248064',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-003'
),
'ENSMUST00000122006' => array(
'start' => '101246429',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-002'
),
'ENSMUST00000128260' => array(
'start' => '101246391',
'end' => '101259546',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-008'
),
'ENSMUST00000129680' => array(
'start' => '101246028',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-001'
),
'ENSMUST00000138229' => array(
'start' => '101246933',
'end' => '101248250',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-007'
),
'ENSMUST00000149006' => array(
'start' => '101246312',
'end' => '101247684',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-004'
),
'ENSMUST00000149585' => array(
'start' => '101246432',
'end' => '101248250',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-005'
),
'ENSMUST00000151830' => array(
'start' => '101246567',
'end' => '101247636',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-006'
),
'ENSMUST00000007533' => array(
'start' => '101253707',
'end' => '101258049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-002'
),
'ENSMUST00000042477' => array(
'start' => '101253707',
'end' => '101259549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-001'
),
'ENSMUST00000100414' => array(
'start' => '101253729',
'end' => '101259545',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-003'
),
'ENSMUST00000107280' => array(
'start' => '101253735',
'end' => '101259323',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-007'
),
'ENSMUST00000121331' => array(
'start' => '101253753',
'end' => '101259056',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-004'
),
'ENSMUST00000123529' => array(
'start' => '101253764',
'end' => '101259210',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps25-005'
),
'ENSMUST00000144306' => array(
'start' => '101253730',
'end' => '101258916',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps25-006'
)
),
'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_0004JZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004JZ_0001' => array(
'genes_in_region' => array(
'ENSG00000131475' => array(
[maximum depth reached]
),
'ENSG00000131477' => array(
[maximum depth reached]
),
'ENSG00000197291' => 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 => 'Bladder',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Placenta',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(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 => 'Adrenal',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Kidney',
(int) 36 => 'Testis',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Bladder',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Breast',
(int) 51 => 'Liver',
(int) 52 => 'Brain',
(int) 53 => 'Colon',
(int) 54 => 'Kidney',
(int) 55 => 'Muscle',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Lung',
(int) 61 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000131475' => 'vacuolar protein sorting 25 homolog (S. cerevisiae)',
'ENSG00000131477' => 'receptor (G protein-coupled) activity modifying protein 2',
'ENSG00000197291' => 'RAMP2 antisense RNA 1',
'ENSMUSG00000001240' => 'receptor (calcitonin) activity modifying protein 2',
'ENSMUSG00000078656' => 'vacuolar protein sorting 25 (yeast)'
)
$gene_name_arr = array(
'ENSG00000131475' => 'VPS25',
'ENSG00000131477' => 'RAMP2',
'ENSG00000197291' => 'RAMP2-AS1',
'ENSMUSG00000001240' => 'Ramp2',
'ENSMUSG00000078656' => 'Vps25'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JZ_0001',
'tax_id' => '9606',
'chromosome' => '17',
'seq_start' => '42758447',
'seq_end' => '42779599',
'region_length' => '21152',
'region_type' => 'CGP',
'el_id' => 'ENSG00000131477-ENSG00000131475'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JZ_0002',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '101246028',
'seq_end' => '101259549',
'region_length' => '13521',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001240-ENSMUSG00000078656'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 14 => 'Bladder',
(int) 22 => 'Brain',
(int) 31 => 'Breast',
(int) 40 => 'Colon',
(int) 47 => 'Heart',
(int) 55 => 'Kidney',
(int) 64 => 'Liver',
(int) 73 => 'Lung',
(int) 80 => 'Muscle',
(int) 87 => 'Ovary',
(int) 96 => 'Placenta',
(int) 104 => '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) 32
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000253794' => array(
'start' => '42773436',
'end' => '42779599',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-001'
),
'ENST00000589219' => array(
'start' => '42773464',
'end' => '42775348',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-006'
),
'ENST00000589520' => array(
'start' => '42773508',
'end' => '42779374',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-005'
),
'ENST00000589577' => array(
'start' => '42773469',
'end' => '42776320',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'VPS25-004'
),
'ENST00000590339' => array(
'start' => '42773480',
'end' => '42779006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'VPS25-002'
),
'ENST00000591584' => array(
'start' => '42773458',
'end' => '42774328',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'VPS25-003'
),
'ENST00000253796' => array(
'start' => '42761194',
'end' => '42763036',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-001'
),
'ENST00000587142' => array(
'start' => '42761258',
'end' => '42762854',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-002'
),
'ENST00000588576' => array(
'start' => '42761258',
'end' => '42763002',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-003'
),
'ENST00000588928' => array(
'start' => '42760805',
'end' => '42762698',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-005'
),
'ENST00000589683' => array(
'start' => '42760775',
'end' => '42763041',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RAMP2-004'
),
'ENST00000591972' => array(
'start' => '42758447',
'end' => '42761899',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RAMP2-006'
),
'ENST00000587694' => array(
'start' => '42753931',
'end' => '42761117',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-003'
),
'ENST00000589716' => array(
'start' => '42753914',
'end' => '42761257',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-004'
),
'ENST00000591082' => array(
'start' => '42756199',
'end' => '42761119',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-005'
),
'ENST00000592195' => array(
'start' => '42758295',
'end' => '42761011',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-002'
),
'ENST00000592670' => array(
'start' => '42753914',
'end' => '42761103',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RAMP2-AS1-001'
),
'ENSMUST00000107282' => array(
'start' => '101247093',
'end' => '101248064',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-003'
),
'ENSMUST00000122006' => array(
'start' => '101246429',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-002'
),
'ENSMUST00000128260' => array(
'start' => '101246391',
'end' => '101259546',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-008'
),
'ENSMUST00000129680' => array(
'start' => '101246028',
'end' => '101248250',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-001'
),
'ENSMUST00000138229' => array(
'start' => '101246933',
'end' => '101248250',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-007'
),
'ENSMUST00000149006' => array(
'start' => '101246312',
'end' => '101247684',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Ramp2-004'
),
'ENSMUST00000149585' => array(
'start' => '101246432',
'end' => '101248250',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Ramp2-005'
),
'ENSMUST00000151830' => array(
'start' => '101246567',
'end' => '101247636',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ramp2-006'
),
'ENSMUST00000007533' => array(
'start' => '101253707',
'end' => '101258049',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-002'
),
'ENSMUST00000042477' => array(
'start' => '101253707',
'end' => '101259549',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-001'
),
'ENSMUST00000100414' => array(
'start' => '101253729',
'end' => '101259545',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-003'
),
'ENSMUST00000107280' => array(
'start' => '101253735',
'end' => '101259323',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-007'
),
'ENSMUST00000121331' => array(
'start' => '101253753',
'end' => '101259056',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Vps25-004'
),
'ENSMUST00000123529' => array(
'start' => '101253764',
'end' => '101259210',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Vps25-005'
),
'ENSMUST00000144306' => array(
'start' => '101253730',
'end' => '101258916',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Vps25-006'
)
)
$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_0004JZ_0001' => array(
'genes_in_region' => array(
'ENSG00000131475' => array(
[maximum depth reached]
),
'ENSG00000131477' => array(
[maximum depth reached]
),
'ENSG00000197291' => 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 => 'Bladder',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Placenta',
(int) 18 => 'Testis',
(int) 19 => 'Adipose',
(int) 20 => 'Adrenal',
(int) 21 => 'Brain',
(int) 22 => 'Breast',
(int) 23 => 'Colon',
(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 => 'Adrenal',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Kidney',
(int) 36 => 'Testis',
(int) 37 => 'Bladder',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Bladder',
(int) 48 => 'Heart',
(int) 49 => 'Liver',
(int) 50 => 'Breast',
(int) 51 => 'Liver',
(int) 52 => 'Brain',
(int) 53 => 'Colon',
(int) 54 => 'Kidney',
(int) 55 => 'Muscle',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Heart',
(int) 59 => 'Kidney',
(int) 60 => 'Lung',
(int) 61 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004JZ_0002',
'tax_id' => '10090',
'chromosome' => '11',
'seq_start' => '101246028',
'seq_end' => '101259549',
'region_length' => '13521',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000001240-ENSMUSG00000078656'
)
)
$gene_el = array(
'ENST00000587694' => array(
'Breast' => array(
'average_FPKM' => '0.539',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.290',
'stddev_FPKM' => '0.00'
)
),
'ENST00000589716' => array(
'Brain' => array(
'average_FPKM' => '0.405',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.211',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
)
),
'ENST00000591082' => array(
'Muscle' => array(
'average_FPKM' => '0.963',
'stddev_FPKM' => '0.00'
)
),
'ENST00000592195' => array(),
'ENST00000592670' => array(
'Bladder' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.132',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.156',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.381',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.655',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000197291'
$is_first = false
$tran_el = array(
'Bladder' => array(
'average_FPKM' => '0.069',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.387',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.132',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.156',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.381',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.655',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000592670'
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
(VPS25)