| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000031970-ENSMUSG00000040220 |
CGP |
10090 |
8:123504718-123536649  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_00005T_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_00005T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000003249' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSG00000141013' => 'growth arrest-specific 8',
'ENSG00000221819' => 'GAS8 antisense RNA 1',
'ENSG00000222019' => 'urate (hydroxyiso-) hydrolase, pseudogene',
'ENSMUSG00000031970' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSMUSG00000040220' => 'growth arrest specific 8',
'ENSMUSG00000088632' => 'predicted gene, 22314'
),
'gene_name_arr' => array(
'ENSG00000003249' => 'DBNDD1',
'ENSG00000141013' => 'GAS8',
'ENSG00000221819' => 'C16orf3',
'ENSG00000222019' => 'URAHP',
'ENSMUSG00000031970' => 'Dbndd1',
'ENSMUSG00000040220' => 'Gas8',
'ENSMUSG00000088632' => 'Gm22314'
),
'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) 3 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Brain',
(int) 12 => 'Breast',
(int) 18 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 36 => 'Lung',
(int) 40 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 57 => '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) 40,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000002501' => array(
'start' => '90004865',
'end' => '90019473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-001'
),
'ENST00000304733' => array(
'start' => '90004865',
'end' => '90010121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-002'
),
'ENST00000392973' => array(
'start' => '90004873',
'end' => '90010211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-004'
),
'ENST00000568330' => array(
'start' => '90006480',
'end' => '90019880',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DBNDD1-006'
),
'ENST00000568662' => array(
'start' => '90006219',
'end' => '90009072',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DBNDD1-007'
),
'ENST00000568838' => array(
'start' => '90006189',
'end' => '90020128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-003'
),
'ENST00000623401' => array(
'start' => '90004873',
'end' => '90007761',
'transcript_biotype' => 'TEC',
'transcript_name' => 'DBNDD1-005'
),
'ENST00000268699' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-001'
),
'ENST00000536122' => array(
'start' => '90019629',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-201'
),
'ENST00000537797' => array(
'start' => '90022683',
'end' => '90036926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-005'
),
'ENST00000540721' => array(
'start' => '90022664',
'end' => '90042428',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-004'
),
'ENST00000561675' => array(
'start' => '90019731',
'end' => '90032858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-014'
),
'ENST00000563936' => array(
'start' => '90019643',
'end' => '90032856',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-008'
),
'ENST00000563980' => array(
'start' => '90019629',
'end' => '90031252',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-010'
),
'ENST00000564392' => array(
'start' => '90022086',
'end' => '90032790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-011'
),
'ENST00000564789' => array(
'start' => '90040043',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-018'
),
'ENST00000564802' => array(
'start' => '90035732',
'end' => '90037347',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-015'
),
'ENST00000564853' => array(
'start' => '90022670',
'end' => '90027996',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-012'
),
'ENST00000565000' => array(
'start' => '90035781',
'end' => '90036766',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-016'
),
'ENST00000565062' => array(
'start' => '90022653',
'end' => '90037046',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-003'
),
'ENST00000565957' => array(
'start' => '90019637',
'end' => '90031406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-007'
),
'ENST00000566266' => array(
'start' => '90022683',
'end' => '90044975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-002'
),
'ENST00000568284' => array(
'start' => '90042377',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-019'
),
'ENST00000568664' => array(
'start' => '90019730',
'end' => '90031499',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-013'
),
'ENST00000568705' => array(
'start' => '90019693',
'end' => '90032892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-009'
),
'ENST00000569399' => array(
'start' => '90036196',
'end' => '90040509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-017'
),
'ENST00000569558' => array(
'start' => '90029541',
'end' => '90044961',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-006'
),
'ENST00000620723' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-202'
),
'ENST00000408886' => array(
'start' => '90028908',
'end' => '90029342',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-001'
),
'ENST00000623094' => array(
'start' => '90028908',
'end' => '90029901',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-201'
),
'ENST00000409768' => array(
'start' => '90043429',
'end' => '90044610',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-004'
),
'ENST00000409873' => array(
'start' => '90039761',
'end' => '90047625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-001'
),
'ENST00000517889' => array(
'start' => '90042902',
'end' => '90047773',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-002'
),
'ENST00000521551' => array(
'start' => '90043802',
'end' => '90047190',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-003'
),
'ENST00000610227' => array(
'start' => '90043914',
'end' => '90047597',
'transcript_biotype' => 'transcribed_unprocessed_pseudogene',
'transcript_name' => 'URAHP-005'
),
'ENSMUST00000176155' => array(
'start' => '123505687',
'end' => '123515463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-002'
),
'ENSMUST00000176286' => array(
'start' => '123504718',
'end' => '123515455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-001'
),
'ENSMUST00000177240' => array(
'start' => '123505687',
'end' => '123515390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-003'
),
'ENSMUST00000093043' => array(
'start' => '123518835',
'end' => '123536649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gas8-201'
),
'ENSMUST00000158007' => array(
'start' => '123523260',
'end' => '123523540',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22314-201'
)
),
'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_00005T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00005T_0001' => array(
'genes_in_region' => array(
'ENSG00000003249' => array(
[maximum depth reached]
),
'ENSG00000141013' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Breast',
(int) 26 => 'Kidney',
(int) 27 => 'Ovary',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Breast',
(int) 45 => 'Liver',
(int) 46 => 'Bladder',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Ovary',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Kidney',
(int) 53 => 'Lung',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Muscle',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000003249' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSG00000141013' => 'growth arrest-specific 8',
'ENSG00000221819' => 'GAS8 antisense RNA 1',
'ENSG00000222019' => 'urate (hydroxyiso-) hydrolase, pseudogene',
'ENSMUSG00000031970' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSMUSG00000040220' => 'growth arrest specific 8',
'ENSMUSG00000088632' => 'predicted gene, 22314'
)
$gene_name_arr = array(
'ENSG00000003249' => 'DBNDD1',
'ENSG00000141013' => 'GAS8',
'ENSG00000221819' => 'C16orf3',
'ENSG00000222019' => 'URAHP',
'ENSMUSG00000031970' => 'Dbndd1',
'ENSMUSG00000040220' => 'Gas8',
'ENSMUSG00000088632' => 'Gm22314'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005T_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '90004865',
'seq_end' => '90044975',
'region_length' => '40110',
'region_type' => 'CGP',
'el_id' => 'ENSG00000003249-ENSG00000141013'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123504718',
'seq_end' => '123536649',
'region_length' => '31931',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031970-ENSMUSG00000040220'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Brain',
(int) 12 => 'Breast',
(int) 18 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 36 => 'Lung',
(int) 40 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 57 => '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) 40
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000002501' => array(
'start' => '90004865',
'end' => '90019473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-001'
),
'ENST00000304733' => array(
'start' => '90004865',
'end' => '90010121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-002'
),
'ENST00000392973' => array(
'start' => '90004873',
'end' => '90010211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-004'
),
'ENST00000568330' => array(
'start' => '90006480',
'end' => '90019880',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DBNDD1-006'
),
'ENST00000568662' => array(
'start' => '90006219',
'end' => '90009072',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DBNDD1-007'
),
'ENST00000568838' => array(
'start' => '90006189',
'end' => '90020128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-003'
),
'ENST00000623401' => array(
'start' => '90004873',
'end' => '90007761',
'transcript_biotype' => 'TEC',
'transcript_name' => 'DBNDD1-005'
),
'ENST00000268699' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-001'
),
'ENST00000536122' => array(
'start' => '90019629',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-201'
),
'ENST00000537797' => array(
'start' => '90022683',
'end' => '90036926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-005'
),
'ENST00000540721' => array(
'start' => '90022664',
'end' => '90042428',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-004'
),
'ENST00000561675' => array(
'start' => '90019731',
'end' => '90032858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-014'
),
'ENST00000563936' => array(
'start' => '90019643',
'end' => '90032856',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-008'
),
'ENST00000563980' => array(
'start' => '90019629',
'end' => '90031252',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-010'
),
'ENST00000564392' => array(
'start' => '90022086',
'end' => '90032790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-011'
),
'ENST00000564789' => array(
'start' => '90040043',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-018'
),
'ENST00000564802' => array(
'start' => '90035732',
'end' => '90037347',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-015'
),
'ENST00000564853' => array(
'start' => '90022670',
'end' => '90027996',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-012'
),
'ENST00000565000' => array(
'start' => '90035781',
'end' => '90036766',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-016'
),
'ENST00000565062' => array(
'start' => '90022653',
'end' => '90037046',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-003'
),
'ENST00000565957' => array(
'start' => '90019637',
'end' => '90031406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-007'
),
'ENST00000566266' => array(
'start' => '90022683',
'end' => '90044975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-002'
),
'ENST00000568284' => array(
'start' => '90042377',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-019'
),
'ENST00000568664' => array(
'start' => '90019730',
'end' => '90031499',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-013'
),
'ENST00000568705' => array(
'start' => '90019693',
'end' => '90032892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-009'
),
'ENST00000569399' => array(
'start' => '90036196',
'end' => '90040509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-017'
),
'ENST00000569558' => array(
'start' => '90029541',
'end' => '90044961',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-006'
),
'ENST00000620723' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-202'
),
'ENST00000408886' => array(
'start' => '90028908',
'end' => '90029342',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-001'
),
'ENST00000623094' => array(
'start' => '90028908',
'end' => '90029901',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-201'
),
'ENST00000409768' => array(
'start' => '90043429',
'end' => '90044610',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-004'
),
'ENST00000409873' => array(
'start' => '90039761',
'end' => '90047625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-001'
),
'ENST00000517889' => array(
'start' => '90042902',
'end' => '90047773',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-002'
),
'ENST00000521551' => array(
'start' => '90043802',
'end' => '90047190',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-003'
),
'ENST00000610227' => array(
'start' => '90043914',
'end' => '90047597',
'transcript_biotype' => 'transcribed_unprocessed_pseudogene',
'transcript_name' => 'URAHP-005'
),
'ENSMUST00000176155' => array(
'start' => '123505687',
'end' => '123515463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-002'
),
'ENSMUST00000176286' => array(
'start' => '123504718',
'end' => '123515455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-001'
),
'ENSMUST00000177240' => array(
'start' => '123505687',
'end' => '123515390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-003'
),
'ENSMUST00000093043' => array(
'start' => '123518835',
'end' => '123536649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gas8-201'
),
'ENSMUST00000158007' => array(
'start' => '123523260',
'end' => '123523540',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22314-201'
)
)
$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_00005T_0001' => array(
'genes_in_region' => array(
'ENSG00000003249' => array(
[maximum depth reached]
),
'ENSG00000141013' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Breast',
(int) 26 => 'Kidney',
(int) 27 => 'Ovary',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Breast',
(int) 45 => 'Liver',
(int) 46 => 'Bladder',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Ovary',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Kidney',
(int) 53 => 'Lung',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Muscle',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00005T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123504718',
'seq_end' => '123536649',
'region_length' => '31931',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031970-ENSMUSG00000040220'
)
)
$gene_el = array(
'ENST00000268699' => array(
'Adipose' => array(
'average_FPKM' => '1.265',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '3.166',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '3.328',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.622',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.962',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '1.905',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '3.093',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.782',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '1.618',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.167',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '5.338',
'stddev_FPKM' => '0.54'
),
'Placenta' => array(
'average_FPKM' => '1.032',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '5.878',
'stddev_FPKM' => '0.77'
)
),
'ENST00000536122' => array(
'Breast' => array(
'average_FPKM' => '0.294',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '2.225',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.108',
'stddev_FPKM' => '0.00'
)
),
'ENST00000537797' => array(),
'ENST00000540721' => array(
'Adipose' => array(
'average_FPKM' => '3.293',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '5.225',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '4.883',
'stddev_FPKM' => '2.79'
),
'Breast' => array(
'average_FPKM' => '2.441',
'stddev_FPKM' => '1.94'
),
'Colon' => array(
'average_FPKM' => '0.330',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '2.811',
'stddev_FPKM' => '0.98'
),
'Kidney' => array(
'average_FPKM' => '3.453',
'stddev_FPKM' => '2.73'
),
'Liver' => array(
'average_FPKM' => '1.013',
'stddev_FPKM' => '0.01'
),
'Lung' => array(
'average_FPKM' => '2.667',
'stddev_FPKM' => '2.16'
),
'Muscle' => array(
'average_FPKM' => '1.979',
'stddev_FPKM' => '0.66'
),
'Ovary' => array(
'average_FPKM' => '0.397',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '1.482',
'stddev_FPKM' => '0.65'
),
'Testis' => array(
'average_FPKM' => '18.088',
'stddev_FPKM' => '7.08'
)
),
'ENST00000561675' => array(
'Ovary' => array(
'average_FPKM' => '1.962',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '3.965',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '29.415',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563936' => array(
'Breast' => array(
'average_FPKM' => '1.749',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.687',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563980' => array(),
'ENST00000564392' => array(),
'ENST00000564789' => array(),
'ENST00000564802' => array(
'Bladder' => array(
'average_FPKM' => '6.039',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564853' => array(),
'ENST00000565000' => array(),
'ENST00000565062' => array(),
'ENST00000565957' => array(),
'ENST00000566266' => array(
'Brain' => array(
'average_FPKM' => '0.879',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568284' => array(),
'ENST00000568664' => array(
'Colon' => array(
'average_FPKM' => '1.708',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568705' => array(),
'ENST00000569399' => array(
'Ovary' => array(
'average_FPKM' => '0.477',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569558' => array(
'Breast' => array(
'average_FPKM' => '0.288',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.079',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.328',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.314',
'stddev_FPKM' => '0.00'
)
),
'ENST00000620723' => array()
)
$gene_key = 'ENSG00000141013'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000620723'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00005T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000003249' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSG00000141013' => 'growth arrest-specific 8',
'ENSG00000221819' => 'GAS8 antisense RNA 1',
'ENSG00000222019' => 'urate (hydroxyiso-) hydrolase, pseudogene',
'ENSMUSG00000031970' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSMUSG00000040220' => 'growth arrest specific 8',
'ENSMUSG00000088632' => 'predicted gene, 22314'
),
'gene_name_arr' => array(
'ENSG00000003249' => 'DBNDD1',
'ENSG00000141013' => 'GAS8',
'ENSG00000221819' => 'C16orf3',
'ENSG00000222019' => 'URAHP',
'ENSMUSG00000031970' => 'Dbndd1',
'ENSMUSG00000040220' => 'Gas8',
'ENSMUSG00000088632' => 'Gm22314'
),
'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) 3 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Brain',
(int) 12 => 'Breast',
(int) 18 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 36 => 'Lung',
(int) 40 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 57 => '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) 40,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000002501' => array(
'start' => '90004865',
'end' => '90019473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-001'
),
'ENST00000304733' => array(
'start' => '90004865',
'end' => '90010121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-002'
),
'ENST00000392973' => array(
'start' => '90004873',
'end' => '90010211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-004'
),
'ENST00000568330' => array(
'start' => '90006480',
'end' => '90019880',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DBNDD1-006'
),
'ENST00000568662' => array(
'start' => '90006219',
'end' => '90009072',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DBNDD1-007'
),
'ENST00000568838' => array(
'start' => '90006189',
'end' => '90020128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-003'
),
'ENST00000623401' => array(
'start' => '90004873',
'end' => '90007761',
'transcript_biotype' => 'TEC',
'transcript_name' => 'DBNDD1-005'
),
'ENST00000268699' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-001'
),
'ENST00000536122' => array(
'start' => '90019629',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-201'
),
'ENST00000537797' => array(
'start' => '90022683',
'end' => '90036926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-005'
),
'ENST00000540721' => array(
'start' => '90022664',
'end' => '90042428',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-004'
),
'ENST00000561675' => array(
'start' => '90019731',
'end' => '90032858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-014'
),
'ENST00000563936' => array(
'start' => '90019643',
'end' => '90032856',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-008'
),
'ENST00000563980' => array(
'start' => '90019629',
'end' => '90031252',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-010'
),
'ENST00000564392' => array(
'start' => '90022086',
'end' => '90032790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-011'
),
'ENST00000564789' => array(
'start' => '90040043',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-018'
),
'ENST00000564802' => array(
'start' => '90035732',
'end' => '90037347',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-015'
),
'ENST00000564853' => array(
'start' => '90022670',
'end' => '90027996',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-012'
),
'ENST00000565000' => array(
'start' => '90035781',
'end' => '90036766',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-016'
),
'ENST00000565062' => array(
'start' => '90022653',
'end' => '90037046',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-003'
),
'ENST00000565957' => array(
'start' => '90019637',
'end' => '90031406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-007'
),
'ENST00000566266' => array(
'start' => '90022683',
'end' => '90044975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-002'
),
'ENST00000568284' => array(
'start' => '90042377',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-019'
),
'ENST00000568664' => array(
'start' => '90019730',
'end' => '90031499',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-013'
),
'ENST00000568705' => array(
'start' => '90019693',
'end' => '90032892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-009'
),
'ENST00000569399' => array(
'start' => '90036196',
'end' => '90040509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-017'
),
'ENST00000569558' => array(
'start' => '90029541',
'end' => '90044961',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-006'
),
'ENST00000620723' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-202'
),
'ENST00000408886' => array(
'start' => '90028908',
'end' => '90029342',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-001'
),
'ENST00000623094' => array(
'start' => '90028908',
'end' => '90029901',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-201'
),
'ENST00000409768' => array(
'start' => '90043429',
'end' => '90044610',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-004'
),
'ENST00000409873' => array(
'start' => '90039761',
'end' => '90047625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-001'
),
'ENST00000517889' => array(
'start' => '90042902',
'end' => '90047773',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-002'
),
'ENST00000521551' => array(
'start' => '90043802',
'end' => '90047190',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-003'
),
'ENST00000610227' => array(
'start' => '90043914',
'end' => '90047597',
'transcript_biotype' => 'transcribed_unprocessed_pseudogene',
'transcript_name' => 'URAHP-005'
),
'ENSMUST00000176155' => array(
'start' => '123505687',
'end' => '123515463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-002'
),
'ENSMUST00000176286' => array(
'start' => '123504718',
'end' => '123515455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-001'
),
'ENSMUST00000177240' => array(
'start' => '123505687',
'end' => '123515390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-003'
),
'ENSMUST00000093043' => array(
'start' => '123518835',
'end' => '123536649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gas8-201'
),
'ENSMUST00000158007' => array(
'start' => '123523260',
'end' => '123523540',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22314-201'
)
),
'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_00005T_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00005T_0001' => array(
'genes_in_region' => array(
'ENSG00000003249' => array(
[maximum depth reached]
),
'ENSG00000141013' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Breast',
(int) 26 => 'Kidney',
(int) 27 => 'Ovary',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Breast',
(int) 45 => 'Liver',
(int) 46 => 'Bladder',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Ovary',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Kidney',
(int) 53 => 'Lung',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Muscle',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000003249' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSG00000141013' => 'growth arrest-specific 8',
'ENSG00000221819' => 'GAS8 antisense RNA 1',
'ENSG00000222019' => 'urate (hydroxyiso-) hydrolase, pseudogene',
'ENSMUSG00000031970' => 'dysbindin (dystrobrevin binding protein 1) domain containing 1',
'ENSMUSG00000040220' => 'growth arrest specific 8',
'ENSMUSG00000088632' => 'predicted gene, 22314'
)
$gene_name_arr = array(
'ENSG00000003249' => 'DBNDD1',
'ENSG00000141013' => 'GAS8',
'ENSG00000221819' => 'C16orf3',
'ENSG00000222019' => 'URAHP',
'ENSMUSG00000031970' => 'Dbndd1',
'ENSMUSG00000040220' => 'Gas8',
'ENSMUSG00000088632' => 'Gm22314'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005T_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '90004865',
'seq_end' => '90044975',
'region_length' => '40110',
'region_type' => 'CGP',
'el_id' => 'ENSG00000003249-ENSG00000141013'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123504718',
'seq_end' => '123536649',
'region_length' => '31931',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031970-ENSMUSG00000040220'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 7 => 'Bladder',
(int) 8 => 'Brain',
(int) 12 => 'Breast',
(int) 18 => 'Colon',
(int) 24 => 'Heart',
(int) 27 => 'Kidney',
(int) 32 => 'Liver',
(int) 36 => 'Lung',
(int) 40 => 'Muscle',
(int) 45 => 'Ovary',
(int) 52 => 'Placenta',
(int) 57 => '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) 40
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000002501' => array(
'start' => '90004865',
'end' => '90019473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-001'
),
'ENST00000304733' => array(
'start' => '90004865',
'end' => '90010121',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-002'
),
'ENST00000392973' => array(
'start' => '90004873',
'end' => '90010211',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-004'
),
'ENST00000568330' => array(
'start' => '90006480',
'end' => '90019880',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'DBNDD1-006'
),
'ENST00000568662' => array(
'start' => '90006219',
'end' => '90009072',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'DBNDD1-007'
),
'ENST00000568838' => array(
'start' => '90006189',
'end' => '90020128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'DBNDD1-003'
),
'ENST00000623401' => array(
'start' => '90004873',
'end' => '90007761',
'transcript_biotype' => 'TEC',
'transcript_name' => 'DBNDD1-005'
),
'ENST00000268699' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-001'
),
'ENST00000536122' => array(
'start' => '90019629',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-201'
),
'ENST00000537797' => array(
'start' => '90022683',
'end' => '90036926',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-005'
),
'ENST00000540721' => array(
'start' => '90022664',
'end' => '90042428',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-004'
),
'ENST00000561675' => array(
'start' => '90019731',
'end' => '90032858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-014'
),
'ENST00000563936' => array(
'start' => '90019643',
'end' => '90032856',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-008'
),
'ENST00000563980' => array(
'start' => '90019629',
'end' => '90031252',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-010'
),
'ENST00000564392' => array(
'start' => '90022086',
'end' => '90032790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-011'
),
'ENST00000564789' => array(
'start' => '90040043',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-018'
),
'ENST00000564802' => array(
'start' => '90035732',
'end' => '90037347',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-015'
),
'ENST00000564853' => array(
'start' => '90022670',
'end' => '90027996',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-012'
),
'ENST00000565000' => array(
'start' => '90035781',
'end' => '90036766',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-016'
),
'ENST00000565062' => array(
'start' => '90022653',
'end' => '90037046',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-003'
),
'ENST00000565957' => array(
'start' => '90019637',
'end' => '90031406',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-007'
),
'ENST00000566266' => array(
'start' => '90022683',
'end' => '90044975',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'GAS8-002'
),
'ENST00000568284' => array(
'start' => '90042377',
'end' => '90043472',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-019'
),
'ENST00000568664' => array(
'start' => '90019730',
'end' => '90031499',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-013'
),
'ENST00000568705' => array(
'start' => '90019693',
'end' => '90032892',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'GAS8-009'
),
'ENST00000569399' => array(
'start' => '90036196',
'end' => '90040509',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-017'
),
'ENST00000569558' => array(
'start' => '90029541',
'end' => '90044961',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'GAS8-006'
),
'ENST00000620723' => array(
'start' => '90022600',
'end' => '90044971',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'GAS8-202'
),
'ENST00000408886' => array(
'start' => '90028908',
'end' => '90029342',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-001'
),
'ENST00000623094' => array(
'start' => '90028908',
'end' => '90029901',
'transcript_biotype' => 'antisense',
'transcript_name' => 'C16orf3-201'
),
'ENST00000409768' => array(
'start' => '90043429',
'end' => '90044610',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-004'
),
'ENST00000409873' => array(
'start' => '90039761',
'end' => '90047625',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-001'
),
'ENST00000517889' => array(
'start' => '90042902',
'end' => '90047773',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-002'
),
'ENST00000521551' => array(
'start' => '90043802',
'end' => '90047190',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'URAHP-003'
),
'ENST00000610227' => array(
'start' => '90043914',
'end' => '90047597',
'transcript_biotype' => 'transcribed_unprocessed_pseudogene',
'transcript_name' => 'URAHP-005'
),
'ENSMUST00000176155' => array(
'start' => '123505687',
'end' => '123515463',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-002'
),
'ENSMUST00000176286' => array(
'start' => '123504718',
'end' => '123515455',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-001'
),
'ENSMUST00000177240' => array(
'start' => '123505687',
'end' => '123515390',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Dbndd1-003'
),
'ENSMUST00000093043' => array(
'start' => '123518835',
'end' => '123536649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gas8-201'
),
'ENSMUST00000158007' => array(
'start' => '123523260',
'end' => '123523540',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'Gm22314-201'
)
)
$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_00005T_0001' => array(
'genes_in_region' => array(
'ENSG00000003249' => array(
[maximum depth reached]
),
'ENSG00000141013' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Heart',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Liver',
(int) 11 => 'Muscle',
(int) 12 => 'Adipose',
(int) 13 => 'Adrenal',
(int) 14 => 'Brain',
(int) 15 => 'Breast',
(int) 16 => 'Colon',
(int) 17 => 'Heart',
(int) 18 => 'Kidney',
(int) 19 => 'Liver',
(int) 20 => 'Lung',
(int) 21 => 'Muscle',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Testis',
(int) 25 => 'Breast',
(int) 26 => 'Kidney',
(int) 27 => 'Ovary',
(int) 28 => 'Adipose',
(int) 29 => 'Adrenal',
(int) 30 => 'Brain',
(int) 31 => 'Breast',
(int) 32 => 'Colon',
(int) 33 => 'Heart',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Lung',
(int) 37 => 'Muscle',
(int) 38 => 'Ovary',
(int) 39 => 'Placenta',
(int) 40 => 'Testis',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Breast',
(int) 45 => 'Liver',
(int) 46 => 'Bladder',
(int) 47 => 'Brain',
(int) 48 => 'Colon',
(int) 49 => 'Ovary',
(int) 50 => 'Breast',
(int) 51 => 'Colon',
(int) 52 => 'Kidney',
(int) 53 => 'Lung',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Colon',
(int) 57 => 'Muscle',
(int) 58 => 'Ovary',
(int) 59 => 'Placenta',
(int) 60 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00005T_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123504718',
'seq_end' => '123536649',
'region_length' => '31931',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031970-ENSMUSG00000040220'
)
)
$gene_el = array(
'ENST00000268699' => array(
'Adipose' => array(
'average_FPKM' => '1.265',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '3.166',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '3.328',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '2.622',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.962',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '1.905',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '3.093',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.782',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '1.618',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.167',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '5.338',
'stddev_FPKM' => '0.54'
),
'Placenta' => array(
'average_FPKM' => '1.032',
'stddev_FPKM' => '0.10'
),
'Testis' => array(
'average_FPKM' => '5.878',
'stddev_FPKM' => '0.77'
)
),
'ENST00000536122' => array(
'Breast' => array(
'average_FPKM' => '0.294',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '2.225',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.108',
'stddev_FPKM' => '0.00'
)
),
'ENST00000537797' => array(),
'ENST00000540721' => array(
'Adipose' => array(
'average_FPKM' => '3.293',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '5.225',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '4.883',
'stddev_FPKM' => '2.79'
),
'Breast' => array(
'average_FPKM' => '2.441',
'stddev_FPKM' => '1.94'
),
'Colon' => array(
'average_FPKM' => '0.330',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '2.811',
'stddev_FPKM' => '0.98'
),
'Kidney' => array(
'average_FPKM' => '3.453',
'stddev_FPKM' => '2.73'
),
'Liver' => array(
'average_FPKM' => '1.013',
'stddev_FPKM' => '0.01'
),
'Lung' => array(
'average_FPKM' => '2.667',
'stddev_FPKM' => '2.16'
),
'Muscle' => array(
'average_FPKM' => '1.979',
'stddev_FPKM' => '0.66'
),
'Ovary' => array(
'average_FPKM' => '0.397',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '1.482',
'stddev_FPKM' => '0.65'
),
'Testis' => array(
'average_FPKM' => '18.088',
'stddev_FPKM' => '7.08'
)
),
'ENST00000561675' => array(
'Ovary' => array(
'average_FPKM' => '1.962',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '3.965',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '29.415',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563936' => array(
'Breast' => array(
'average_FPKM' => '1.749',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '1.687',
'stddev_FPKM' => '0.00'
)
),
'ENST00000563980' => array(),
'ENST00000564392' => array(),
'ENST00000564789' => array(),
'ENST00000564802' => array(
'Bladder' => array(
'average_FPKM' => '6.039',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564853' => array(),
'ENST00000565000' => array(),
'ENST00000565062' => array(),
'ENST00000565957' => array(),
'ENST00000566266' => array(
'Brain' => array(
'average_FPKM' => '0.879',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568284' => array(),
'ENST00000568664' => array(
'Colon' => array(
'average_FPKM' => '1.708',
'stddev_FPKM' => '0.00'
)
),
'ENST00000568705' => array(),
'ENST00000569399' => array(
'Ovary' => array(
'average_FPKM' => '0.477',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569558' => array(
'Breast' => array(
'average_FPKM' => '0.288',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.079',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.328',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.314',
'stddev_FPKM' => '0.00'
)
),
'ENST00000620723' => array()
)
$gene_key = 'ENSG00000141013'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000620723'
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
(DBNDD1)