Notice (8): Undefined index: CIL_0000MQ_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_0000MQ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000010946' => 'cystathionine-beta-synthase b',
'ENSDARG00000015325' => 'U2(RNU2) small nuclear RNA auxiliary factor 1',
'ENSG00000160200' => 'cystathionine-beta-synthase',
'ENSG00000160201' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSG00000274276' => 'cystathionine-beta-synthase',
'ENSG00000275895' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSMUSG00000024039' => 'cystathionine beta-synthase',
'ENSMUSG00000061613' => 'U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1'
),
'gene_name_arr' => array(
'ENSDARG00000010946' => 'cbsb',
'ENSDARG00000015325' => 'u2af1',
'ENSG00000160200' => 'CBS',
'ENSG00000160201' => 'U2AF1',
'ENSG00000274276' => 'CBS',
'ENSG00000275895' => 'U2AF1',
'ENSMUSG00000024039' => 'Cbs',
'ENSMUSG00000061613' => 'U2af1'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 31 => 'Brain',
(int) 51 => 'Breast',
(int) 64 => 'Colon',
(int) 76 => 'Heart',
(int) 93 => 'Kidney',
(int) 110 => 'Liver',
(int) 127 => 'Lung',
(int) 140 => 'Muscle',
(int) 154 => 'Ovary',
(int) 174 => 'Placenta',
(int) 193 => '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) 58,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000026275' => array(
'start' => '9404591',
'end' => '9450364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-201'
),
'ENSDART00000121665' => array(
'start' => '9405249',
'end' => '9450353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-001'
),
'ENSDART00000021191' => array(
'start' => '9451858',
'end' => '9464189',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'u2af1-001'
),
'ENST00000352178' => array(
'start' => '43053191',
'end' => '43076378',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000359624' => array(
'start' => '43053191',
'end' => '43076362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000398158' => array(
'start' => '43053191',
'end' => '43075831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000398165' => array(
'start' => '43053191',
'end' => '43075945',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-003'
),
'ENST00000430013' => array(
'start' => '43055598',
'end' => '43060546',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-014'
),
'ENST00000441030' => array(
'start' => '43065616',
'end' => '43076943',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-007'
),
'ENST00000451248' => array(
'start' => '43053755',
'end' => '43058941',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-016'
),
'ENST00000458223' => array(
'start' => '43055583',
'end' => '43058954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-015'
),
'ENST00000461686' => array(
'start' => '43053191',
'end' => '43068404',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-005'
),
'ENST00000462349' => array(
'start' => '43053789',
'end' => '43059739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-013'
),
'ENST00000465732' => array(
'start' => '43068321',
'end' => '43075864',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-009'
),
'ENST00000470912' => array(
'start' => '43066243',
'end' => '43075945',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000478709' => array(
'start' => '43075107',
'end' => '43076288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-017'
),
'ENST00000486098' => array(
'start' => '43061919',
'end' => '43063248',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-012'
),
'ENST00000488526' => array(
'start' => '43068404',
'end' => '43073508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-010'
),
'ENST00000491776' => array(
'start' => '43055072',
'end' => '43060520',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000496485' => array(
'start' => '43059276',
'end' => '43064227',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-011'
),
'ENST00000291552' => array(
'start' => '43092956',
'end' => '43107587',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-001'
),
'ENST00000380276' => array(
'start' => '43092956',
'end' => '43107565',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000398137' => array(
'start' => '43092957',
'end' => '43107578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-201'
),
'ENST00000459639' => array(
'start' => '43092956',
'end' => '43105252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-004'
),
'ENST00000463599' => array(
'start' => '43095702',
'end' => '43104476',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-009'
),
'ENST00000464750' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-003'
),
'ENST00000468039' => array(
'start' => '43100453',
'end' => '43101907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-011'
),
'ENST00000471250' => array(
'start' => '43092956',
'end' => '43095943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-008'
),
'ENST00000475639' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-005'
),
'ENST00000478282' => array(
'start' => '43092956',
'end' => '43096390',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-007'
),
'ENST00000486519' => array(
'start' => '43093190',
'end' => '43107570',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'U2AF1-010'
),
'ENST00000496462' => array(
'start' => '43097622',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-006'
),
'ENST00000398168' => array(
'start' => '6444869',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000617706' => array(
'start' => '6444873',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-201'
),
'ENST00000618024' => array(
'start' => '6444869',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000622914' => array(
'start' => '6447132',
'end' => '6467534',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-005'
),
'ENST00000623939' => array(
'start' => '6456880',
'end' => '6461713',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-007'
),
'ENST00000624406' => array(
'start' => '6444869',
'end' => '6467509',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-009'
),
'ENST00000624691' => array(
'start' => '6444869',
'end' => '6460082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000624808' => array(
'start' => '6447261',
'end' => '6450632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-003'
),
'ENST00000624921' => array(
'start' => '6457901',
'end' => '6467483',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000624934' => array(
'start' => '6445433',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000610664' => array(
'start' => '6484623',
'end' => '6499200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-003'
),
'ENST00000619610' => array(
'start' => '6484709',
'end' => '6499202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000620065' => array(
'start' => '6484626',
'end' => '6499202',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-001'
),
'ENST00000623375' => array(
'start' => '6484623',
'end' => '6496930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-005'
),
'ENST00000624739' => array(
'start' => '6484661',
'end' => '6499261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-004'
),
'ENSMUST00000067801' => array(
'start' => '31612623',
'end' => '31637199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-001'
),
'ENSMUST00000078509' => array(
'start' => '31612641',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-002'
),
'ENSMUST00000118504' => array(
'start' => '31612640',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-003'
),
'ENSMUST00000128351' => array(
'start' => '31620947',
'end' => '31626188',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-006'
),
'ENSMUST00000135425' => array(
'start' => '31625131',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-005'
),
'ENSMUST00000143982' => array(
'start' => '31621472',
'end' => '31623058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-007'
),
'ENSMUST00000151597' => array(
'start' => '31617165',
'end' => '31617873',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbs-008'
),
'ENSMUST00000151718' => array(
'start' => '31627525',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-009'
),
'ENSMUST00000155814' => array(
'start' => '31625077',
'end' => '31636790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-004'
),
'ENSMUST00000014684' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-201'
),
'ENSMUST00000166526' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-202'
)
),
'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_0000MQ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000MQ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000010946' => array(
[maximum depth reached]
),
'ENSDARG00000015325' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Muscle'
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000024039' => array(
[maximum depth reached]
),
'ENSMUSG00000061613' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Muscle',
(int) 46 => 'Muscle',
(int) 47 => 'Placenta',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Liver',
(int) 60 => 'Lung',
(int) 61 => 'Muscle',
(int) 62 => 'Ovary',
(int) 63 => 'Placenta',
(int) 64 => 'Testis',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Muscle',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000010946' => 'cystathionine-beta-synthase b',
'ENSDARG00000015325' => 'U2(RNU2) small nuclear RNA auxiliary factor 1',
'ENSG00000160200' => 'cystathionine-beta-synthase',
'ENSG00000160201' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSG00000274276' => 'cystathionine-beta-synthase',
'ENSG00000275895' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSMUSG00000024039' => 'cystathionine beta-synthase',
'ENSMUSG00000061613' => 'U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1'
)
$gene_name_arr = array(
'ENSDARG00000010946' => 'cbsb',
'ENSDARG00000015325' => 'u2af1',
'ENSG00000160200' => 'CBS',
'ENSG00000160201' => 'U2AF1',
'ENSG00000274276' => 'CBS',
'ENSG00000275895' => 'U2AF1',
'ENSMUSG00000024039' => 'Cbs',
'ENSMUSG00000061613' => 'U2af1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0001',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '9404591',
'seq_end' => '9464189',
'region_length' => '59598',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000010946-ENSDARG00000015325'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0002',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '43053191',
'seq_end' => '43107587',
'region_length' => '54396',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160200-ENSG00000160201'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0003',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '6444869',
'seq_end' => '6499261',
'region_length' => '54392',
'region_type' => 'CGP',
'el_id' => 'ENSG00000274276-ENSG00000275895'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0004',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '31612623',
'seq_end' => '31658754',
'region_length' => '46131',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000024039-ENSMUSG00000061613'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 31 => 'Brain',
(int) 51 => 'Breast',
(int) 64 => 'Colon',
(int) 76 => 'Heart',
(int) 93 => 'Kidney',
(int) 110 => 'Liver',
(int) 127 => 'Lung',
(int) 140 => 'Muscle',
(int) 154 => 'Ovary',
(int) 174 => 'Placenta',
(int) 193 => '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) 58
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000026275' => array(
'start' => '9404591',
'end' => '9450364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-201'
),
'ENSDART00000121665' => array(
'start' => '9405249',
'end' => '9450353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-001'
),
'ENSDART00000021191' => array(
'start' => '9451858',
'end' => '9464189',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'u2af1-001'
),
'ENST00000352178' => array(
'start' => '43053191',
'end' => '43076378',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000359624' => array(
'start' => '43053191',
'end' => '43076362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000398158' => array(
'start' => '43053191',
'end' => '43075831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000398165' => array(
'start' => '43053191',
'end' => '43075945',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-003'
),
'ENST00000430013' => array(
'start' => '43055598',
'end' => '43060546',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-014'
),
'ENST00000441030' => array(
'start' => '43065616',
'end' => '43076943',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-007'
),
'ENST00000451248' => array(
'start' => '43053755',
'end' => '43058941',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-016'
),
'ENST00000458223' => array(
'start' => '43055583',
'end' => '43058954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-015'
),
'ENST00000461686' => array(
'start' => '43053191',
'end' => '43068404',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-005'
),
'ENST00000462349' => array(
'start' => '43053789',
'end' => '43059739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-013'
),
'ENST00000465732' => array(
'start' => '43068321',
'end' => '43075864',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-009'
),
'ENST00000470912' => array(
'start' => '43066243',
'end' => '43075945',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000478709' => array(
'start' => '43075107',
'end' => '43076288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-017'
),
'ENST00000486098' => array(
'start' => '43061919',
'end' => '43063248',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-012'
),
'ENST00000488526' => array(
'start' => '43068404',
'end' => '43073508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-010'
),
'ENST00000491776' => array(
'start' => '43055072',
'end' => '43060520',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000496485' => array(
'start' => '43059276',
'end' => '43064227',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-011'
),
'ENST00000291552' => array(
'start' => '43092956',
'end' => '43107587',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-001'
),
'ENST00000380276' => array(
'start' => '43092956',
'end' => '43107565',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000398137' => array(
'start' => '43092957',
'end' => '43107578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-201'
),
'ENST00000459639' => array(
'start' => '43092956',
'end' => '43105252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-004'
),
'ENST00000463599' => array(
'start' => '43095702',
'end' => '43104476',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-009'
),
'ENST00000464750' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-003'
),
'ENST00000468039' => array(
'start' => '43100453',
'end' => '43101907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-011'
),
'ENST00000471250' => array(
'start' => '43092956',
'end' => '43095943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-008'
),
'ENST00000475639' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-005'
),
'ENST00000478282' => array(
'start' => '43092956',
'end' => '43096390',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-007'
),
'ENST00000486519' => array(
'start' => '43093190',
'end' => '43107570',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'U2AF1-010'
),
'ENST00000496462' => array(
'start' => '43097622',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-006'
),
'ENST00000398168' => array(
'start' => '6444869',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000617706' => array(
'start' => '6444873',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-201'
),
'ENST00000618024' => array(
'start' => '6444869',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000622914' => array(
'start' => '6447132',
'end' => '6467534',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-005'
),
'ENST00000623939' => array(
'start' => '6456880',
'end' => '6461713',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-007'
),
'ENST00000624406' => array(
'start' => '6444869',
'end' => '6467509',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-009'
),
'ENST00000624691' => array(
'start' => '6444869',
'end' => '6460082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000624808' => array(
'start' => '6447261',
'end' => '6450632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-003'
),
'ENST00000624921' => array(
'start' => '6457901',
'end' => '6467483',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000624934' => array(
'start' => '6445433',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000610664' => array(
'start' => '6484623',
'end' => '6499200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-003'
),
'ENST00000619610' => array(
'start' => '6484709',
'end' => '6499202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000620065' => array(
'start' => '6484626',
'end' => '6499202',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-001'
),
'ENST00000623375' => array(
'start' => '6484623',
'end' => '6496930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-005'
),
'ENST00000624739' => array(
'start' => '6484661',
'end' => '6499261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-004'
),
'ENSMUST00000067801' => array(
'start' => '31612623',
'end' => '31637199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-001'
),
'ENSMUST00000078509' => array(
'start' => '31612641',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-002'
),
'ENSMUST00000118504' => array(
'start' => '31612640',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-003'
),
'ENSMUST00000128351' => array(
'start' => '31620947',
'end' => '31626188',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-006'
),
'ENSMUST00000135425' => array(
'start' => '31625131',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-005'
),
'ENSMUST00000143982' => array(
'start' => '31621472',
'end' => '31623058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-007'
),
'ENSMUST00000151597' => array(
'start' => '31617165',
'end' => '31617873',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbs-008'
),
'ENSMUST00000151718' => array(
'start' => '31627525',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-009'
),
'ENSMUST00000155814' => array(
'start' => '31625077',
'end' => '31636790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-004'
),
'ENSMUST00000014684' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-201'
),
'ENSMUST00000166526' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-202'
)
)
$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_0000MQ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000010946' => array(
[maximum depth reached]
),
'ENSDARG00000015325' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Muscle'
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000024039' => array(
[maximum depth reached]
),
'ENSMUSG00000061613' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Muscle',
(int) 46 => 'Muscle',
(int) 47 => 'Placenta',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Liver',
(int) 60 => 'Lung',
(int) 61 => 'Muscle',
(int) 62 => 'Ovary',
(int) 63 => 'Placenta',
(int) 64 => 'Testis',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Muscle',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0002',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '43053191',
'seq_end' => '43107587',
'region_length' => '54396',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160200-ENSG00000160201'
)
)
$gene_el = array(
'ENSDART00000021191' => array(
'Brain' => array(
'average_FPKM' => '13.770',
'stddev_FPKM' => '10.57'
),
'Heart' => array(
'average_FPKM' => '21.445',
'stddev_FPKM' => '2.67'
),
'Kidney' => array(
'average_FPKM' => '18.245',
'stddev_FPKM' => '6.79'
),
'Liver' => array(
'average_FPKM' => '3.088',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '11.340',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000015325'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '13.770',
'stddev_FPKM' => '10.57'
),
'Heart' => array(
'average_FPKM' => '21.445',
'stddev_FPKM' => '2.67'
),
'Kidney' => array(
'average_FPKM' => '18.245',
'stddev_FPKM' => '6.79'
),
'Liver' => array(
'average_FPKM' => '3.088',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '11.340',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000021191'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0000MQ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000010946' => 'cystathionine-beta-synthase b',
'ENSDARG00000015325' => 'U2(RNU2) small nuclear RNA auxiliary factor 1',
'ENSG00000160200' => 'cystathionine-beta-synthase',
'ENSG00000160201' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSG00000274276' => 'cystathionine-beta-synthase',
'ENSG00000275895' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSMUSG00000024039' => 'cystathionine beta-synthase',
'ENSMUSG00000061613' => 'U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1'
),
'gene_name_arr' => array(
'ENSDARG00000010946' => 'cbsb',
'ENSDARG00000015325' => 'u2af1',
'ENSG00000160200' => 'CBS',
'ENSG00000160201' => 'U2AF1',
'ENSG00000274276' => 'CBS',
'ENSG00000275895' => 'U2AF1',
'ENSMUSG00000024039' => 'Cbs',
'ENSMUSG00000061613' => 'U2af1'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 3 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 31 => 'Brain',
(int) 51 => 'Breast',
(int) 64 => 'Colon',
(int) 76 => 'Heart',
(int) 93 => 'Kidney',
(int) 110 => 'Liver',
(int) 127 => 'Lung',
(int) 140 => 'Muscle',
(int) 154 => 'Ovary',
(int) 174 => 'Placenta',
(int) 193 => '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) 58,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000026275' => array(
'start' => '9404591',
'end' => '9450364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-201'
),
'ENSDART00000121665' => array(
'start' => '9405249',
'end' => '9450353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-001'
),
'ENSDART00000021191' => array(
'start' => '9451858',
'end' => '9464189',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'u2af1-001'
),
'ENST00000352178' => array(
'start' => '43053191',
'end' => '43076378',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000359624' => array(
'start' => '43053191',
'end' => '43076362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000398158' => array(
'start' => '43053191',
'end' => '43075831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000398165' => array(
'start' => '43053191',
'end' => '43075945',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-003'
),
'ENST00000430013' => array(
'start' => '43055598',
'end' => '43060546',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-014'
),
'ENST00000441030' => array(
'start' => '43065616',
'end' => '43076943',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-007'
),
'ENST00000451248' => array(
'start' => '43053755',
'end' => '43058941',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-016'
),
'ENST00000458223' => array(
'start' => '43055583',
'end' => '43058954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-015'
),
'ENST00000461686' => array(
'start' => '43053191',
'end' => '43068404',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-005'
),
'ENST00000462349' => array(
'start' => '43053789',
'end' => '43059739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-013'
),
'ENST00000465732' => array(
'start' => '43068321',
'end' => '43075864',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-009'
),
'ENST00000470912' => array(
'start' => '43066243',
'end' => '43075945',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000478709' => array(
'start' => '43075107',
'end' => '43076288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-017'
),
'ENST00000486098' => array(
'start' => '43061919',
'end' => '43063248',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-012'
),
'ENST00000488526' => array(
'start' => '43068404',
'end' => '43073508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-010'
),
'ENST00000491776' => array(
'start' => '43055072',
'end' => '43060520',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000496485' => array(
'start' => '43059276',
'end' => '43064227',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-011'
),
'ENST00000291552' => array(
'start' => '43092956',
'end' => '43107587',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-001'
),
'ENST00000380276' => array(
'start' => '43092956',
'end' => '43107565',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000398137' => array(
'start' => '43092957',
'end' => '43107578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-201'
),
'ENST00000459639' => array(
'start' => '43092956',
'end' => '43105252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-004'
),
'ENST00000463599' => array(
'start' => '43095702',
'end' => '43104476',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-009'
),
'ENST00000464750' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-003'
),
'ENST00000468039' => array(
'start' => '43100453',
'end' => '43101907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-011'
),
'ENST00000471250' => array(
'start' => '43092956',
'end' => '43095943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-008'
),
'ENST00000475639' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-005'
),
'ENST00000478282' => array(
'start' => '43092956',
'end' => '43096390',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-007'
),
'ENST00000486519' => array(
'start' => '43093190',
'end' => '43107570',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'U2AF1-010'
),
'ENST00000496462' => array(
'start' => '43097622',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-006'
),
'ENST00000398168' => array(
'start' => '6444869',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000617706' => array(
'start' => '6444873',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-201'
),
'ENST00000618024' => array(
'start' => '6444869',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000622914' => array(
'start' => '6447132',
'end' => '6467534',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-005'
),
'ENST00000623939' => array(
'start' => '6456880',
'end' => '6461713',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-007'
),
'ENST00000624406' => array(
'start' => '6444869',
'end' => '6467509',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-009'
),
'ENST00000624691' => array(
'start' => '6444869',
'end' => '6460082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000624808' => array(
'start' => '6447261',
'end' => '6450632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-003'
),
'ENST00000624921' => array(
'start' => '6457901',
'end' => '6467483',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000624934' => array(
'start' => '6445433',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000610664' => array(
'start' => '6484623',
'end' => '6499200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-003'
),
'ENST00000619610' => array(
'start' => '6484709',
'end' => '6499202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000620065' => array(
'start' => '6484626',
'end' => '6499202',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-001'
),
'ENST00000623375' => array(
'start' => '6484623',
'end' => '6496930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-005'
),
'ENST00000624739' => array(
'start' => '6484661',
'end' => '6499261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-004'
),
'ENSMUST00000067801' => array(
'start' => '31612623',
'end' => '31637199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-001'
),
'ENSMUST00000078509' => array(
'start' => '31612641',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-002'
),
'ENSMUST00000118504' => array(
'start' => '31612640',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-003'
),
'ENSMUST00000128351' => array(
'start' => '31620947',
'end' => '31626188',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-006'
),
'ENSMUST00000135425' => array(
'start' => '31625131',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-005'
),
'ENSMUST00000143982' => array(
'start' => '31621472',
'end' => '31623058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-007'
),
'ENSMUST00000151597' => array(
'start' => '31617165',
'end' => '31617873',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbs-008'
),
'ENSMUST00000151718' => array(
'start' => '31627525',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-009'
),
'ENSMUST00000155814' => array(
'start' => '31625077',
'end' => '31636790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-004'
),
'ENSMUST00000014684' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-201'
),
'ENSMUST00000166526' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-202'
)
),
'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_0000MQ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0000MQ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000010946' => array(
[maximum depth reached]
),
'ENSDARG00000015325' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Muscle'
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000024039' => array(
[maximum depth reached]
),
'ENSMUSG00000061613' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Muscle',
(int) 46 => 'Muscle',
(int) 47 => 'Placenta',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Liver',
(int) 60 => 'Lung',
(int) 61 => 'Muscle',
(int) 62 => 'Ovary',
(int) 63 => 'Placenta',
(int) 64 => 'Testis',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Muscle',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000010946' => 'cystathionine-beta-synthase b',
'ENSDARG00000015325' => 'U2(RNU2) small nuclear RNA auxiliary factor 1',
'ENSG00000160200' => 'cystathionine-beta-synthase',
'ENSG00000160201' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSG00000274276' => 'cystathionine-beta-synthase',
'ENSG00000275895' => 'U2 small nuclear RNA auxiliary factor 1',
'ENSMUSG00000024039' => 'cystathionine beta-synthase',
'ENSMUSG00000061613' => 'U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1'
)
$gene_name_arr = array(
'ENSDARG00000010946' => 'cbsb',
'ENSDARG00000015325' => 'u2af1',
'ENSG00000160200' => 'CBS',
'ENSG00000160201' => 'U2AF1',
'ENSG00000274276' => 'CBS',
'ENSG00000275895' => 'U2AF1',
'ENSMUSG00000024039' => 'Cbs',
'ENSMUSG00000061613' => 'U2af1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0001',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '9404591',
'seq_end' => '9464189',
'region_length' => '59598',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000010946-ENSDARG00000015325'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0002',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '43053191',
'seq_end' => '43107587',
'region_length' => '54396',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160200-ENSG00000160201'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0003',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '6444869',
'seq_end' => '6499261',
'region_length' => '54392',
'region_type' => 'CGP',
'el_id' => 'ENSG00000274276-ENSG00000275895'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0004',
'tax_id' => '10090',
'chromosome' => '17',
'seq_start' => '31612623',
'seq_end' => '31658754',
'region_length' => '46131',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000024039-ENSMUSG00000061613'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 11 => 'Adrenal',
(int) 23 => 'Bladder',
(int) 31 => 'Brain',
(int) 51 => 'Breast',
(int) 64 => 'Colon',
(int) 76 => 'Heart',
(int) 93 => 'Kidney',
(int) 110 => 'Liver',
(int) 127 => 'Lung',
(int) 140 => 'Muscle',
(int) 154 => 'Ovary',
(int) 174 => 'Placenta',
(int) 193 => '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) 58
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000026275' => array(
'start' => '9404591',
'end' => '9450364',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-201'
),
'ENSDART00000121665' => array(
'start' => '9405249',
'end' => '9450353',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'cbsb-001'
),
'ENSDART00000021191' => array(
'start' => '9451858',
'end' => '9464189',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'u2af1-001'
),
'ENST00000352178' => array(
'start' => '43053191',
'end' => '43076378',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000359624' => array(
'start' => '43053191',
'end' => '43076362',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000398158' => array(
'start' => '43053191',
'end' => '43075831',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000398165' => array(
'start' => '43053191',
'end' => '43075945',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-003'
),
'ENST00000430013' => array(
'start' => '43055598',
'end' => '43060546',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-014'
),
'ENST00000441030' => array(
'start' => '43065616',
'end' => '43076943',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-007'
),
'ENST00000451248' => array(
'start' => '43053755',
'end' => '43058941',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-016'
),
'ENST00000458223' => array(
'start' => '43055583',
'end' => '43058954',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-015'
),
'ENST00000461686' => array(
'start' => '43053191',
'end' => '43068404',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-005'
),
'ENST00000462349' => array(
'start' => '43053789',
'end' => '43059739',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-013'
),
'ENST00000465732' => array(
'start' => '43068321',
'end' => '43075864',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-009'
),
'ENST00000470912' => array(
'start' => '43066243',
'end' => '43075945',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000478709' => array(
'start' => '43075107',
'end' => '43076288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-017'
),
'ENST00000486098' => array(
'start' => '43061919',
'end' => '43063248',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-012'
),
'ENST00000488526' => array(
'start' => '43068404',
'end' => '43073508',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-010'
),
'ENST00000491776' => array(
'start' => '43055072',
'end' => '43060520',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000496485' => array(
'start' => '43059276',
'end' => '43064227',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-011'
),
'ENST00000291552' => array(
'start' => '43092956',
'end' => '43107587',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-001'
),
'ENST00000380276' => array(
'start' => '43092956',
'end' => '43107565',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000398137' => array(
'start' => '43092957',
'end' => '43107578',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-201'
),
'ENST00000459639' => array(
'start' => '43092956',
'end' => '43105252',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-004'
),
'ENST00000463599' => array(
'start' => '43095702',
'end' => '43104476',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-009'
),
'ENST00000464750' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-003'
),
'ENST00000468039' => array(
'start' => '43100453',
'end' => '43101907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-011'
),
'ENST00000471250' => array(
'start' => '43092956',
'end' => '43095943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-008'
),
'ENST00000475639' => array(
'start' => '43092956',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-005'
),
'ENST00000478282' => array(
'start' => '43092956',
'end' => '43096390',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-007'
),
'ENST00000486519' => array(
'start' => '43093190',
'end' => '43107570',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'U2AF1-010'
),
'ENST00000496462' => array(
'start' => '43097622',
'end' => '43107524',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-006'
),
'ENST00000398168' => array(
'start' => '6444869',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-001'
),
'ENST00000617706' => array(
'start' => '6444873',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-201'
),
'ENST00000618024' => array(
'start' => '6444869',
'end' => '6468040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-002'
),
'ENST00000622914' => array(
'start' => '6447132',
'end' => '6467534',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-005'
),
'ENST00000623939' => array(
'start' => '6456880',
'end' => '6461713',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-007'
),
'ENST00000624406' => array(
'start' => '6444869',
'end' => '6467509',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-009'
),
'ENST00000624691' => array(
'start' => '6444869',
'end' => '6460082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBS-006'
),
'ENST00000624808' => array(
'start' => '6447261',
'end' => '6450632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-003'
),
'ENST00000624921' => array(
'start' => '6457901',
'end' => '6467483',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'CBS-008'
),
'ENST00000624934' => array(
'start' => '6445433',
'end' => '6467532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBS-004'
),
'ENST00000610664' => array(
'start' => '6484623',
'end' => '6499200',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-003'
),
'ENST00000619610' => array(
'start' => '6484709',
'end' => '6499202',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-002'
),
'ENST00000620065' => array(
'start' => '6484626',
'end' => '6499202',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'U2AF1-001'
),
'ENST00000623375' => array(
'start' => '6484623',
'end' => '6496930',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2AF1-005'
),
'ENST00000624739' => array(
'start' => '6484661',
'end' => '6499261',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'U2AF1-004'
),
'ENSMUST00000067801' => array(
'start' => '31612623',
'end' => '31637199',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-001'
),
'ENSMUST00000078509' => array(
'start' => '31612641',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-002'
),
'ENSMUST00000118504' => array(
'start' => '31612640',
'end' => '31637165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-003'
),
'ENSMUST00000128351' => array(
'start' => '31620947',
'end' => '31626188',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-006'
),
'ENSMUST00000135425' => array(
'start' => '31625131',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-005'
),
'ENSMUST00000143982' => array(
'start' => '31621472',
'end' => '31623058',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbs-007'
),
'ENSMUST00000151597' => array(
'start' => '31617165',
'end' => '31617873',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Cbs-008'
),
'ENSMUST00000151718' => array(
'start' => '31627525',
'end' => '31636649',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-009'
),
'ENSMUST00000155814' => array(
'start' => '31625077',
'end' => '31636790',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbs-004'
),
'ENSMUST00000014684' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-201'
),
'ENSMUST00000166526' => array(
'start' => '31647082',
'end' => '31658754',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'U2af1-202'
)
)
$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_0000MQ_0001' => array(
'genes_in_region' => array(
'ENSDARG00000010946' => array(
[maximum depth reached]
),
'ENSDARG00000015325' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Brain',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Brain',
(int) 9 => 'Heart',
(int) 10 => 'Kidney',
(int) 11 => 'Liver',
(int) 12 => 'Muscle'
)
),
'CIL_0000MQ_0004' => array(
'genes_in_region' => array(
'ENSMUSG00000024039' => array(
[maximum depth reached]
),
'ENSMUSG00000061613' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Adipose',
(int) 14 => 'Adrenal',
(int) 15 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Colon',
(int) 19 => 'Heart',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Placenta',
(int) 26 => 'Testis',
(int) 27 => 'Adipose',
(int) 28 => 'Adrenal',
(int) 29 => 'Bladder',
(int) 30 => 'Breast',
(int) 31 => 'Colon',
(int) 32 => 'Heart',
(int) 33 => 'Kidney',
(int) 34 => 'Liver',
(int) 35 => 'Lung',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Placenta',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Muscle',
(int) 46 => 'Muscle',
(int) 47 => 'Placenta',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Adipose',
(int) 52 => 'Adrenal',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Heart',
(int) 58 => 'Kidney',
(int) 59 => 'Liver',
(int) 60 => 'Lung',
(int) 61 => 'Muscle',
(int) 62 => 'Ovary',
(int) 63 => 'Placenta',
(int) 64 => 'Testis',
(int) 65 => 'Bladder',
(int) 66 => 'Brain',
(int) 67 => 'Heart',
(int) 68 => 'Kidney',
(int) 69 => 'Liver',
(int) 70 => 'Muscle',
(int) 71 => 'Ovary',
(int) 72 => 'Placenta',
(int) 73 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0000MQ_0002',
'tax_id' => '9606',
'chromosome' => '21',
'seq_start' => '43053191',
'seq_end' => '43107587',
'region_length' => '54396',
'region_type' => 'CGP',
'el_id' => 'ENSG00000160200-ENSG00000160201'
)
)
$gene_el = array(
'ENSDART00000021191' => array(
'Brain' => array(
'average_FPKM' => '13.770',
'stddev_FPKM' => '10.57'
),
'Heart' => array(
'average_FPKM' => '21.445',
'stddev_FPKM' => '2.67'
),
'Kidney' => array(
'average_FPKM' => '18.245',
'stddev_FPKM' => '6.79'
),
'Liver' => array(
'average_FPKM' => '3.088',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '11.340',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000015325'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '13.770',
'stddev_FPKM' => '10.57'
),
'Heart' => array(
'average_FPKM' => '21.445',
'stddev_FPKM' => '2.67'
),
'Kidney' => array(
'average_FPKM' => '18.245',
'stddev_FPKM' => '6.79'
),
'Liver' => array(
'average_FPKM' => '3.088',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '11.340',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000021191'
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
| Source ID |
Type |
Tax ID |
Position |
| ENSG00000160200-ENSG00000160201 |
CGP |
9606 |
21:43053191-43107587  |
| Gene | Transcript | Position | Biotype |
|---|
(cbsb)