| Source ID |
Type |
Tax ID |
Position |
| HDAC9 |
UCNEbase |
7955 |
9:46995335-46995457  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007LO_0004 [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_0007LO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000048052' => 'histone deacetylase 9',
'ENSG00000122691' => 'twist family bHLH transcription factor 1',
'ENSG00000146618' => 'Fer3-like bHLH transcription factor',
'ENSG00000222164' => 'RNA, 7SK small nuclear pseudogene 266',
'ENSG00000223838' => null,
'ENSG00000226522' => null,
'ENSG00000229533' => null,
'ENSG00000232492' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 13',
'ENSG00000232821' => null,
'ENSG00000236536' => null,
'ENSMUSG00000004698' => 'histone deacetylase 9',
'ENSMUSG00000035799' => 'twist basic helix-loop-helix transcription factor 1',
'ENSMUSG00000046518' => 'Fer3-like (Drosophila)',
'ENSMUSG00000095406' => 'predicted gene, 18025',
'ENSDARG00000076010' => 'twist1b'
),
'gene_name_arr' => array(
'ENSG00000048052' => 'HDAC9',
'ENSG00000122691' => 'TWIST1',
'ENSG00000146618' => 'FERD3L',
'ENSG00000222164' => 'RN7SKP266',
'ENSG00000223838' => 'AC007091.1',
'ENSG00000226522' => 'AC004744.3',
'ENSG00000229533' => 'AC003986.5',
'ENSG00000232492' => 'NPM1P13',
'ENSG00000232821' => 'AC003986.6',
'ENSG00000236536' => 'AC003986.7',
'ENSMUSG00000004698' => 'Hdac9',
'ENSMUSG00000035799' => 'Twist1',
'ENSMUSG00000046518' => 'Ferd3l',
'ENSMUSG00000095406' => 'Gm18025',
'ENSDARG00000076010' => 'twist1b'
),
'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) 6 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 19 => 'Brain',
(int) 32 => 'Breast',
(int) 43 => 'Colon',
(int) 48 => 'Heart',
(int) 58 => 'Kidney',
(int) 70 => 'Liver',
(int) 79 => 'Lung',
(int) 84 => 'Muscle',
(int) 91 => 'Ovary',
(int) 99 => 'Placenta',
(int) 105 => '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) 46,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000401921' => array(
'start' => '18496262',
'end' => '18996197',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-017'
),
'ENST00000405010' => array(
'start' => '18495746',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-002'
),
'ENST00000406072' => array(
'start' => '18496167',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-004'
),
'ENST00000406451' => array(
'start' => '18495746',
'end' => '19002416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-001'
),
'ENST00000411993' => array(
'start' => '18290188',
'end' => '18327758',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-026'
),
'ENST00000413380' => array(
'start' => '18495710',
'end' => '18591544',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-011'
),
'ENST00000413509' => array(
'start' => '18290422',
'end' => '18590486',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-008'
),
'ENST00000417496' => array(
'start' => '18086949',
'end' => '18666923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-005'
),
'ENST00000425071' => array(
'start' => '18151775',
'end' => '18327612',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-027'
),
'ENST00000428307' => array(
'start' => '18495756',
'end' => '18667105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-025'
),
'ENST00000430454' => array(
'start' => '18495715',
'end' => '18590376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-010'
),
'ENST00000432645' => array(
'start' => '18496303',
'end' => '18954316',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-023'
),
'ENST00000433709' => array(
'start' => '18290092',
'end' => '18585326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-006'
),
'ENST00000441542' => array(
'start' => '18496303',
'end' => '18996062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-021'
),
'ENST00000441986' => array(
'start' => '18496497',
'end' => '18591533',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-013'
),
'ENST00000446646' => array(
'start' => '18496176',
'end' => '18591544',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'HDAC9-012'
),
'ENST00000455069' => array(
'start' => '18087883',
'end' => '18162628',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-028'
),
'ENST00000456174' => array(
'start' => '18509273',
'end' => '18666900',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-015'
),
'ENST00000461159' => array(
'start' => '18290422',
'end' => '18829392',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-016'
),
'ENST00000461409' => array(
'start' => '18495761',
'end' => '18506036',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-009'
),
'ENST00000471887' => array(
'start' => '18502608',
'end' => '18518071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-014'
),
'ENST00000474742' => array(
'start' => '18290450',
'end' => '18496746',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-007'
),
'ENST00000476135' => array(
'start' => '18495739',
'end' => '18590354',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-003'
),
'ENST00000483142' => array(
'start' => '18835909',
'end' => '18907034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-019'
),
'ENST00000490851' => array(
'start' => '18793159',
'end' => '18997299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-020'
),
'ENST00000496026' => array(
'start' => '18851400',
'end' => '18996343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-018'
),
'ENST00000523867' => array(
'start' => '18496303',
'end' => '18835649',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-024'
),
'ENST00000524023' => array(
'start' => '18509313',
'end' => '18666979',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-022'
),
'ENST00000622668' => array(
'start' => '18495746',
'end' => '18668837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-201'
),
'ENST00000242261' => array(
'start' => '19115468',
'end' => '19117672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TWIST1-001'
),
'ENST00000354571' => array(
'start' => '19113047',
'end' => '19117118',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-003'
),
'ENST00000443687' => array(
'start' => '19020991',
'end' => '19116924',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-002'
),
'ENST00000275461' => array(
'start' => '19144782',
'end' => '19145421',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FERD3L-001'
),
'ENST00000410232' => array(
'start' => '18807993',
'end' => '18808279',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP266-201'
),
'ENST00000412563' => array(
'start' => '19353534',
'end' => '19578606',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007091.1-001'
),
'ENST00000447057' => array(
'start' => '18892096',
'end' => '18899433',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC004744.3-001'
),
'ENST00000452700' => array(
'start' => '19144293',
'end' => '19146253',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.5-001'
),
'ENST00000452663' => array(
'start' => '18948898',
'end' => '18949762',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P13-001'
),
'ENST00000419944' => array(
'start' => '19112474',
'end' => '19114271',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.6-001'
),
'ENST00000417460' => array(
'start' => '19119933',
'end' => '19121916',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.7-001'
),
'ENSMUST00000110819' => array(
'start' => '34371503',
'end' => '34528889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hdac9-201'
),
'ENSMUST00000049089' => array(
'start' => '33957671',
'end' => '33959817',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Twist1-201'
),
'ENSMUST00000061035' => array(
'start' => '33928425',
'end' => '33929310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ferd3l-201'
),
'ENSMUST00000166546' => array(
'start' => '34290274',
'end' => '34291092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm18025-201'
),
'ENSDART00000052927' => array(
'start' => '21820281',
'end' => '21821887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-001'
),
'ENSDART00000149901' => array(
'start' => '21820281',
'end' => '21821746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-002'
)
),
'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_0007LO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007LO_0001' => array(
'genes_in_region' => array(
'ENSG00000122691' => array(
[maximum depth reached]
),
'ENSG00000146618' => array(
[maximum depth reached]
),
'ENSG00000222164' => array(
[maximum depth reached]
),
'ENSG00000223838' => array(
[maximum depth reached]
),
'ENSG00000226522' => array(
[maximum depth reached]
),
'ENSG00000229533' => array(
[maximum depth reached]
),
'ENSG00000232492' => array(
[maximum depth reached]
),
'ENSG00000232821' => array(
[maximum depth reached]
),
'ENSG00000236536' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Bladder',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Brain',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Testis',
(int) 22 => 'Bladder',
(int) 23 => 'Muscle',
(int) 24 => 'Breast',
(int) 25 => 'Liver',
(int) 26 => 'Kidney',
(int) 27 => 'Muscle',
(int) 28 => 'Testis',
(int) 29 => 'Brain',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Breast',
(int) 47 => 'Kidney',
(int) 48 => 'Placenta',
(int) 49 => 'Brain',
(int) 50 => 'Heart',
(int) 51 => 'Bladder',
(int) 52 => 'Testis',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Brain',
(int) 56 => 'Testis',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Kidney',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Adipose',
(int) 65 => 'Adrenal',
(int) 66 => 'Breast',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000004698' => array(
[maximum depth reached]
),
'ENSMUSG00000035799' => array(
[maximum depth reached]
),
'ENSMUSG00000046518' => array(
[maximum depth reached]
),
'ENSMUSG00000095406' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
'ENSDARG00000076010' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Kidney',
(int) 2 => 'Brain',
(int) 3 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSG00000048052' => 'histone deacetylase 9',
'ENSG00000122691' => 'twist family bHLH transcription factor 1',
'ENSG00000146618' => 'Fer3-like bHLH transcription factor',
'ENSG00000222164' => 'RNA, 7SK small nuclear pseudogene 266',
'ENSG00000223838' => null,
'ENSG00000226522' => null,
'ENSG00000229533' => null,
'ENSG00000232492' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 13',
'ENSG00000232821' => null,
'ENSG00000236536' => null,
'ENSMUSG00000004698' => 'histone deacetylase 9',
'ENSMUSG00000035799' => 'twist basic helix-loop-helix transcription factor 1',
'ENSMUSG00000046518' => 'Fer3-like (Drosophila)',
'ENSMUSG00000095406' => 'predicted gene, 18025',
'ENSDARG00000076010' => 'twist1b'
)
$gene_name_arr = array(
'ENSG00000048052' => 'HDAC9',
'ENSG00000122691' => 'TWIST1',
'ENSG00000146618' => 'FERD3L',
'ENSG00000222164' => 'RN7SKP266',
'ENSG00000223838' => 'AC007091.1',
'ENSG00000226522' => 'AC004744.3',
'ENSG00000229533' => 'AC003986.5',
'ENSG00000232492' => 'NPM1P13',
'ENSG00000232821' => 'AC003986.6',
'ENSG00000236536' => 'AC003986.7',
'ENSMUSG00000004698' => 'Hdac9',
'ENSMUSG00000035799' => 'Twist1',
'ENSMUSG00000046518' => 'Ferd3l',
'ENSMUSG00000095406' => 'Gm18025',
'ENSDARG00000076010' => 'twist1b'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0001',
'tax_id' => '9606',
'chromosome' => '7',
'seq_start' => '18643621',
'seq_end' => '19413840',
'region_length' => '770219',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '33675251',
'seq_end' => '34394390',
'region_length' => '719139',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '21759330',
'seq_end' => '21846762',
'region_length' => '87432',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '46995335',
'seq_end' => '46995457',
'region_length' => '122',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 19 => 'Brain',
(int) 32 => 'Breast',
(int) 43 => 'Colon',
(int) 48 => 'Heart',
(int) 58 => 'Kidney',
(int) 70 => 'Liver',
(int) 79 => 'Lung',
(int) 84 => 'Muscle',
(int) 91 => 'Ovary',
(int) 99 => 'Placenta',
(int) 105 => '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) 46
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000401921' => array(
'start' => '18496262',
'end' => '18996197',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-017'
),
'ENST00000405010' => array(
'start' => '18495746',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-002'
),
'ENST00000406072' => array(
'start' => '18496167',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-004'
),
'ENST00000406451' => array(
'start' => '18495746',
'end' => '19002416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-001'
),
'ENST00000411993' => array(
'start' => '18290188',
'end' => '18327758',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-026'
),
'ENST00000413380' => array(
'start' => '18495710',
'end' => '18591544',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-011'
),
'ENST00000413509' => array(
'start' => '18290422',
'end' => '18590486',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-008'
),
'ENST00000417496' => array(
'start' => '18086949',
'end' => '18666923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-005'
),
'ENST00000425071' => array(
'start' => '18151775',
'end' => '18327612',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-027'
),
'ENST00000428307' => array(
'start' => '18495756',
'end' => '18667105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-025'
),
'ENST00000430454' => array(
'start' => '18495715',
'end' => '18590376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-010'
),
'ENST00000432645' => array(
'start' => '18496303',
'end' => '18954316',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-023'
),
'ENST00000433709' => array(
'start' => '18290092',
'end' => '18585326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-006'
),
'ENST00000441542' => array(
'start' => '18496303',
'end' => '18996062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-021'
),
'ENST00000441986' => array(
'start' => '18496497',
'end' => '18591533',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-013'
),
'ENST00000446646' => array(
'start' => '18496176',
'end' => '18591544',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'HDAC9-012'
),
'ENST00000455069' => array(
'start' => '18087883',
'end' => '18162628',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-028'
),
'ENST00000456174' => array(
'start' => '18509273',
'end' => '18666900',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-015'
),
'ENST00000461159' => array(
'start' => '18290422',
'end' => '18829392',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-016'
),
'ENST00000461409' => array(
'start' => '18495761',
'end' => '18506036',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-009'
),
'ENST00000471887' => array(
'start' => '18502608',
'end' => '18518071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-014'
),
'ENST00000474742' => array(
'start' => '18290450',
'end' => '18496746',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-007'
),
'ENST00000476135' => array(
'start' => '18495739',
'end' => '18590354',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-003'
),
'ENST00000483142' => array(
'start' => '18835909',
'end' => '18907034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-019'
),
'ENST00000490851' => array(
'start' => '18793159',
'end' => '18997299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-020'
),
'ENST00000496026' => array(
'start' => '18851400',
'end' => '18996343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-018'
),
'ENST00000523867' => array(
'start' => '18496303',
'end' => '18835649',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-024'
),
'ENST00000524023' => array(
'start' => '18509313',
'end' => '18666979',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-022'
),
'ENST00000622668' => array(
'start' => '18495746',
'end' => '18668837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-201'
),
'ENST00000242261' => array(
'start' => '19115468',
'end' => '19117672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TWIST1-001'
),
'ENST00000354571' => array(
'start' => '19113047',
'end' => '19117118',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-003'
),
'ENST00000443687' => array(
'start' => '19020991',
'end' => '19116924',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-002'
),
'ENST00000275461' => array(
'start' => '19144782',
'end' => '19145421',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FERD3L-001'
),
'ENST00000410232' => array(
'start' => '18807993',
'end' => '18808279',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP266-201'
),
'ENST00000412563' => array(
'start' => '19353534',
'end' => '19578606',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007091.1-001'
),
'ENST00000447057' => array(
'start' => '18892096',
'end' => '18899433',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC004744.3-001'
),
'ENST00000452700' => array(
'start' => '19144293',
'end' => '19146253',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.5-001'
),
'ENST00000452663' => array(
'start' => '18948898',
'end' => '18949762',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P13-001'
),
'ENST00000419944' => array(
'start' => '19112474',
'end' => '19114271',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.6-001'
),
'ENST00000417460' => array(
'start' => '19119933',
'end' => '19121916',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.7-001'
),
'ENSMUST00000110819' => array(
'start' => '34371503',
'end' => '34528889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hdac9-201'
),
'ENSMUST00000049089' => array(
'start' => '33957671',
'end' => '33959817',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Twist1-201'
),
'ENSMUST00000061035' => array(
'start' => '33928425',
'end' => '33929310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ferd3l-201'
),
'ENSMUST00000166546' => array(
'start' => '34290274',
'end' => '34291092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm18025-201'
),
'ENSDART00000052927' => array(
'start' => '21820281',
'end' => '21821887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-001'
),
'ENSDART00000149901' => array(
'start' => '21820281',
'end' => '21821746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-002'
)
)
$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_0007LO_0001' => array(
'genes_in_region' => array(
'ENSG00000122691' => array(
[maximum depth reached]
),
'ENSG00000146618' => array(
[maximum depth reached]
),
'ENSG00000222164' => array(
[maximum depth reached]
),
'ENSG00000223838' => array(
[maximum depth reached]
),
'ENSG00000226522' => array(
[maximum depth reached]
),
'ENSG00000229533' => array(
[maximum depth reached]
),
'ENSG00000232492' => array(
[maximum depth reached]
),
'ENSG00000232821' => array(
[maximum depth reached]
),
'ENSG00000236536' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Bladder',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Brain',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Testis',
(int) 22 => 'Bladder',
(int) 23 => 'Muscle',
(int) 24 => 'Breast',
(int) 25 => 'Liver',
(int) 26 => 'Kidney',
(int) 27 => 'Muscle',
(int) 28 => 'Testis',
(int) 29 => 'Brain',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Breast',
(int) 47 => 'Kidney',
(int) 48 => 'Placenta',
(int) 49 => 'Brain',
(int) 50 => 'Heart',
(int) 51 => 'Bladder',
(int) 52 => 'Testis',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Brain',
(int) 56 => 'Testis',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Kidney',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Adipose',
(int) 65 => 'Adrenal',
(int) 66 => 'Breast',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000004698' => array(
[maximum depth reached]
),
'ENSMUSG00000035799' => array(
[maximum depth reached]
),
'ENSMUSG00000046518' => array(
[maximum depth reached]
),
'ENSMUSG00000095406' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
'ENSDARG00000076010' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Kidney',
(int) 2 => 'Brain',
(int) 3 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '46995335',
'seq_end' => '46995457',
'region_length' => '122',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
)
$gene_el = array(
'ENSDART00000052927' => array(
'Heart' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.312',
'stddev_FPKM' => '0.06'
)
),
'ENSDART00000149901' => array(
'Brain' => array(
'average_FPKM' => '0.145',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.229',
'stddev_FPKM' => '0.15'
)
)
)
$gene_key = 'ENSDARG00000076010'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.145',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.229',
'stddev_FPKM' => '0.15'
)
)
$tran_key = 'ENSDART00000149901'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007LO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000048052' => 'histone deacetylase 9',
'ENSG00000122691' => 'twist family bHLH transcription factor 1',
'ENSG00000146618' => 'Fer3-like bHLH transcription factor',
'ENSG00000222164' => 'RNA, 7SK small nuclear pseudogene 266',
'ENSG00000223838' => null,
'ENSG00000226522' => null,
'ENSG00000229533' => null,
'ENSG00000232492' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 13',
'ENSG00000232821' => null,
'ENSG00000236536' => null,
'ENSMUSG00000004698' => 'histone deacetylase 9',
'ENSMUSG00000035799' => 'twist basic helix-loop-helix transcription factor 1',
'ENSMUSG00000046518' => 'Fer3-like (Drosophila)',
'ENSMUSG00000095406' => 'predicted gene, 18025',
'ENSDARG00000076010' => 'twist1b'
),
'gene_name_arr' => array(
'ENSG00000048052' => 'HDAC9',
'ENSG00000122691' => 'TWIST1',
'ENSG00000146618' => 'FERD3L',
'ENSG00000222164' => 'RN7SKP266',
'ENSG00000223838' => 'AC007091.1',
'ENSG00000226522' => 'AC004744.3',
'ENSG00000229533' => 'AC003986.5',
'ENSG00000232492' => 'NPM1P13',
'ENSG00000232821' => 'AC003986.6',
'ENSG00000236536' => 'AC003986.7',
'ENSMUSG00000004698' => 'Hdac9',
'ENSMUSG00000035799' => 'Twist1',
'ENSMUSG00000046518' => 'Ferd3l',
'ENSMUSG00000095406' => 'Gm18025',
'ENSDARG00000076010' => 'twist1b'
),
'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) 6 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 19 => 'Brain',
(int) 32 => 'Breast',
(int) 43 => 'Colon',
(int) 48 => 'Heart',
(int) 58 => 'Kidney',
(int) 70 => 'Liver',
(int) 79 => 'Lung',
(int) 84 => 'Muscle',
(int) 91 => 'Ovary',
(int) 99 => 'Placenta',
(int) 105 => '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) 46,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000401921' => array(
'start' => '18496262',
'end' => '18996197',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-017'
),
'ENST00000405010' => array(
'start' => '18495746',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-002'
),
'ENST00000406072' => array(
'start' => '18496167',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-004'
),
'ENST00000406451' => array(
'start' => '18495746',
'end' => '19002416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-001'
),
'ENST00000411993' => array(
'start' => '18290188',
'end' => '18327758',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-026'
),
'ENST00000413380' => array(
'start' => '18495710',
'end' => '18591544',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-011'
),
'ENST00000413509' => array(
'start' => '18290422',
'end' => '18590486',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-008'
),
'ENST00000417496' => array(
'start' => '18086949',
'end' => '18666923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-005'
),
'ENST00000425071' => array(
'start' => '18151775',
'end' => '18327612',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-027'
),
'ENST00000428307' => array(
'start' => '18495756',
'end' => '18667105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-025'
),
'ENST00000430454' => array(
'start' => '18495715',
'end' => '18590376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-010'
),
'ENST00000432645' => array(
'start' => '18496303',
'end' => '18954316',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-023'
),
'ENST00000433709' => array(
'start' => '18290092',
'end' => '18585326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-006'
),
'ENST00000441542' => array(
'start' => '18496303',
'end' => '18996062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-021'
),
'ENST00000441986' => array(
'start' => '18496497',
'end' => '18591533',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-013'
),
'ENST00000446646' => array(
'start' => '18496176',
'end' => '18591544',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'HDAC9-012'
),
'ENST00000455069' => array(
'start' => '18087883',
'end' => '18162628',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-028'
),
'ENST00000456174' => array(
'start' => '18509273',
'end' => '18666900',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-015'
),
'ENST00000461159' => array(
'start' => '18290422',
'end' => '18829392',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-016'
),
'ENST00000461409' => array(
'start' => '18495761',
'end' => '18506036',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-009'
),
'ENST00000471887' => array(
'start' => '18502608',
'end' => '18518071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-014'
),
'ENST00000474742' => array(
'start' => '18290450',
'end' => '18496746',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-007'
),
'ENST00000476135' => array(
'start' => '18495739',
'end' => '18590354',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-003'
),
'ENST00000483142' => array(
'start' => '18835909',
'end' => '18907034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-019'
),
'ENST00000490851' => array(
'start' => '18793159',
'end' => '18997299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-020'
),
'ENST00000496026' => array(
'start' => '18851400',
'end' => '18996343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-018'
),
'ENST00000523867' => array(
'start' => '18496303',
'end' => '18835649',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-024'
),
'ENST00000524023' => array(
'start' => '18509313',
'end' => '18666979',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-022'
),
'ENST00000622668' => array(
'start' => '18495746',
'end' => '18668837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-201'
),
'ENST00000242261' => array(
'start' => '19115468',
'end' => '19117672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TWIST1-001'
),
'ENST00000354571' => array(
'start' => '19113047',
'end' => '19117118',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-003'
),
'ENST00000443687' => array(
'start' => '19020991',
'end' => '19116924',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-002'
),
'ENST00000275461' => array(
'start' => '19144782',
'end' => '19145421',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FERD3L-001'
),
'ENST00000410232' => array(
'start' => '18807993',
'end' => '18808279',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP266-201'
),
'ENST00000412563' => array(
'start' => '19353534',
'end' => '19578606',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007091.1-001'
),
'ENST00000447057' => array(
'start' => '18892096',
'end' => '18899433',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC004744.3-001'
),
'ENST00000452700' => array(
'start' => '19144293',
'end' => '19146253',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.5-001'
),
'ENST00000452663' => array(
'start' => '18948898',
'end' => '18949762',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P13-001'
),
'ENST00000419944' => array(
'start' => '19112474',
'end' => '19114271',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.6-001'
),
'ENST00000417460' => array(
'start' => '19119933',
'end' => '19121916',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.7-001'
),
'ENSMUST00000110819' => array(
'start' => '34371503',
'end' => '34528889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hdac9-201'
),
'ENSMUST00000049089' => array(
'start' => '33957671',
'end' => '33959817',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Twist1-201'
),
'ENSMUST00000061035' => array(
'start' => '33928425',
'end' => '33929310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ferd3l-201'
),
'ENSMUST00000166546' => array(
'start' => '34290274',
'end' => '34291092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm18025-201'
),
'ENSDART00000052927' => array(
'start' => '21820281',
'end' => '21821887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-001'
),
'ENSDART00000149901' => array(
'start' => '21820281',
'end' => '21821746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-002'
)
),
'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_0007LO_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007LO_0001' => array(
'genes_in_region' => array(
'ENSG00000122691' => array(
[maximum depth reached]
),
'ENSG00000146618' => array(
[maximum depth reached]
),
'ENSG00000222164' => array(
[maximum depth reached]
),
'ENSG00000223838' => array(
[maximum depth reached]
),
'ENSG00000226522' => array(
[maximum depth reached]
),
'ENSG00000229533' => array(
[maximum depth reached]
),
'ENSG00000232492' => array(
[maximum depth reached]
),
'ENSG00000232821' => array(
[maximum depth reached]
),
'ENSG00000236536' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Bladder',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Brain',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Testis',
(int) 22 => 'Bladder',
(int) 23 => 'Muscle',
(int) 24 => 'Breast',
(int) 25 => 'Liver',
(int) 26 => 'Kidney',
(int) 27 => 'Muscle',
(int) 28 => 'Testis',
(int) 29 => 'Brain',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Breast',
(int) 47 => 'Kidney',
(int) 48 => 'Placenta',
(int) 49 => 'Brain',
(int) 50 => 'Heart',
(int) 51 => 'Bladder',
(int) 52 => 'Testis',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Brain',
(int) 56 => 'Testis',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Kidney',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Adipose',
(int) 65 => 'Adrenal',
(int) 66 => 'Breast',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000004698' => array(
[maximum depth reached]
),
'ENSMUSG00000035799' => array(
[maximum depth reached]
),
'ENSMUSG00000046518' => array(
[maximum depth reached]
),
'ENSMUSG00000095406' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
'ENSDARG00000076010' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Kidney',
(int) 2 => 'Brain',
(int) 3 => 'Heart'
)
)
)
$gene_desc_arr = array(
'ENSG00000048052' => 'histone deacetylase 9',
'ENSG00000122691' => 'twist family bHLH transcription factor 1',
'ENSG00000146618' => 'Fer3-like bHLH transcription factor',
'ENSG00000222164' => 'RNA, 7SK small nuclear pseudogene 266',
'ENSG00000223838' => null,
'ENSG00000226522' => null,
'ENSG00000229533' => null,
'ENSG00000232492' => 'nucleophosmin 1 (nucleolar phosphoprotein B23, numatrin) pseudogene 13',
'ENSG00000232821' => null,
'ENSG00000236536' => null,
'ENSMUSG00000004698' => 'histone deacetylase 9',
'ENSMUSG00000035799' => 'twist basic helix-loop-helix transcription factor 1',
'ENSMUSG00000046518' => 'Fer3-like (Drosophila)',
'ENSMUSG00000095406' => 'predicted gene, 18025',
'ENSDARG00000076010' => 'twist1b'
)
$gene_name_arr = array(
'ENSG00000048052' => 'HDAC9',
'ENSG00000122691' => 'TWIST1',
'ENSG00000146618' => 'FERD3L',
'ENSG00000222164' => 'RN7SKP266',
'ENSG00000223838' => 'AC007091.1',
'ENSG00000226522' => 'AC004744.3',
'ENSG00000229533' => 'AC003986.5',
'ENSG00000232492' => 'NPM1P13',
'ENSG00000232821' => 'AC003986.6',
'ENSG00000236536' => 'AC003986.7',
'ENSMUSG00000004698' => 'Hdac9',
'ENSMUSG00000035799' => 'Twist1',
'ENSMUSG00000046518' => 'Ferd3l',
'ENSMUSG00000095406' => 'Gm18025',
'ENSDARG00000076010' => 'twist1b'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0001',
'tax_id' => '9606',
'chromosome' => '7',
'seq_start' => '18643621',
'seq_end' => '19413840',
'region_length' => '770219',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0002',
'tax_id' => '10090',
'chromosome' => '12',
'seq_start' => '33675251',
'seq_end' => '34394390',
'region_length' => '719139',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0003',
'tax_id' => '7955',
'chromosome' => '16',
'seq_start' => '21759330',
'seq_end' => '21846762',
'region_length' => '87432',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '46995335',
'seq_end' => '46995457',
'region_length' => '122',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 13 => 'Bladder',
(int) 19 => 'Brain',
(int) 32 => 'Breast',
(int) 43 => 'Colon',
(int) 48 => 'Heart',
(int) 58 => 'Kidney',
(int) 70 => 'Liver',
(int) 79 => 'Lung',
(int) 84 => 'Muscle',
(int) 91 => 'Ovary',
(int) 99 => 'Placenta',
(int) 105 => '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) 46
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000401921' => array(
'start' => '18496262',
'end' => '18996197',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-017'
),
'ENST00000405010' => array(
'start' => '18495746',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-002'
),
'ENST00000406072' => array(
'start' => '18496167',
'end' => '18668843',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-004'
),
'ENST00000406451' => array(
'start' => '18495746',
'end' => '19002416',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-001'
),
'ENST00000411993' => array(
'start' => '18290188',
'end' => '18327758',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-026'
),
'ENST00000413380' => array(
'start' => '18495710',
'end' => '18591544',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-011'
),
'ENST00000413509' => array(
'start' => '18290422',
'end' => '18590486',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-008'
),
'ENST00000417496' => array(
'start' => '18086949',
'end' => '18666923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-005'
),
'ENST00000425071' => array(
'start' => '18151775',
'end' => '18327612',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-027'
),
'ENST00000428307' => array(
'start' => '18495756',
'end' => '18667105',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-025'
),
'ENST00000430454' => array(
'start' => '18495715',
'end' => '18590376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-010'
),
'ENST00000432645' => array(
'start' => '18496303',
'end' => '18954316',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-023'
),
'ENST00000433709' => array(
'start' => '18290092',
'end' => '18585326',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-006'
),
'ENST00000441542' => array(
'start' => '18496303',
'end' => '18996062',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-021'
),
'ENST00000441986' => array(
'start' => '18496497',
'end' => '18591533',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-013'
),
'ENST00000446646' => array(
'start' => '18496176',
'end' => '18591544',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'HDAC9-012'
),
'ENST00000455069' => array(
'start' => '18087883',
'end' => '18162628',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-028'
),
'ENST00000456174' => array(
'start' => '18509273',
'end' => '18666900',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-015'
),
'ENST00000461159' => array(
'start' => '18290422',
'end' => '18829392',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-016'
),
'ENST00000461409' => array(
'start' => '18495761',
'end' => '18506036',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-009'
),
'ENST00000471887' => array(
'start' => '18502608',
'end' => '18518071',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-014'
),
'ENST00000474742' => array(
'start' => '18290450',
'end' => '18496746',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-007'
),
'ENST00000476135' => array(
'start' => '18495739',
'end' => '18590354',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-003'
),
'ENST00000483142' => array(
'start' => '18835909',
'end' => '18907034',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-019'
),
'ENST00000490851' => array(
'start' => '18793159',
'end' => '18997299',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-020'
),
'ENST00000496026' => array(
'start' => '18851400',
'end' => '18996343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'HDAC9-018'
),
'ENST00000523867' => array(
'start' => '18496303',
'end' => '18835649',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'HDAC9-024'
),
'ENST00000524023' => array(
'start' => '18509313',
'end' => '18666979',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-022'
),
'ENST00000622668' => array(
'start' => '18495746',
'end' => '18668837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'HDAC9-201'
),
'ENST00000242261' => array(
'start' => '19115468',
'end' => '19117672',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TWIST1-001'
),
'ENST00000354571' => array(
'start' => '19113047',
'end' => '19117118',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-003'
),
'ENST00000443687' => array(
'start' => '19020991',
'end' => '19116924',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TWIST1-002'
),
'ENST00000275461' => array(
'start' => '19144782',
'end' => '19145421',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FERD3L-001'
),
'ENST00000410232' => array(
'start' => '18807993',
'end' => '18808279',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SKP266-201'
),
'ENST00000412563' => array(
'start' => '19353534',
'end' => '19578606',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC007091.1-001'
),
'ENST00000447057' => array(
'start' => '18892096',
'end' => '18899433',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC004744.3-001'
),
'ENST00000452700' => array(
'start' => '19144293',
'end' => '19146253',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.5-001'
),
'ENST00000452663' => array(
'start' => '18948898',
'end' => '18949762',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'NPM1P13-001'
),
'ENST00000419944' => array(
'start' => '19112474',
'end' => '19114271',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.6-001'
),
'ENST00000417460' => array(
'start' => '19119933',
'end' => '19121916',
'transcript_biotype' => 'antisense',
'transcript_name' => 'AC003986.7-001'
),
'ENSMUST00000110819' => array(
'start' => '34371503',
'end' => '34528889',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hdac9-201'
),
'ENSMUST00000049089' => array(
'start' => '33957671',
'end' => '33959817',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Twist1-201'
),
'ENSMUST00000061035' => array(
'start' => '33928425',
'end' => '33929310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Ferd3l-201'
),
'ENSMUST00000166546' => array(
'start' => '34290274',
'end' => '34291092',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm18025-201'
),
'ENSDART00000052927' => array(
'start' => '21820281',
'end' => '21821887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-001'
),
'ENSDART00000149901' => array(
'start' => '21820281',
'end' => '21821746',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'twist1b-002'
)
)
$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_0007LO_0001' => array(
'genes_in_region' => array(
'ENSG00000122691' => array(
[maximum depth reached]
),
'ENSG00000146618' => array(
[maximum depth reached]
),
'ENSG00000222164' => array(
[maximum depth reached]
),
'ENSG00000223838' => array(
[maximum depth reached]
),
'ENSG00000226522' => array(
[maximum depth reached]
),
'ENSG00000229533' => array(
[maximum depth reached]
),
'ENSG00000232492' => array(
[maximum depth reached]
),
'ENSG00000232821' => array(
[maximum depth reached]
),
'ENSG00000236536' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adrenal',
(int) 1 => 'Brain',
(int) 2 => 'Breast',
(int) 3 => 'Colon',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Bladder',
(int) 9 => 'Breast',
(int) 10 => 'Heart',
(int) 11 => 'Kidney',
(int) 12 => 'Lung',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Brain',
(int) 17 => 'Heart',
(int) 18 => 'Liver',
(int) 19 => 'Heart',
(int) 20 => 'Liver',
(int) 21 => 'Testis',
(int) 22 => 'Bladder',
(int) 23 => 'Muscle',
(int) 24 => 'Breast',
(int) 25 => 'Liver',
(int) 26 => 'Kidney',
(int) 27 => 'Muscle',
(int) 28 => 'Testis',
(int) 29 => 'Brain',
(int) 30 => 'Kidney',
(int) 31 => 'Ovary',
(int) 32 => 'Adipose',
(int) 33 => 'Adrenal',
(int) 34 => 'Brain',
(int) 35 => 'Breast',
(int) 36 => 'Colon',
(int) 37 => 'Heart',
(int) 38 => 'Kidney',
(int) 39 => 'Liver',
(int) 40 => 'Lung',
(int) 41 => 'Muscle',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Adrenal',
(int) 46 => 'Breast',
(int) 47 => 'Kidney',
(int) 48 => 'Placenta',
(int) 49 => 'Brain',
(int) 50 => 'Heart',
(int) 51 => 'Bladder',
(int) 52 => 'Testis',
(int) 53 => 'Testis',
(int) 54 => 'Adipose',
(int) 55 => 'Brain',
(int) 56 => 'Testis',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Kidney',
(int) 60 => 'Brain',
(int) 61 => 'Breast',
(int) 62 => 'Kidney',
(int) 63 => 'Liver',
(int) 64 => 'Adipose',
(int) 65 => 'Adrenal',
(int) 66 => 'Breast',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007LO_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000004698' => array(
[maximum depth reached]
),
'ENSMUSG00000035799' => array(
[maximum depth reached]
),
'ENSMUSG00000046518' => array(
[maximum depth reached]
),
'ENSMUSG00000095406' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Brain',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Bladder',
(int) 33 => 'Brain',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Heart',
(int) 37 => 'Kidney',
(int) 38 => 'Liver',
(int) 39 => 'Lung',
(int) 40 => 'Muscle',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis'
)
),
'CIL_0007LO_0003' => array(
'genes_in_region' => array(
'ENSDARG00000076010' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Heart',
(int) 1 => 'Kidney',
(int) 2 => 'Brain',
(int) 3 => 'Heart'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007LO_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '46995335',
'seq_end' => '46995457',
'region_length' => '122',
'region_type' => 'UCNEbase',
'el_id' => 'HDAC9'
)
)
$gene_el = array(
'ENSDART00000052927' => array(
'Heart' => array(
'average_FPKM' => '0.162',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.312',
'stddev_FPKM' => '0.06'
)
),
'ENSDART00000149901' => array(
'Brain' => array(
'average_FPKM' => '0.145',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.229',
'stddev_FPKM' => '0.15'
)
)
)
$gene_key = 'ENSDARG00000076010'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.145',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.229',
'stddev_FPKM' => '0.15'
)
)
$tran_key = 'ENSDART00000149901'
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
(TWIST1)