Notice (8): Undefined index: CIL_0007O4_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_0007O4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000115896' => 'phospholipase C-like 1',
'ENSG00000225421' => null,
'ENSG00000231557' => null,
'ENSG00000236653' => null,
'ENSG00000252511' => null,
'ENSG00000119042' => 'SATB homeobox 2',
'ENSG00000230407' => null,
'ENSG00000238698' => 'RNA, U7 small nuclear 147 pseudogene',
'ENSG00000257045' => null,
'ENSMUSG00000038331' => 'special AT-rich sequence binding protein 2',
'ENSMUSG00000045336' => 'heat shock transcription factor, Y linked 2',
'ENSMUSG00000099950' => 'RIKEN cDNA 9130227L01 gene',
'ENSMUSG00000100372' => 'RIKEN cDNA 1700003I22 gene',
'ENSMUSG00000100944' => 'predicted gene 28900',
'ENSMUSG00000101332' => 'predicted gene 28240'
),
'gene_name_arr' => array(
'ENSG00000115896' => 'PLCL1',
'ENSG00000225421' => 'AC019330.1',
'ENSG00000231557' => 'AC018717.1',
'ENSG00000236653' => 'AC005235.1',
'ENSG00000252511' => 'AC019330.2',
'ENSG00000119042' => 'SATB2',
'ENSG00000230407' => 'AC018717.2',
'ENSG00000238698' => 'RNU7-147P',
'ENSG00000257045' => 'RP11-486F17.1',
'ENSMUSG00000038331' => 'Satb2',
'ENSMUSG00000045336' => 'Hsfy2',
'ENSMUSG00000099950' => 'RP24-421N21.1',
'ENSMUSG00000100372' => 'RP23-258N15.1',
'ENSMUSG00000100944' => 'RP23-478I8.1',
'ENSMUSG00000101332' => 'RP24-146K19.1'
),
'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) 9 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 27 => 'Brain',
(int) 45 => 'Breast',
(int) 60 => 'Colon',
(int) 70 => 'Heart',
(int) 86 => 'Kidney',
(int) 98 => 'Liver',
(int) 109 => 'Lung',
(int) 116 => 'Muscle',
(int) 129 => 'Ovary',
(int) 139 => 'Placenta',
(int) 149 => '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) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000428675' => array(
'start' => '197804702',
'end' => '198148401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-006'
),
'ENST00000435320' => array(
'start' => '197804702',
'end' => '198149884',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PLCL1-001'
),
'ENST00000437704' => array(
'start' => '198083749',
'end' => '198149884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-201'
),
'ENST00000472193' => array(
'start' => '198346829',
'end' => '198572581',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-005'
),
'ENST00000487695' => array(
'start' => '197810258',
'end' => '198146932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-002'
),
'ENST00000625084' => array(
'start' => '198149375',
'end' => '198355486',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-007'
),
'ENST00000440609' => array(
'start' => '198553195',
'end' => '198772356',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC019330.1-001'
),
'ENST00000456031' => array(
'start' => '198882573',
'end' => '199071791',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC018717.1-001'
),
'ENST00000443261' => array(
'start' => '198374476',
'end' => '198375097',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-003'
),
'ENST00000451266' => array(
'start' => '198301408',
'end' => '198314714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-002'
),
'ENST00000456248' => array(
'start' => '198299363',
'end' => '198374549',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-001'
),
'ENST00000516702' => array(
'start' => '198566645',
'end' => '198566729',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC019330.2-201'
),
'ENST00000260926' => array(
'start' => '199269508',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-003'
),
'ENST00000417098' => array(
'start' => '199269500',
'end' => '199458096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-001'
),
'ENST00000428695' => array(
'start' => '199271975',
'end' => '199456088',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-007'
),
'ENST00000440919' => array(
'start' => '199395831',
'end' => '199457612',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SATB2-005'
),
'ENST00000443023' => array(
'start' => '199269508',
'end' => '199458745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-010'
),
'ENST00000457245' => array(
'start' => '199272150',
'end' => '199471266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-002'
),
'ENST00000463386' => array(
'start' => '199456053',
'end' => '199465167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-004'
),
'ENST00000473517' => array(
'start' => '199308860',
'end' => '199329035',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-009'
),
'ENST00000483346' => array(
'start' => '199346866',
'end' => '199368943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-006'
),
'ENST00000484124' => array(
'start' => '199368610',
'end' => '199423915',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-008'
),
'ENST00000614512' => array(
'start' => '199269500',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-201'
),
'ENST00000457712' => array(
'start' => '199108584',
'end' => '199110088',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018717.2-001'
),
'ENST00000459118' => array(
'start' => '199191059',
'end' => '199191120',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU7-147P-201'
),
'ENST00000489557' => array(
'start' => '199325310',
'end' => '199329362',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-486F17.1-001'
),
'ENSMUST00000042857' => array(
'start' => '56793981',
'end' => '56972502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-002'
),
'ENSMUST00000114415' => array(
'start' => '56793986',
'end' => '56971858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-001'
),
'ENSMUST00000176759' => array(
'start' => '56948134',
'end' => '56969840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-005'
),
'ENSMUST00000177282' => array(
'start' => '56969740',
'end' => '56978650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-004'
),
'ENSMUST00000177424' => array(
'start' => '56793988',
'end' => '56969872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-003'
),
'ENSMUST00000062085' => array(
'start' => '56636044',
'end' => '56637435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hsfy2-001'
),
'ENSMUST00000188040' => array(
'start' => '55960914',
'end' => '55972328',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-002'
),
'ENSMUST00000189293' => array(
'start' => '55931241',
'end' => '55972098',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-001'
),
'ENSMUST00000186048' => array(
'start' => '56018978',
'end' => '56020203',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-001'
),
'ENSMUST00000190280' => array(
'start' => '56019023',
'end' => '56020137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-002'
),
'ENSMUST00000185232' => array(
'start' => '56451407',
'end' => '56451562',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-478I8.1-001'
),
'ENSMUST00000187560' => array(
'start' => '56531824',
'end' => '56533876',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-146K19.1-001'
)
),
'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_0007O4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007O4_0001' => array(
'genes_in_region' => array(
'ENSG00000115896' => array(
[maximum depth reached]
),
'ENSG00000225421' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
),
'ENSG00000236653' => array(
[maximum depth reached]
),
'ENSG00000252511' => 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 => 'Liver',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Liver',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Bladder',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Breast',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Brain',
(int) 43 => 'Testis',
(int) 44 => 'Adipose',
(int) 45 => 'Adrenal',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Muscle',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Heart',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain'
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
'ENSG00000119042' => array(
[maximum depth reached]
),
'ENSG00000230407' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Placenta',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 9 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 12 => 'Heart',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Heart',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Breast',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Testis',
(int) 41 => 'Brain',
(int) 42 => 'Heart'
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000038331' => array(
[maximum depth reached]
),
'ENSMUSG00000045336' => array(
[maximum depth reached]
),
'ENSMUSG00000099950' => array(
[maximum depth reached]
),
'ENSMUSG00000100372' => array(
[maximum depth reached]
),
'ENSMUSG00000101332' => 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 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Bladder',
(int) 29 => 'Brain',
(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 => 'Kidney',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Bladder',
(int) 46 => 'Brain',
(int) 47 => 'Colon',
(int) 48 => 'Kidney',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Kidney',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Lung',
(int) 63 => 'Testis',
(int) 64 => 'Colon',
(int) 65 => 'Testis',
(int) 66 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSG00000115896' => 'phospholipase C-like 1',
'ENSG00000225421' => null,
'ENSG00000231557' => null,
'ENSG00000236653' => null,
'ENSG00000252511' => null,
'ENSG00000119042' => 'SATB homeobox 2',
'ENSG00000230407' => null,
'ENSG00000238698' => 'RNA, U7 small nuclear 147 pseudogene',
'ENSG00000257045' => null,
'ENSMUSG00000038331' => 'special AT-rich sequence binding protein 2',
'ENSMUSG00000045336' => 'heat shock transcription factor, Y linked 2',
'ENSMUSG00000099950' => 'RIKEN cDNA 9130227L01 gene',
'ENSMUSG00000100372' => 'RIKEN cDNA 1700003I22 gene',
'ENSMUSG00000100944' => 'predicted gene 28900',
'ENSMUSG00000101332' => 'predicted gene 28240'
)
$gene_name_arr = array(
'ENSG00000115896' => 'PLCL1',
'ENSG00000225421' => 'AC019330.1',
'ENSG00000231557' => 'AC018717.1',
'ENSG00000236653' => 'AC005235.1',
'ENSG00000252511' => 'AC019330.2',
'ENSG00000119042' => 'SATB2',
'ENSG00000230407' => 'AC018717.2',
'ENSG00000238698' => 'RNU7-147P',
'ENSG00000257045' => 'RP11-486F17.1',
'ENSMUSG00000038331' => 'Satb2',
'ENSMUSG00000045336' => 'Hsfy2',
'ENSMUSG00000099950' => 'RP24-421N21.1',
'ENSMUSG00000100372' => 'RP23-258N15.1',
'ENSMUSG00000100944' => 'RP23-478I8.1',
'ENSMUSG00000101332' => 'RP24-146K19.1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '198337641',
'seq_end' => '198996572',
'region_length' => '658931',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0002',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '198996573',
'seq_end' => '199448043',
'region_length' => '451470',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0003',
'tax_id' => '10090',
'chromosome' => '1',
'seq_start' => '55914497',
'seq_end' => '56961323',
'region_length' => '1046826',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '33565048',
'seq_end' => '33565253',
'region_length' => '205',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 27 => 'Brain',
(int) 45 => 'Breast',
(int) 60 => 'Colon',
(int) 70 => 'Heart',
(int) 86 => 'Kidney',
(int) 98 => 'Liver',
(int) 109 => 'Lung',
(int) 116 => 'Muscle',
(int) 129 => 'Ovary',
(int) 139 => 'Placenta',
(int) 149 => '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) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000428675' => array(
'start' => '197804702',
'end' => '198148401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-006'
),
'ENST00000435320' => array(
'start' => '197804702',
'end' => '198149884',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PLCL1-001'
),
'ENST00000437704' => array(
'start' => '198083749',
'end' => '198149884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-201'
),
'ENST00000472193' => array(
'start' => '198346829',
'end' => '198572581',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-005'
),
'ENST00000487695' => array(
'start' => '197810258',
'end' => '198146932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-002'
),
'ENST00000625084' => array(
'start' => '198149375',
'end' => '198355486',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-007'
),
'ENST00000440609' => array(
'start' => '198553195',
'end' => '198772356',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC019330.1-001'
),
'ENST00000456031' => array(
'start' => '198882573',
'end' => '199071791',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC018717.1-001'
),
'ENST00000443261' => array(
'start' => '198374476',
'end' => '198375097',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-003'
),
'ENST00000451266' => array(
'start' => '198301408',
'end' => '198314714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-002'
),
'ENST00000456248' => array(
'start' => '198299363',
'end' => '198374549',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-001'
),
'ENST00000516702' => array(
'start' => '198566645',
'end' => '198566729',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC019330.2-201'
),
'ENST00000260926' => array(
'start' => '199269508',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-003'
),
'ENST00000417098' => array(
'start' => '199269500',
'end' => '199458096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-001'
),
'ENST00000428695' => array(
'start' => '199271975',
'end' => '199456088',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-007'
),
'ENST00000440919' => array(
'start' => '199395831',
'end' => '199457612',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SATB2-005'
),
'ENST00000443023' => array(
'start' => '199269508',
'end' => '199458745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-010'
),
'ENST00000457245' => array(
'start' => '199272150',
'end' => '199471266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-002'
),
'ENST00000463386' => array(
'start' => '199456053',
'end' => '199465167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-004'
),
'ENST00000473517' => array(
'start' => '199308860',
'end' => '199329035',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-009'
),
'ENST00000483346' => array(
'start' => '199346866',
'end' => '199368943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-006'
),
'ENST00000484124' => array(
'start' => '199368610',
'end' => '199423915',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-008'
),
'ENST00000614512' => array(
'start' => '199269500',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-201'
),
'ENST00000457712' => array(
'start' => '199108584',
'end' => '199110088',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018717.2-001'
),
'ENST00000459118' => array(
'start' => '199191059',
'end' => '199191120',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU7-147P-201'
),
'ENST00000489557' => array(
'start' => '199325310',
'end' => '199329362',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-486F17.1-001'
),
'ENSMUST00000042857' => array(
'start' => '56793981',
'end' => '56972502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-002'
),
'ENSMUST00000114415' => array(
'start' => '56793986',
'end' => '56971858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-001'
),
'ENSMUST00000176759' => array(
'start' => '56948134',
'end' => '56969840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-005'
),
'ENSMUST00000177282' => array(
'start' => '56969740',
'end' => '56978650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-004'
),
'ENSMUST00000177424' => array(
'start' => '56793988',
'end' => '56969872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-003'
),
'ENSMUST00000062085' => array(
'start' => '56636044',
'end' => '56637435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hsfy2-001'
),
'ENSMUST00000188040' => array(
'start' => '55960914',
'end' => '55972328',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-002'
),
'ENSMUST00000189293' => array(
'start' => '55931241',
'end' => '55972098',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-001'
),
'ENSMUST00000186048' => array(
'start' => '56018978',
'end' => '56020203',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-001'
),
'ENSMUST00000190280' => array(
'start' => '56019023',
'end' => '56020137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-002'
),
'ENSMUST00000185232' => array(
'start' => '56451407',
'end' => '56451562',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-478I8.1-001'
),
'ENSMUST00000187560' => array(
'start' => '56531824',
'end' => '56533876',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-146K19.1-001'
)
)
$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_0007O4_0001' => array(
'genes_in_region' => array(
'ENSG00000115896' => array(
[maximum depth reached]
),
'ENSG00000225421' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
),
'ENSG00000236653' => array(
[maximum depth reached]
),
'ENSG00000252511' => 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 => 'Liver',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Liver',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Bladder',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Breast',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Brain',
(int) 43 => 'Testis',
(int) 44 => 'Adipose',
(int) 45 => 'Adrenal',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Muscle',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Heart',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain'
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
'ENSG00000119042' => array(
[maximum depth reached]
),
'ENSG00000230407' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Placenta',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 9 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 12 => 'Heart',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Heart',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Breast',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Testis',
(int) 41 => 'Brain',
(int) 42 => 'Heart'
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000038331' => array(
[maximum depth reached]
),
'ENSMUSG00000045336' => array(
[maximum depth reached]
),
'ENSMUSG00000099950' => array(
[maximum depth reached]
),
'ENSMUSG00000100372' => array(
[maximum depth reached]
),
'ENSMUSG00000101332' => 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 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Bladder',
(int) 29 => 'Brain',
(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 => 'Kidney',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Bladder',
(int) 46 => 'Brain',
(int) 47 => 'Colon',
(int) 48 => 'Kidney',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Kidney',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Lung',
(int) 63 => 'Testis',
(int) 64 => 'Colon',
(int) 65 => 'Testis',
(int) 66 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '33565048',
'seq_end' => '33565253',
'region_length' => '205',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
)
$gene_el = array(
'ENSMUST00000187560' => array(
'Brain' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000101332'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000187560'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007O4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000115896' => 'phospholipase C-like 1',
'ENSG00000225421' => null,
'ENSG00000231557' => null,
'ENSG00000236653' => null,
'ENSG00000252511' => null,
'ENSG00000119042' => 'SATB homeobox 2',
'ENSG00000230407' => null,
'ENSG00000238698' => 'RNA, U7 small nuclear 147 pseudogene',
'ENSG00000257045' => null,
'ENSMUSG00000038331' => 'special AT-rich sequence binding protein 2',
'ENSMUSG00000045336' => 'heat shock transcription factor, Y linked 2',
'ENSMUSG00000099950' => 'RIKEN cDNA 9130227L01 gene',
'ENSMUSG00000100372' => 'RIKEN cDNA 1700003I22 gene',
'ENSMUSG00000100944' => 'predicted gene 28900',
'ENSMUSG00000101332' => 'predicted gene 28240'
),
'gene_name_arr' => array(
'ENSG00000115896' => 'PLCL1',
'ENSG00000225421' => 'AC019330.1',
'ENSG00000231557' => 'AC018717.1',
'ENSG00000236653' => 'AC005235.1',
'ENSG00000252511' => 'AC019330.2',
'ENSG00000119042' => 'SATB2',
'ENSG00000230407' => 'AC018717.2',
'ENSG00000238698' => 'RNU7-147P',
'ENSG00000257045' => 'RP11-486F17.1',
'ENSMUSG00000038331' => 'Satb2',
'ENSMUSG00000045336' => 'Hsfy2',
'ENSMUSG00000099950' => 'RP24-421N21.1',
'ENSMUSG00000100372' => 'RP23-258N15.1',
'ENSMUSG00000100944' => 'RP23-478I8.1',
'ENSMUSG00000101332' => 'RP24-146K19.1'
),
'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) 9 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 27 => 'Brain',
(int) 45 => 'Breast',
(int) 60 => 'Colon',
(int) 70 => 'Heart',
(int) 86 => 'Kidney',
(int) 98 => 'Liver',
(int) 109 => 'Lung',
(int) 116 => 'Muscle',
(int) 129 => 'Ovary',
(int) 139 => 'Placenta',
(int) 149 => '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) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000428675' => array(
'start' => '197804702',
'end' => '198148401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-006'
),
'ENST00000435320' => array(
'start' => '197804702',
'end' => '198149884',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PLCL1-001'
),
'ENST00000437704' => array(
'start' => '198083749',
'end' => '198149884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-201'
),
'ENST00000472193' => array(
'start' => '198346829',
'end' => '198572581',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-005'
),
'ENST00000487695' => array(
'start' => '197810258',
'end' => '198146932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-002'
),
'ENST00000625084' => array(
'start' => '198149375',
'end' => '198355486',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-007'
),
'ENST00000440609' => array(
'start' => '198553195',
'end' => '198772356',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC019330.1-001'
),
'ENST00000456031' => array(
'start' => '198882573',
'end' => '199071791',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC018717.1-001'
),
'ENST00000443261' => array(
'start' => '198374476',
'end' => '198375097',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-003'
),
'ENST00000451266' => array(
'start' => '198301408',
'end' => '198314714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-002'
),
'ENST00000456248' => array(
'start' => '198299363',
'end' => '198374549',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-001'
),
'ENST00000516702' => array(
'start' => '198566645',
'end' => '198566729',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC019330.2-201'
),
'ENST00000260926' => array(
'start' => '199269508',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-003'
),
'ENST00000417098' => array(
'start' => '199269500',
'end' => '199458096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-001'
),
'ENST00000428695' => array(
'start' => '199271975',
'end' => '199456088',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-007'
),
'ENST00000440919' => array(
'start' => '199395831',
'end' => '199457612',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SATB2-005'
),
'ENST00000443023' => array(
'start' => '199269508',
'end' => '199458745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-010'
),
'ENST00000457245' => array(
'start' => '199272150',
'end' => '199471266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-002'
),
'ENST00000463386' => array(
'start' => '199456053',
'end' => '199465167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-004'
),
'ENST00000473517' => array(
'start' => '199308860',
'end' => '199329035',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-009'
),
'ENST00000483346' => array(
'start' => '199346866',
'end' => '199368943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-006'
),
'ENST00000484124' => array(
'start' => '199368610',
'end' => '199423915',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-008'
),
'ENST00000614512' => array(
'start' => '199269500',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-201'
),
'ENST00000457712' => array(
'start' => '199108584',
'end' => '199110088',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018717.2-001'
),
'ENST00000459118' => array(
'start' => '199191059',
'end' => '199191120',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU7-147P-201'
),
'ENST00000489557' => array(
'start' => '199325310',
'end' => '199329362',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-486F17.1-001'
),
'ENSMUST00000042857' => array(
'start' => '56793981',
'end' => '56972502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-002'
),
'ENSMUST00000114415' => array(
'start' => '56793986',
'end' => '56971858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-001'
),
'ENSMUST00000176759' => array(
'start' => '56948134',
'end' => '56969840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-005'
),
'ENSMUST00000177282' => array(
'start' => '56969740',
'end' => '56978650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-004'
),
'ENSMUST00000177424' => array(
'start' => '56793988',
'end' => '56969872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-003'
),
'ENSMUST00000062085' => array(
'start' => '56636044',
'end' => '56637435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hsfy2-001'
),
'ENSMUST00000188040' => array(
'start' => '55960914',
'end' => '55972328',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-002'
),
'ENSMUST00000189293' => array(
'start' => '55931241',
'end' => '55972098',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-001'
),
'ENSMUST00000186048' => array(
'start' => '56018978',
'end' => '56020203',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-001'
),
'ENSMUST00000190280' => array(
'start' => '56019023',
'end' => '56020137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-002'
),
'ENSMUST00000185232' => array(
'start' => '56451407',
'end' => '56451562',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-478I8.1-001'
),
'ENSMUST00000187560' => array(
'start' => '56531824',
'end' => '56533876',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-146K19.1-001'
)
),
'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_0007O4_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007O4_0001' => array(
'genes_in_region' => array(
'ENSG00000115896' => array(
[maximum depth reached]
),
'ENSG00000225421' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
),
'ENSG00000236653' => array(
[maximum depth reached]
),
'ENSG00000252511' => 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 => 'Liver',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Liver',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Bladder',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Breast',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Brain',
(int) 43 => 'Testis',
(int) 44 => 'Adipose',
(int) 45 => 'Adrenal',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Muscle',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Heart',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain'
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
'ENSG00000119042' => array(
[maximum depth reached]
),
'ENSG00000230407' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Placenta',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 9 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 12 => 'Heart',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Heart',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Breast',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Testis',
(int) 41 => 'Brain',
(int) 42 => 'Heart'
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000038331' => array(
[maximum depth reached]
),
'ENSMUSG00000045336' => array(
[maximum depth reached]
),
'ENSMUSG00000099950' => array(
[maximum depth reached]
),
'ENSMUSG00000100372' => array(
[maximum depth reached]
),
'ENSMUSG00000101332' => 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 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Bladder',
(int) 29 => 'Brain',
(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 => 'Kidney',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Bladder',
(int) 46 => 'Brain',
(int) 47 => 'Colon',
(int) 48 => 'Kidney',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Kidney',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Lung',
(int) 63 => 'Testis',
(int) 64 => 'Colon',
(int) 65 => 'Testis',
(int) 66 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSG00000115896' => 'phospholipase C-like 1',
'ENSG00000225421' => null,
'ENSG00000231557' => null,
'ENSG00000236653' => null,
'ENSG00000252511' => null,
'ENSG00000119042' => 'SATB homeobox 2',
'ENSG00000230407' => null,
'ENSG00000238698' => 'RNA, U7 small nuclear 147 pseudogene',
'ENSG00000257045' => null,
'ENSMUSG00000038331' => 'special AT-rich sequence binding protein 2',
'ENSMUSG00000045336' => 'heat shock transcription factor, Y linked 2',
'ENSMUSG00000099950' => 'RIKEN cDNA 9130227L01 gene',
'ENSMUSG00000100372' => 'RIKEN cDNA 1700003I22 gene',
'ENSMUSG00000100944' => 'predicted gene 28900',
'ENSMUSG00000101332' => 'predicted gene 28240'
)
$gene_name_arr = array(
'ENSG00000115896' => 'PLCL1',
'ENSG00000225421' => 'AC019330.1',
'ENSG00000231557' => 'AC018717.1',
'ENSG00000236653' => 'AC005235.1',
'ENSG00000252511' => 'AC019330.2',
'ENSG00000119042' => 'SATB2',
'ENSG00000230407' => 'AC018717.2',
'ENSG00000238698' => 'RNU7-147P',
'ENSG00000257045' => 'RP11-486F17.1',
'ENSMUSG00000038331' => 'Satb2',
'ENSMUSG00000045336' => 'Hsfy2',
'ENSMUSG00000099950' => 'RP24-421N21.1',
'ENSMUSG00000100372' => 'RP23-258N15.1',
'ENSMUSG00000100944' => 'RP23-478I8.1',
'ENSMUSG00000101332' => 'RP24-146K19.1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0001',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '198337641',
'seq_end' => '198996572',
'region_length' => '658931',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0002',
'tax_id' => '9606',
'chromosome' => '2',
'seq_start' => '198996573',
'seq_end' => '199448043',
'region_length' => '451470',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0003',
'tax_id' => '10090',
'chromosome' => '1',
'seq_start' => '55914497',
'seq_end' => '56961323',
'region_length' => '1046826',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '33565048',
'seq_end' => '33565253',
'region_length' => '205',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 9 => 'Adrenal',
(int) 18 => 'Bladder',
(int) 27 => 'Brain',
(int) 45 => 'Breast',
(int) 60 => 'Colon',
(int) 70 => 'Heart',
(int) 86 => 'Kidney',
(int) 98 => 'Liver',
(int) 109 => 'Lung',
(int) 116 => 'Muscle',
(int) 129 => 'Ovary',
(int) 139 => 'Placenta',
(int) 149 => '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) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000428675' => array(
'start' => '197804702',
'end' => '198148401',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-006'
),
'ENST00000435320' => array(
'start' => '197804702',
'end' => '198149884',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'PLCL1-001'
),
'ENST00000437704' => array(
'start' => '198083749',
'end' => '198149884',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-201'
),
'ENST00000472193' => array(
'start' => '198346829',
'end' => '198572581',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-005'
),
'ENST00000487695' => array(
'start' => '197810258',
'end' => '198146932',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'PLCL1-002'
),
'ENST00000625084' => array(
'start' => '198149375',
'end' => '198355486',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'PLCL1-007'
),
'ENST00000440609' => array(
'start' => '198553195',
'end' => '198772356',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC019330.1-001'
),
'ENST00000456031' => array(
'start' => '198882573',
'end' => '199071791',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC018717.1-001'
),
'ENST00000443261' => array(
'start' => '198374476',
'end' => '198375097',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-003'
),
'ENST00000451266' => array(
'start' => '198301408',
'end' => '198314714',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-002'
),
'ENST00000456248' => array(
'start' => '198299363',
'end' => '198374549',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'AC005235.1-001'
),
'ENST00000516702' => array(
'start' => '198566645',
'end' => '198566729',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC019330.2-201'
),
'ENST00000260926' => array(
'start' => '199269508',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-003'
),
'ENST00000417098' => array(
'start' => '199269500',
'end' => '199458096',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-001'
),
'ENST00000428695' => array(
'start' => '199271975',
'end' => '199456088',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-007'
),
'ENST00000440919' => array(
'start' => '199395831',
'end' => '199457612',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SATB2-005'
),
'ENST00000443023' => array(
'start' => '199269508',
'end' => '199458745',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-010'
),
'ENST00000457245' => array(
'start' => '199272150',
'end' => '199471266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-002'
),
'ENST00000463386' => array(
'start' => '199456053',
'end' => '199465167',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-004'
),
'ENST00000473517' => array(
'start' => '199308860',
'end' => '199329035',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-009'
),
'ENST00000483346' => array(
'start' => '199346866',
'end' => '199368943',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SATB2-006'
),
'ENST00000484124' => array(
'start' => '199368610',
'end' => '199423915',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SATB2-008'
),
'ENST00000614512' => array(
'start' => '199269500',
'end' => '199465108',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SATB2-201'
),
'ENST00000457712' => array(
'start' => '199108584',
'end' => '199110088',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'AC018717.2-001'
),
'ENST00000459118' => array(
'start' => '199191059',
'end' => '199191120',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU7-147P-201'
),
'ENST00000489557' => array(
'start' => '199325310',
'end' => '199329362',
'transcript_biotype' => 'antisense',
'transcript_name' => 'RP11-486F17.1-001'
),
'ENSMUST00000042857' => array(
'start' => '56793981',
'end' => '56972502',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-002'
),
'ENSMUST00000114415' => array(
'start' => '56793986',
'end' => '56971858',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-001'
),
'ENSMUST00000176759' => array(
'start' => '56948134',
'end' => '56969840',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-005'
),
'ENSMUST00000177282' => array(
'start' => '56969740',
'end' => '56978650',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-004'
),
'ENSMUST00000177424' => array(
'start' => '56793988',
'end' => '56969872',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Satb2-003'
),
'ENSMUST00000062085' => array(
'start' => '56636044',
'end' => '56637435',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Hsfy2-001'
),
'ENSMUST00000188040' => array(
'start' => '55960914',
'end' => '55972328',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-002'
),
'ENSMUST00000189293' => array(
'start' => '55931241',
'end' => '55972098',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-421N21.1-001'
),
'ENSMUST00000186048' => array(
'start' => '56018978',
'end' => '56020203',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-001'
),
'ENSMUST00000190280' => array(
'start' => '56019023',
'end' => '56020137',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP23-258N15.1-002'
),
'ENSMUST00000185232' => array(
'start' => '56451407',
'end' => '56451562',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP23-478I8.1-001'
),
'ENSMUST00000187560' => array(
'start' => '56531824',
'end' => '56533876',
'transcript_biotype' => 'lincRNA',
'transcript_name' => 'RP24-146K19.1-001'
)
)
$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_0007O4_0001' => array(
'genes_in_region' => array(
'ENSG00000115896' => array(
[maximum depth reached]
),
'ENSG00000225421' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
),
'ENSG00000236653' => array(
[maximum depth reached]
),
'ENSG00000252511' => 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 => 'Liver',
(int) 15 => 'Adipose',
(int) 16 => 'Adrenal',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Colon',
(int) 21 => 'Heart',
(int) 22 => 'Kidney',
(int) 23 => 'Liver',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis',
(int) 28 => 'Bladder',
(int) 29 => 'Breast',
(int) 30 => 'Colon',
(int) 31 => 'Heart',
(int) 32 => 'Kidney',
(int) 33 => 'Liver',
(int) 34 => 'Lung',
(int) 35 => 'Muscle',
(int) 36 => 'Ovary',
(int) 37 => 'Testis',
(int) 38 => 'Breast',
(int) 39 => 'Testis',
(int) 40 => 'Brain',
(int) 41 => 'Heart',
(int) 42 => 'Brain',
(int) 43 => 'Testis',
(int) 44 => 'Adipose',
(int) 45 => 'Adrenal',
(int) 46 => 'Brain',
(int) 47 => 'Breast',
(int) 48 => 'Heart',
(int) 49 => 'Kidney',
(int) 50 => 'Muscle',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Heart',
(int) 55 => 'Adrenal',
(int) 56 => 'Brain'
)
),
'CIL_0007O4_0002' => array(
'genes_in_region' => array(
'ENSG00000119042' => array(
[maximum depth reached]
),
'ENSG00000230407' => array(
[maximum depth reached]
),
'ENSG00000231557' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Colon',
(int) 2 => 'Heart',
(int) 3 => 'Liver',
(int) 4 => 'Muscle',
(int) 5 => 'Placenta',
(int) 6 => 'Adipose',
(int) 7 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 9 => 'Brain',
(int) 10 => 'Breast',
(int) 11 => 'Colon',
(int) 12 => 'Heart',
(int) 13 => 'Muscle',
(int) 14 => 'Ovary',
(int) 15 => 'Placenta',
(int) 16 => 'Testis',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Heart',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Adipose',
(int) 23 => 'Adrenal',
(int) 24 => 'Breast',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Testis',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Breast',
(int) 38 => 'Ovary',
(int) 39 => 'Testis',
(int) 40 => 'Testis',
(int) 41 => 'Brain',
(int) 42 => 'Heart'
)
),
'CIL_0007O4_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000038331' => array(
[maximum depth reached]
),
'ENSMUSG00000045336' => array(
[maximum depth reached]
),
'ENSMUSG00000099950' => array(
[maximum depth reached]
),
'ENSMUSG00000100372' => array(
[maximum depth reached]
),
'ENSMUSG00000101332' => 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 => 'Bladder',
(int) 16 => 'Brain',
(int) 17 => 'Breast',
(int) 18 => 'Heart',
(int) 19 => 'Kidney',
(int) 20 => 'Liver',
(int) 21 => 'Lung',
(int) 22 => 'Muscle',
(int) 23 => 'Ovary',
(int) 24 => 'Placenta',
(int) 25 => 'Testis',
(int) 26 => 'Adipose',
(int) 27 => 'Adrenal',
(int) 28 => 'Bladder',
(int) 29 => 'Brain',
(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 => 'Kidney',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Bladder',
(int) 46 => 'Brain',
(int) 47 => 'Colon',
(int) 48 => 'Kidney',
(int) 49 => 'Muscle',
(int) 50 => 'Ovary',
(int) 51 => 'Placenta',
(int) 52 => 'Testis',
(int) 53 => 'Bladder',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Colon',
(int) 57 => 'Kidney',
(int) 58 => 'Liver',
(int) 59 => 'Muscle',
(int) 60 => 'Placenta',
(int) 61 => 'Testis',
(int) 62 => 'Lung',
(int) 63 => 'Testis',
(int) 64 => 'Colon',
(int) 65 => 'Testis',
(int) 66 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007O4_0004',
'tax_id' => '7955',
'chromosome' => '9',
'seq_start' => '33565048',
'seq_end' => '33565253',
'region_length' => '205',
'region_type' => 'UCNEbase',
'el_id' => 'SATB2'
)
)
$gene_el = array(
'ENSMUST00000187560' => array(
'Brain' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSMUSG00000101332'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.004',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSMUST00000187560'
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 |
| SATB2 |
UCNEbase |
7955 |
9:33565048-33565253  |
| Gene | Transcript | Position | Biotype |
|---|
(PLCL1)