| Source ID |
Type |
Tax ID |
Position |
| hs854 |
VISTA |
10090 |
6:98668191-99269077  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007PZ_0002 [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($region_arr[$accession["region_elements"]["region_element_id"]]['genes_in_region'] as $gene_key => $gene_el): ?>
$viewFile = '/var/www/c-it-loci/app/View/Region/show.ctp'
$dataForView = array(
'region_arr' => array(
'CIL_0007PZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000114861' => 'forkhead box P1',
'ENSG00000206939' => 'RNA, U6 small nuclear 281, pseudogene',
'ENSG00000221382' => null,
'ENSG00000240156' => 'cytochrome c oxidase subunit VIc pseudogene 6',
'ENSG00000243873' => 'high mobility group box 1 pseudogene 36',
'ENSG00000244203' => 'FOXP1 antisense RNA 1',
'ENSG00000277539' => null,
'ENSMUSG00000030067' => 'forkhead box P1',
'ENSMUSG00000030068' => 'predicted gene 20696'
),
'gene_name_arr' => array(
'ENSG00000114861' => 'FOXP1',
'ENSG00000206939' => 'RNU6-281P',
'ENSG00000221382' => 'AC096971.1',
'ENSG00000240156' => 'COX6CP6',
'ENSG00000243873' => 'HMGB1P36',
'ENSG00000244203' => 'FOXP1-AS1',
'ENSG00000277539' => 'RP11-298C2.1',
'ENSMUSG00000030067' => 'Foxp1',
'ENSMUSG00000030068' => 'Gm20696'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 30 => 'Breast',
(int) 42 => 'Colon',
(int) 52 => 'Heart',
(int) 61 => 'Kidney',
(int) 69 => 'Liver',
(int) 78 => 'Lung',
(int) 88 => 'Muscle',
(int) 96 => 'Ovary',
(int) 112 => 'Placenta',
(int) 120 => '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) 63,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000318779' => array(
'start' => '71197882',
'end' => '71583939',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-014'
),
'ENST00000318789' => array(
'start' => '70954693',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-001'
),
'ENST00000327590' => array(
'start' => '70959191',
'end' => '71493555',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FOXP1-003'
),
'ENST00000460805' => array(
'start' => '70959191',
'end' => '70966352',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FOXP1-022'
),
'ENST00000468577' => array(
'start' => '70959247',
'end' => '71198381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-012'
),
'ENST00000470112' => array(
'start' => '71296085',
'end' => '71306015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-018'
),
'ENST00000471386' => array(
'start' => '71493426',
'end' => '71583739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-016'
),
'ENST00000472382' => array(
'start' => '71040278',
'end' => '71053773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-020'
),
'ENST00000475937' => array(
'start' => '70956745',
'end' => '71543557',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-004'
),
'ENST00000484350' => array(
'start' => '70959211',
'end' => '71304760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-005'
),
'ENST00000485326' => array(
'start' => '71015549',
'end' => '71064926',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-021'
),
'ENST00000491238' => array(
'start' => '70959191',
'end' => '71130837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-011'
),
'ENST00000493010' => array(
'start' => '71299835',
'end' => '71360760',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-017'
),
'ENST00000493089' => array(
'start' => '70959204',
'end' => '71583753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-002'
),
'ENST00000497355' => array(
'start' => '70959191',
'end' => '71130593',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-009'
),
'ENST00000497553' => array(
'start' => '71046937',
'end' => '71065767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-019'
),
'ENST00000498154' => array(
'start' => '71493426',
'end' => '71581953',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-015'
),
'ENST00000498215' => array(
'start' => '70959204',
'end' => '71245165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-006'
),
'ENST00000610810' => array(
'start' => '71053703',
'end' => '71306029',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-023'
),
'ENST00000614176' => array(
'start' => '70954715',
'end' => '71064923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-201'
),
'ENST00000614183' => array(
'start' => '70968848',
'end' => '70978029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-025'
),
'ENST00000615603' => array(
'start' => '70954715',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-202'
),
'ENST00000622151' => array(
'start' => '71197882',
'end' => '71210869',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-024'
),
'ENST00000384212' => array(
'start' => '70808350',
'end' => '70808452',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-281P-201'
),
'ENST00000408455' => array(
'start' => '70878660',
'end' => '70878792',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC096971.1-201'
),
'ENST00000490840' => array(
'start' => '70751123',
'end' => '70751350',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'COX6CP6-001'
),
'ENST00000487709' => array(
'start' => '70753854',
'end' => '70754573',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P36-001'
),
'ENST00000465742' => array(
'start' => '71289769',
'end' => '71305853',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXP1-AS1-001'
),
'ENST00000620572' => array(
'start' => '71276087',
'end' => '71289616',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-298C2.1-001'
),
'ENSMUST00000074346' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-001'
),
'ENSMUST00000075832' => array(
'start' => '99152058',
'end' => '99266515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-005'
),
'ENSMUST00000113321' => array(
'start' => '99006685',
'end' => '99028266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-009'
),
'ENSMUST00000113322' => array(
'start' => '98925342',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-201'
),
'ENSMUST00000113324' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-007'
),
'ENSMUST00000113326' => array(
'start' => '98925338',
'end' => '99266515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-004'
),
'ENSMUST00000113328' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-006'
),
'ENSMUST00000113329' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-008'
),
'ENSMUST00000123992' => array(
'start' => '99003393',
'end' => '99044459',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-013'
),
'ENSMUST00000124058' => array(
'start' => '98945534',
'end' => '99028313',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-011'
),
'ENSMUST00000131967' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-003'
),
'ENSMUST00000138754' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-002'
),
'ENSMUST00000142164' => array(
'start' => '98952201',
'end' => '99003680',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-010'
),
'ENSMUST00000154163' => array(
'start' => '99003200',
'end' => '99028942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-012'
),
'ENSMUST00000175670' => array(
'start' => '99016550',
'end' => '99027991',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-029'
),
'ENSMUST00000175838' => array(
'start' => '99435236',
'end' => '99522721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-032'
),
'ENSMUST00000175880' => array(
'start' => '98930171',
'end' => '98935545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-028'
),
'ENSMUST00000175886' => array(
'start' => '99009933',
'end' => '99096205',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-019'
),
'ENSMUST00000176105' => array(
'start' => '99308377',
'end' => '99436396',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-018'
),
'ENSMUST00000176148' => array(
'start' => '99434751',
'end' => '99445607',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-031'
),
'ENSMUST00000176565' => array(
'start' => '98929189',
'end' => '99520997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-014'
),
'ENSMUST00000176632' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-026'
),
'ENSMUST00000176850' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-027'
),
'ENSMUST00000177208' => array(
'start' => '99075962',
'end' => '99248336',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-030'
),
'ENSMUST00000177227' => array(
'start' => '99162929',
'end' => '99521162',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-033'
),
'ENSMUST00000177229' => array(
'start' => '98930090',
'end' => '99028259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-023'
),
'ENSMUST00000177230' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Foxp1-024'
),
'ENSMUST00000177235' => array(
'start' => '99260357',
'end' => '99522647',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-017'
),
'ENSMUST00000177307' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-020'
),
'ENSMUST00000177410' => array(
'start' => '98925415',
'end' => '98929785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-025'
),
'ENSMUST00000177437' => array(
'start' => '98929466',
'end' => '99028258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-021'
),
'ENSMUST00000177507' => array(
'start' => '99009944',
'end' => '99044442',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-022'
),
'ENSMUST00000155466' => array(
'start' => '99257484',
'end' => '99666797',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Gm20696-001'
),
'ENSMUST00000176255' => array(
'start' => '99434782',
'end' => '99632376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20696-002'
)
),
'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_0007PZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007PZ_0001' => array(
'genes_in_region' => array(
'ENSG00000221382' => array(
[maximum depth reached]
),
'ENSG00000240156' => array(
[maximum depth reached]
),
'ENSG00000243873' => array(
[maximum depth reached]
),
'ENSG00000244203' => array(
[maximum depth reached]
),
'ENSG00000277539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Colon',
(int) 2 => 'Muscle',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Bladder',
(int) 16 => 'Ovary',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Kidney',
(int) 55 => 'Brain',
(int) 56 => 'Heart',
(int) 57 => 'Lung',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Brain',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Testis',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Breast',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000114861' => 'forkhead box P1',
'ENSG00000206939' => 'RNA, U6 small nuclear 281, pseudogene',
'ENSG00000221382' => null,
'ENSG00000240156' => 'cytochrome c oxidase subunit VIc pseudogene 6',
'ENSG00000243873' => 'high mobility group box 1 pseudogene 36',
'ENSG00000244203' => 'FOXP1 antisense RNA 1',
'ENSG00000277539' => null,
'ENSMUSG00000030067' => 'forkhead box P1',
'ENSMUSG00000030068' => 'predicted gene 20696'
)
$gene_name_arr = array(
'ENSG00000114861' => 'FOXP1',
'ENSG00000206939' => 'RNU6-281P',
'ENSG00000221382' => 'AC096971.1',
'ENSG00000240156' => 'COX6CP6',
'ENSG00000243873' => 'HMGB1P36',
'ENSG00000244203' => 'FOXP1-AS1',
'ENSG00000277539' => 'RP11-298C2.1',
'ENSMUSG00000030067' => 'Foxp1',
'ENSMUSG00000030068' => 'Gm20696'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PZ_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '70703225',
'seq_end' => '71304095',
'region_length' => '600870',
'region_type' => 'VISTA',
'el_id' => 'hs854'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PZ_0002',
'tax_id' => '10090',
'chromosome' => '6',
'seq_start' => '98668191',
'seq_end' => '99269077',
'region_length' => '600886',
'region_type' => 'VISTA',
'el_id' => 'hs854'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 30 => 'Breast',
(int) 42 => 'Colon',
(int) 52 => 'Heart',
(int) 61 => 'Kidney',
(int) 69 => 'Liver',
(int) 78 => 'Lung',
(int) 88 => 'Muscle',
(int) 96 => 'Ovary',
(int) 112 => 'Placenta',
(int) 120 => '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) 63
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000318779' => array(
'start' => '71197882',
'end' => '71583939',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-014'
),
'ENST00000318789' => array(
'start' => '70954693',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-001'
),
'ENST00000327590' => array(
'start' => '70959191',
'end' => '71493555',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FOXP1-003'
),
'ENST00000460805' => array(
'start' => '70959191',
'end' => '70966352',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FOXP1-022'
),
'ENST00000468577' => array(
'start' => '70959247',
'end' => '71198381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-012'
),
'ENST00000470112' => array(
'start' => '71296085',
'end' => '71306015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-018'
),
'ENST00000471386' => array(
'start' => '71493426',
'end' => '71583739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-016'
),
'ENST00000472382' => array(
'start' => '71040278',
'end' => '71053773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-020'
),
'ENST00000475937' => array(
'start' => '70956745',
'end' => '71543557',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-004'
),
'ENST00000484350' => array(
'start' => '70959211',
'end' => '71304760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-005'
),
'ENST00000485326' => array(
'start' => '71015549',
'end' => '71064926',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-021'
),
'ENST00000491238' => array(
'start' => '70959191',
'end' => '71130837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-011'
),
'ENST00000493010' => array(
'start' => '71299835',
'end' => '71360760',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-017'
),
'ENST00000493089' => array(
'start' => '70959204',
'end' => '71583753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-002'
),
'ENST00000497355' => array(
'start' => '70959191',
'end' => '71130593',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-009'
),
'ENST00000497553' => array(
'start' => '71046937',
'end' => '71065767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-019'
),
'ENST00000498154' => array(
'start' => '71493426',
'end' => '71581953',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-015'
),
'ENST00000498215' => array(
'start' => '70959204',
'end' => '71245165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-006'
),
'ENST00000610810' => array(
'start' => '71053703',
'end' => '71306029',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-023'
),
'ENST00000614176' => array(
'start' => '70954715',
'end' => '71064923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-201'
),
'ENST00000614183' => array(
'start' => '70968848',
'end' => '70978029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-025'
),
'ENST00000615603' => array(
'start' => '70954715',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-202'
),
'ENST00000622151' => array(
'start' => '71197882',
'end' => '71210869',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-024'
),
'ENST00000384212' => array(
'start' => '70808350',
'end' => '70808452',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-281P-201'
),
'ENST00000408455' => array(
'start' => '70878660',
'end' => '70878792',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC096971.1-201'
),
'ENST00000490840' => array(
'start' => '70751123',
'end' => '70751350',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'COX6CP6-001'
),
'ENST00000487709' => array(
'start' => '70753854',
'end' => '70754573',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P36-001'
),
'ENST00000465742' => array(
'start' => '71289769',
'end' => '71305853',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXP1-AS1-001'
),
'ENST00000620572' => array(
'start' => '71276087',
'end' => '71289616',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-298C2.1-001'
),
'ENSMUST00000074346' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-001'
),
'ENSMUST00000075832' => array(
'start' => '99152058',
'end' => '99266515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-005'
),
'ENSMUST00000113321' => array(
'start' => '99006685',
'end' => '99028266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-009'
),
'ENSMUST00000113322' => array(
'start' => '98925342',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-201'
),
'ENSMUST00000113324' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-007'
),
'ENSMUST00000113326' => array(
'start' => '98925338',
'end' => '99266515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-004'
),
'ENSMUST00000113328' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-006'
),
'ENSMUST00000113329' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-008'
),
'ENSMUST00000123992' => array(
'start' => '99003393',
'end' => '99044459',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-013'
),
'ENSMUST00000124058' => array(
'start' => '98945534',
'end' => '99028313',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-011'
),
'ENSMUST00000131967' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-003'
),
'ENSMUST00000138754' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-002'
),
'ENSMUST00000142164' => array(
'start' => '98952201',
'end' => '99003680',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-010'
),
'ENSMUST00000154163' => array(
'start' => '99003200',
'end' => '99028942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-012'
),
'ENSMUST00000175670' => array(
'start' => '99016550',
'end' => '99027991',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-029'
),
'ENSMUST00000175838' => array(
'start' => '99435236',
'end' => '99522721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-032'
),
'ENSMUST00000175880' => array(
'start' => '98930171',
'end' => '98935545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-028'
),
'ENSMUST00000175886' => array(
'start' => '99009933',
'end' => '99096205',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-019'
),
'ENSMUST00000176105' => array(
'start' => '99308377',
'end' => '99436396',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-018'
),
'ENSMUST00000176148' => array(
'start' => '99434751',
'end' => '99445607',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-031'
),
'ENSMUST00000176565' => array(
'start' => '98929189',
'end' => '99520997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-014'
),
'ENSMUST00000176632' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-026'
),
'ENSMUST00000176850' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-027'
),
'ENSMUST00000177208' => array(
'start' => '99075962',
'end' => '99248336',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-030'
),
'ENSMUST00000177227' => array(
'start' => '99162929',
'end' => '99521162',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-033'
),
'ENSMUST00000177229' => array(
'start' => '98930090',
'end' => '99028259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-023'
),
'ENSMUST00000177230' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Foxp1-024'
),
'ENSMUST00000177235' => array(
'start' => '99260357',
'end' => '99522647',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-017'
),
'ENSMUST00000177307' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-020'
),
'ENSMUST00000177410' => array(
'start' => '98925415',
'end' => '98929785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-025'
),
'ENSMUST00000177437' => array(
'start' => '98929466',
'end' => '99028258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-021'
),
'ENSMUST00000177507' => array(
'start' => '99009944',
'end' => '99044442',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-022'
),
'ENSMUST00000155466' => array(
'start' => '99257484',
'end' => '99666797',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Gm20696-001'
),
'ENSMUST00000176255' => array(
'start' => '99434782',
'end' => '99632376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20696-002'
)
)
$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_0007PZ_0001' => array(
'genes_in_region' => array(
'ENSG00000221382' => array(
[maximum depth reached]
),
'ENSG00000240156' => array(
[maximum depth reached]
),
'ENSG00000243873' => array(
[maximum depth reached]
),
'ENSG00000244203' => array(
[maximum depth reached]
),
'ENSG00000277539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Colon',
(int) 2 => 'Muscle',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Bladder',
(int) 16 => 'Ovary',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Kidney',
(int) 55 => 'Brain',
(int) 56 => 'Heart',
(int) 57 => 'Lung',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Brain',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Testis',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Breast',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PZ_0002',
'tax_id' => '10090',
'chromosome' => '6',
'seq_start' => '98668191',
'seq_end' => '99269077',
'region_length' => '600886',
'region_type' => 'VISTA',
'el_id' => 'hs854'
)
)
$gene_el = array(
'ENST00000620572' => array(
'Adrenal' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.724',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.106',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.405',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.239',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.515',
'stddev_FPKM' => '0.33'
)
)
)
$gene_key = 'ENSG00000277539'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.724',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.106',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.405',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.239',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.515',
'stddev_FPKM' => '0.33'
)
)
$tran_key = 'ENST00000620572'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007PZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000114861' => 'forkhead box P1',
'ENSG00000206939' => 'RNA, U6 small nuclear 281, pseudogene',
'ENSG00000221382' => null,
'ENSG00000240156' => 'cytochrome c oxidase subunit VIc pseudogene 6',
'ENSG00000243873' => 'high mobility group box 1 pseudogene 36',
'ENSG00000244203' => 'FOXP1 antisense RNA 1',
'ENSG00000277539' => null,
'ENSMUSG00000030067' => 'forkhead box P1',
'ENSMUSG00000030068' => 'predicted gene 20696'
),
'gene_name_arr' => array(
'ENSG00000114861' => 'FOXP1',
'ENSG00000206939' => 'RNU6-281P',
'ENSG00000221382' => 'AC096971.1',
'ENSG00000240156' => 'COX6CP6',
'ENSG00000243873' => 'HMGB1P36',
'ENSG00000244203' => 'FOXP1-AS1',
'ENSG00000277539' => 'RP11-298C2.1',
'ENSMUSG00000030067' => 'Foxp1',
'ENSMUSG00000030068' => 'Gm20696'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 30 => 'Breast',
(int) 42 => 'Colon',
(int) 52 => 'Heart',
(int) 61 => 'Kidney',
(int) 69 => 'Liver',
(int) 78 => 'Lung',
(int) 88 => 'Muscle',
(int) 96 => 'Ovary',
(int) 112 => 'Placenta',
(int) 120 => '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) 63,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000318779' => array(
'start' => '71197882',
'end' => '71583939',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-014'
),
'ENST00000318789' => array(
'start' => '70954693',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-001'
),
'ENST00000327590' => array(
'start' => '70959191',
'end' => '71493555',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FOXP1-003'
),
'ENST00000460805' => array(
'start' => '70959191',
'end' => '70966352',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FOXP1-022'
),
'ENST00000468577' => array(
'start' => '70959247',
'end' => '71198381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-012'
),
'ENST00000470112' => array(
'start' => '71296085',
'end' => '71306015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-018'
),
'ENST00000471386' => array(
'start' => '71493426',
'end' => '71583739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-016'
),
'ENST00000472382' => array(
'start' => '71040278',
'end' => '71053773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-020'
),
'ENST00000475937' => array(
'start' => '70956745',
'end' => '71543557',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-004'
),
'ENST00000484350' => array(
'start' => '70959211',
'end' => '71304760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-005'
),
'ENST00000485326' => array(
'start' => '71015549',
'end' => '71064926',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-021'
),
'ENST00000491238' => array(
'start' => '70959191',
'end' => '71130837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-011'
),
'ENST00000493010' => array(
'start' => '71299835',
'end' => '71360760',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-017'
),
'ENST00000493089' => array(
'start' => '70959204',
'end' => '71583753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-002'
),
'ENST00000497355' => array(
'start' => '70959191',
'end' => '71130593',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-009'
),
'ENST00000497553' => array(
'start' => '71046937',
'end' => '71065767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-019'
),
'ENST00000498154' => array(
'start' => '71493426',
'end' => '71581953',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-015'
),
'ENST00000498215' => array(
'start' => '70959204',
'end' => '71245165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-006'
),
'ENST00000610810' => array(
'start' => '71053703',
'end' => '71306029',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-023'
),
'ENST00000614176' => array(
'start' => '70954715',
'end' => '71064923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-201'
),
'ENST00000614183' => array(
'start' => '70968848',
'end' => '70978029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-025'
),
'ENST00000615603' => array(
'start' => '70954715',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-202'
),
'ENST00000622151' => array(
'start' => '71197882',
'end' => '71210869',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-024'
),
'ENST00000384212' => array(
'start' => '70808350',
'end' => '70808452',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-281P-201'
),
'ENST00000408455' => array(
'start' => '70878660',
'end' => '70878792',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC096971.1-201'
),
'ENST00000490840' => array(
'start' => '70751123',
'end' => '70751350',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'COX6CP6-001'
),
'ENST00000487709' => array(
'start' => '70753854',
'end' => '70754573',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P36-001'
),
'ENST00000465742' => array(
'start' => '71289769',
'end' => '71305853',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXP1-AS1-001'
),
'ENST00000620572' => array(
'start' => '71276087',
'end' => '71289616',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-298C2.1-001'
),
'ENSMUST00000074346' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-001'
),
'ENSMUST00000075832' => array(
'start' => '99152058',
'end' => '99266515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-005'
),
'ENSMUST00000113321' => array(
'start' => '99006685',
'end' => '99028266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-009'
),
'ENSMUST00000113322' => array(
'start' => '98925342',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-201'
),
'ENSMUST00000113324' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-007'
),
'ENSMUST00000113326' => array(
'start' => '98925338',
'end' => '99266515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-004'
),
'ENSMUST00000113328' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-006'
),
'ENSMUST00000113329' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-008'
),
'ENSMUST00000123992' => array(
'start' => '99003393',
'end' => '99044459',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-013'
),
'ENSMUST00000124058' => array(
'start' => '98945534',
'end' => '99028313',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-011'
),
'ENSMUST00000131967' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-003'
),
'ENSMUST00000138754' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-002'
),
'ENSMUST00000142164' => array(
'start' => '98952201',
'end' => '99003680',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-010'
),
'ENSMUST00000154163' => array(
'start' => '99003200',
'end' => '99028942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-012'
),
'ENSMUST00000175670' => array(
'start' => '99016550',
'end' => '99027991',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-029'
),
'ENSMUST00000175838' => array(
'start' => '99435236',
'end' => '99522721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-032'
),
'ENSMUST00000175880' => array(
'start' => '98930171',
'end' => '98935545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-028'
),
'ENSMUST00000175886' => array(
'start' => '99009933',
'end' => '99096205',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-019'
),
'ENSMUST00000176105' => array(
'start' => '99308377',
'end' => '99436396',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-018'
),
'ENSMUST00000176148' => array(
'start' => '99434751',
'end' => '99445607',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-031'
),
'ENSMUST00000176565' => array(
'start' => '98929189',
'end' => '99520997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-014'
),
'ENSMUST00000176632' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-026'
),
'ENSMUST00000176850' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-027'
),
'ENSMUST00000177208' => array(
'start' => '99075962',
'end' => '99248336',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-030'
),
'ENSMUST00000177227' => array(
'start' => '99162929',
'end' => '99521162',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-033'
),
'ENSMUST00000177229' => array(
'start' => '98930090',
'end' => '99028259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-023'
),
'ENSMUST00000177230' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Foxp1-024'
),
'ENSMUST00000177235' => array(
'start' => '99260357',
'end' => '99522647',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-017'
),
'ENSMUST00000177307' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-020'
),
'ENSMUST00000177410' => array(
'start' => '98925415',
'end' => '98929785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-025'
),
'ENSMUST00000177437' => array(
'start' => '98929466',
'end' => '99028258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-021'
),
'ENSMUST00000177507' => array(
'start' => '99009944',
'end' => '99044442',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-022'
),
'ENSMUST00000155466' => array(
'start' => '99257484',
'end' => '99666797',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Gm20696-001'
),
'ENSMUST00000176255' => array(
'start' => '99434782',
'end' => '99632376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20696-002'
)
),
'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_0007PZ_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007PZ_0001' => array(
'genes_in_region' => array(
'ENSG00000221382' => array(
[maximum depth reached]
),
'ENSG00000240156' => array(
[maximum depth reached]
),
'ENSG00000243873' => array(
[maximum depth reached]
),
'ENSG00000244203' => array(
[maximum depth reached]
),
'ENSG00000277539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Colon',
(int) 2 => 'Muscle',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Bladder',
(int) 16 => 'Ovary',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Kidney',
(int) 55 => 'Brain',
(int) 56 => 'Heart',
(int) 57 => 'Lung',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Brain',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Testis',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Breast',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000114861' => 'forkhead box P1',
'ENSG00000206939' => 'RNA, U6 small nuclear 281, pseudogene',
'ENSG00000221382' => null,
'ENSG00000240156' => 'cytochrome c oxidase subunit VIc pseudogene 6',
'ENSG00000243873' => 'high mobility group box 1 pseudogene 36',
'ENSG00000244203' => 'FOXP1 antisense RNA 1',
'ENSG00000277539' => null,
'ENSMUSG00000030067' => 'forkhead box P1',
'ENSMUSG00000030068' => 'predicted gene 20696'
)
$gene_name_arr = array(
'ENSG00000114861' => 'FOXP1',
'ENSG00000206939' => 'RNU6-281P',
'ENSG00000221382' => 'AC096971.1',
'ENSG00000240156' => 'COX6CP6',
'ENSG00000243873' => 'HMGB1P36',
'ENSG00000244203' => 'FOXP1-AS1',
'ENSG00000277539' => 'RP11-298C2.1',
'ENSMUSG00000030067' => 'Foxp1',
'ENSMUSG00000030068' => 'Gm20696'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PZ_0001',
'tax_id' => '9606',
'chromosome' => '3',
'seq_start' => '70703225',
'seq_end' => '71304095',
'region_length' => '600870',
'region_type' => 'VISTA',
'el_id' => 'hs854'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PZ_0002',
'tax_id' => '10090',
'chromosome' => '6',
'seq_start' => '98668191',
'seq_end' => '99269077',
'region_length' => '600886',
'region_type' => 'VISTA',
'el_id' => 'hs854'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 6 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 23 => 'Brain',
(int) 30 => 'Breast',
(int) 42 => 'Colon',
(int) 52 => 'Heart',
(int) 61 => 'Kidney',
(int) 69 => 'Liver',
(int) 78 => 'Lung',
(int) 88 => 'Muscle',
(int) 96 => 'Ovary',
(int) 112 => 'Placenta',
(int) 120 => '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) 63
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000318779' => array(
'start' => '71197882',
'end' => '71583939',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-014'
),
'ENST00000318789' => array(
'start' => '70954693',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-001'
),
'ENST00000327590' => array(
'start' => '70959191',
'end' => '71493555',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'FOXP1-003'
),
'ENST00000460805' => array(
'start' => '70959191',
'end' => '70966352',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'FOXP1-022'
),
'ENST00000468577' => array(
'start' => '70959247',
'end' => '71198381',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-012'
),
'ENST00000470112' => array(
'start' => '71296085',
'end' => '71306015',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-018'
),
'ENST00000471386' => array(
'start' => '71493426',
'end' => '71583739',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-016'
),
'ENST00000472382' => array(
'start' => '71040278',
'end' => '71053773',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-020'
),
'ENST00000475937' => array(
'start' => '70956745',
'end' => '71543557',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-004'
),
'ENST00000484350' => array(
'start' => '70959211',
'end' => '71304760',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-005'
),
'ENST00000485326' => array(
'start' => '71015549',
'end' => '71064926',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-021'
),
'ENST00000491238' => array(
'start' => '70959191',
'end' => '71130837',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-011'
),
'ENST00000493010' => array(
'start' => '71299835',
'end' => '71360760',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-017'
),
'ENST00000493089' => array(
'start' => '70959204',
'end' => '71583753',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-002'
),
'ENST00000497355' => array(
'start' => '70959191',
'end' => '71130593',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-009'
),
'ENST00000497553' => array(
'start' => '71046937',
'end' => '71065767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-019'
),
'ENST00000498154' => array(
'start' => '71493426',
'end' => '71581953',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-015'
),
'ENST00000498215' => array(
'start' => '70959204',
'end' => '71245165',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-006'
),
'ENST00000610810' => array(
'start' => '71053703',
'end' => '71306029',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-023'
),
'ENST00000614176' => array(
'start' => '70954715',
'end' => '71064923',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-201'
),
'ENST00000614183' => array(
'start' => '70968848',
'end' => '70978029',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'FOXP1-025'
),
'ENST00000615603' => array(
'start' => '70954715',
'end' => '71583989',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-202'
),
'ENST00000622151' => array(
'start' => '71197882',
'end' => '71210869',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXP1-024'
),
'ENST00000384212' => array(
'start' => '70808350',
'end' => '70808452',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'RNU6-281P-201'
),
'ENST00000408455' => array(
'start' => '70878660',
'end' => '70878792',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC096971.1-201'
),
'ENST00000490840' => array(
'start' => '70751123',
'end' => '70751350',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'COX6CP6-001'
),
'ENST00000487709' => array(
'start' => '70753854',
'end' => '70754573',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'HMGB1P36-001'
),
'ENST00000465742' => array(
'start' => '71289769',
'end' => '71305853',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXP1-AS1-001'
),
'ENST00000620572' => array(
'start' => '71276087',
'end' => '71289616',
'transcript_biotype' => 'sense_intronic',
'transcript_name' => 'RP11-298C2.1-001'
),
'ENSMUST00000074346' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-001'
),
'ENSMUST00000075832' => array(
'start' => '99152058',
'end' => '99266515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-005'
),
'ENSMUST00000113321' => array(
'start' => '99006685',
'end' => '99028266',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-009'
),
'ENSMUST00000113322' => array(
'start' => '98925342',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-201'
),
'ENSMUST00000113324' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-007'
),
'ENSMUST00000113326' => array(
'start' => '98925338',
'end' => '99266515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-004'
),
'ENSMUST00000113328' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-006'
),
'ENSMUST00000113329' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-008'
),
'ENSMUST00000123992' => array(
'start' => '99003393',
'end' => '99044459',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-013'
),
'ENSMUST00000124058' => array(
'start' => '98945534',
'end' => '99028313',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-011'
),
'ENSMUST00000131967' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-003'
),
'ENSMUST00000138754' => array(
'start' => '99161940',
'end' => '99266532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-002'
),
'ENSMUST00000142164' => array(
'start' => '98952201',
'end' => '99003680',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-010'
),
'ENSMUST00000154163' => array(
'start' => '99003200',
'end' => '99028942',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-012'
),
'ENSMUST00000175670' => array(
'start' => '99016550',
'end' => '99027991',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-029'
),
'ENSMUST00000175838' => array(
'start' => '99435236',
'end' => '99522721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-032'
),
'ENSMUST00000175880' => array(
'start' => '98930171',
'end' => '98935545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-028'
),
'ENSMUST00000175886' => array(
'start' => '99009933',
'end' => '99096205',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-019'
),
'ENSMUST00000176105' => array(
'start' => '99308377',
'end' => '99436396',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-018'
),
'ENSMUST00000176148' => array(
'start' => '99434751',
'end' => '99445607',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Foxp1-031'
),
'ENSMUST00000176565' => array(
'start' => '98929189',
'end' => '99520997',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-014'
),
'ENSMUST00000176632' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-026'
),
'ENSMUST00000176850' => array(
'start' => '98930090',
'end' => '99435345',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-027'
),
'ENSMUST00000177208' => array(
'start' => '99075962',
'end' => '99248336',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-030'
),
'ENSMUST00000177227' => array(
'start' => '99162929',
'end' => '99521162',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-033'
),
'ENSMUST00000177229' => array(
'start' => '98930090',
'end' => '99028259',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-023'
),
'ENSMUST00000177230' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Foxp1-024'
),
'ENSMUST00000177235' => array(
'start' => '99260357',
'end' => '99522647',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-017'
),
'ENSMUST00000177307' => array(
'start' => '98930090',
'end' => '99163018',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-020'
),
'ENSMUST00000177410' => array(
'start' => '98925415',
'end' => '98929785',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Foxp1-025'
),
'ENSMUST00000177437' => array(
'start' => '98929466',
'end' => '99028258',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-021'
),
'ENSMUST00000177507' => array(
'start' => '99009944',
'end' => '99044442',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxp1-022'
),
'ENSMUST00000155466' => array(
'start' => '99257484',
'end' => '99666797',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Gm20696-001'
),
'ENSMUST00000176255' => array(
'start' => '99434782',
'end' => '99632376',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Gm20696-002'
)
)
$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_0007PZ_0001' => array(
'genes_in_region' => array(
'ENSG00000221382' => array(
[maximum depth reached]
),
'ENSG00000240156' => array(
[maximum depth reached]
),
'ENSG00000243873' => array(
[maximum depth reached]
),
'ENSG00000244203' => array(
[maximum depth reached]
),
'ENSG00000277539' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Colon',
(int) 2 => 'Muscle',
(int) 3 => 'Brain',
(int) 4 => 'Adipose',
(int) 5 => 'Bladder',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Liver',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Muscle',
(int) 15 => 'Bladder',
(int) 16 => 'Ovary',
(int) 17 => 'Bladder',
(int) 18 => 'Brain',
(int) 19 => 'Breast',
(int) 20 => 'Kidney',
(int) 21 => 'Liver',
(int) 22 => 'Lung',
(int) 23 => 'Muscle',
(int) 24 => 'Ovary',
(int) 25 => 'Bladder',
(int) 26 => 'Breast',
(int) 27 => 'Colon',
(int) 28 => 'Heart',
(int) 29 => 'Liver',
(int) 30 => 'Lung',
(int) 31 => 'Muscle',
(int) 32 => 'Ovary',
(int) 33 => 'Placenta',
(int) 34 => 'Testis',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Muscle',
(int) 45 => 'Ovary',
(int) 46 => 'Placenta',
(int) 47 => 'Testis',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Testis',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Kidney',
(int) 55 => 'Brain',
(int) 56 => 'Heart',
(int) 57 => 'Lung',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Brain',
(int) 61 => 'Colon',
(int) 62 => 'Heart',
(int) 63 => 'Kidney',
(int) 64 => 'Liver',
(int) 65 => 'Lung',
(int) 66 => 'Muscle',
(int) 67 => 'Ovary',
(int) 68 => 'Testis',
(int) 69 => 'Adrenal',
(int) 70 => 'Bladder',
(int) 71 => 'Breast',
(int) 72 => 'Heart',
(int) 73 => 'Kidney',
(int) 74 => 'Ovary',
(int) 75 => 'Placenta',
(int) 76 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PZ_0002',
'tax_id' => '10090',
'chromosome' => '6',
'seq_start' => '98668191',
'seq_end' => '99269077',
'region_length' => '600886',
'region_type' => 'VISTA',
'el_id' => 'hs854'
)
)
$gene_el = array(
'ENST00000620572' => array(
'Adrenal' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.724',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.106',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.405',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.239',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.515',
'stddev_FPKM' => '0.33'
)
)
)
$gene_key = 'ENSG00000277539'
$is_first = false
$tran_el = array(
'Adrenal' => array(
'average_FPKM' => '0.273',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.724',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.106',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.024',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.166',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.405',
'stddev_FPKM' => '0.00'
),
'Placenta' => array(
'average_FPKM' => '0.239',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.515',
'stddev_FPKM' => '0.33'
)
)
$tran_key = 'ENST00000620572'
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
(AC096971.1)