| Source ID |
Type |
Tax ID |
Position |
| ARX |
UCNEbase |
7955 |
Zv9_scaffold3460:16340-16890  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0007PA_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_0007PA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000004848' => 'aristaless related homeobox',
'ENSG00000101868' => 'polymerase (DNA directed), alpha 1, catalytic subunit',
'ENSG00000176812' => null,
'ENSG00000212075' => null,
'ENSG00000214111' => null,
'ENSG00000228519' => null,
'ENSG00000229310' => 'ribonuclease P/MRP 40kDa subunit pseudogene 1',
'ENSG00000240439' => 'RNA, 7SL, cytoplasmic 91, pseudogene',
'ENSMUSG00000006678' => 'polymerase (DNA directed), alpha 1',
'ENSMUSG00000035277' => 'aristaless related homeobox',
'ENSMUSG00000065266' => 'predicted gene, 23454',
'ENSMUSG00000067649' => 'melanoma antigen family B, 18',
'ENSMUSG00000077294' => 'predicted gene, 24123',
'ENSMUSG00000080737' => 'predicted gene 6982',
'ENSMUSG00000088663' => 'predicted gene, 25332',
'ENSMUSG00000093329' => 'predicted gene, 24973',
'ENSMUSG00000095110' => 'RIKEN cDNA 1700003E24 gene',
'ENSMUSG00000096153' => 'cDNA sequence BC061195',
'ENSDARG00000045308' => 'polymerase (DNA directed), alpha 1'
),
'gene_name_arr' => array(
'ENSG00000004848' => 'ARX',
'ENSG00000101868' => 'POLA1',
'ENSG00000176812' => 'RP11-629O4.1',
'ENSG00000212075' => 'AC112778.1',
'ENSG00000214111' => 'RP1-258N20.3',
'ENSG00000228519' => 'RP11-298C3.2',
'ENSG00000229310' => 'RPP40P1',
'ENSG00000240439' => 'RN7SL91P',
'ENSMUSG00000006678' => 'Pola1',
'ENSMUSG00000035277' => 'Arx',
'ENSMUSG00000065266' => 'Gm23454',
'ENSMUSG00000067649' => 'Mageb18',
'ENSMUSG00000077294' => 'Gm24123',
'ENSMUSG00000080737' => 'Gm6982',
'ENSMUSG00000088663' => 'Gm25332',
'ENSMUSG00000093329' => 'Gm24973',
'ENSMUSG00000095110' => '1700003E24Rik',
'ENSMUSG00000096153' => 'BC061195',
'ENSDARG00000045308' => 'pola1'
),
'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) 10 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 22 => 'Brain',
(int) 35 => 'Breast',
(int) 42 => 'Colon',
(int) 50 => 'Heart',
(int) 56 => 'Kidney',
(int) 68 => 'Liver',
(int) 78 => 'Lung',
(int) 83 => 'Muscle',
(int) 96 => 'Ovary',
(int) 111 => 'Placenta',
(int) 119 => '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) 32,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000379044' => array(
'start' => '25003694',
'end' => '25015948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ARX-001'
),
'ENST00000379059' => array(
'start' => '24693947',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-001'
),
'ENST00000379068' => array(
'start' => '24693919',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-005'
),
'ENST00000480125' => array(
'start' => '24745503',
'end' => '24810781',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-002'
),
'ENST00000493342' => array(
'start' => '24726933',
'end' => '24734353',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-003'
),
'ENST00000494204' => array(
'start' => '24812830',
'end' => '24841983',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-004'
),
'ENST00000611764' => array(
'start' => '24693947',
'end' => '24996983',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-201'
),
'ENST00000433306' => array(
'start' => '25194381',
'end' => '25195207',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-629O4.1-001'
),
'ENST00000390786' => array(
'start' => '25206370',
'end' => '25206460',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC112778.1-201'
),
'ENST00000438281' => array(
'start' => '25029545',
'end' => '25030235',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-258N20.3-001'
),
'ENST00000496795' => array(
'start' => '25645722',
'end' => '25646327',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-298C3.2-001'
),
'ENST00000426762' => array(
'start' => '25591353',
'end' => '25591808',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPP40P1-001'
),
'ENST00000469313' => array(
'start' => '25060649',
'end' => '25060939',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL91P-201'
),
'ENSMUST00000006856' => array(
'start' => '93304767',
'end' => '93632155',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Pola1-001'
),
'ENSMUST00000124236' => array(
'start' => '93623298',
'end' => '93632115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-002'
),
'ENSMUST00000127718' => array(
'start' => '93623076',
'end' => '93632143',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Pola1-003'
),
'ENSMUST00000142479' => array(
'start' => '93480490',
'end' => '93490946',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-004'
),
'ENSMUST00000046565' => array(
'start' => '93286529',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-001'
),
'ENSMUST00000113947' => array(
'start' => '93286522',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-002'
),
'ENSMUST00000187010' => array(
'start' => '93286445',
'end' => '93288382',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Arx-003'
),
'ENSMUST00000083332' => array(
'start' => '93251474',
'end' => '93251606',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23454-201'
),
'ENSMUST00000088137' => array(
'start' => '92119201',
'end' => '92120771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-201'
),
'ENSMUST00000113955' => array(
'start' => '92118879',
'end' => '92599572',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-001'
),
'ENSMUST00000104106' => array(
'start' => '93164902',
'end' => '93164984',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24123-201'
),
'ENSMUST00000118752' => array(
'start' => '92593809',
'end' => '92595368',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6982-001'
),
'ENSMUST00000158038' => array(
'start' => '92882451',
'end' => '92882555',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm25332-201'
),
'ENSMUST00000175588' => array(
'start' => '92989095',
'end' => '92989195',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm24973-201'
),
'ENSMUST00000088134' => array(
'start' => '93156154',
'end' => '93156873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700003E24Rik-001'
),
'ENSMUST00000088133' => array(
'start' => '93183227',
'end' => '93183946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BC061195-001'
),
'ENSDART00000127188' => array(
'start' => '24448797',
'end' => '24540473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-001'
),
'ENSDART00000128595' => array(
'start' => '24448900',
'end' => '24540472',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-201'
),
'ENSDART00000138097' => array(
'start' => '24449632',
'end' => '24540473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'pola1-002'
)
),
'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_0007PA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007PA_0001' => array(
'genes_in_region' => array(
'ENSG00000004848' => array(
[maximum depth reached]
),
'ENSG00000101868' => array(
[maximum depth reached]
),
'ENSG00000176812' => array(
[maximum depth reached]
),
'ENSG00000214111' => array(
[maximum depth reached]
),
'ENSG00000228519' => array(
[maximum depth reached]
),
'ENSG00000240439' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Brain',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Colon',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Kidney',
(int) 45 => 'Ovary',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Kidney',
(int) 51 => 'Lung',
(int) 52 => 'Muscle'
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000006678' => array(
[maximum depth reached]
),
'ENSMUSG00000035277' => array(
[maximum depth reached]
),
'ENSMUSG00000067649' => array(
[maximum depth reached]
),
'ENSMUSG00000080737' => array(
[maximum depth reached]
),
'ENSMUSG00000095110' => array(
[maximum depth reached]
),
'ENSMUSG00000096153' => 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 => 'Adrenal',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Ovary',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Testis',
(int) 29 => 'Adipose',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Adipose',
(int) 43 => 'Brain',
(int) 44 => 'Kidney',
(int) 45 => 'Muscle',
(int) 46 => 'Adipose',
(int) 47 => 'Brain',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Testis',
(int) 52 => 'Adipose',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Muscle',
(int) 57 => 'Ovary',
(int) 58 => 'Testis',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Brain',
(int) 62 => 'Liver',
(int) 63 => 'Ovary',
(int) 64 => 'Testis',
(int) 65 => 'Kidney',
(int) 66 => 'Liver',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000045308' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Heart',
(int) 9 => 'Liver'
)
)
)
$gene_desc_arr = array(
'ENSG00000004848' => 'aristaless related homeobox',
'ENSG00000101868' => 'polymerase (DNA directed), alpha 1, catalytic subunit',
'ENSG00000176812' => null,
'ENSG00000212075' => null,
'ENSG00000214111' => null,
'ENSG00000228519' => null,
'ENSG00000229310' => 'ribonuclease P/MRP 40kDa subunit pseudogene 1',
'ENSG00000240439' => 'RNA, 7SL, cytoplasmic 91, pseudogene',
'ENSMUSG00000006678' => 'polymerase (DNA directed), alpha 1',
'ENSMUSG00000035277' => 'aristaless related homeobox',
'ENSMUSG00000065266' => 'predicted gene, 23454',
'ENSMUSG00000067649' => 'melanoma antigen family B, 18',
'ENSMUSG00000077294' => 'predicted gene, 24123',
'ENSMUSG00000080737' => 'predicted gene 6982',
'ENSMUSG00000088663' => 'predicted gene, 25332',
'ENSMUSG00000093329' => 'predicted gene, 24973',
'ENSMUSG00000095110' => 'RIKEN cDNA 1700003E24 gene',
'ENSMUSG00000096153' => 'cDNA sequence BC061195',
'ENSDARG00000045308' => 'polymerase (DNA directed), alpha 1'
)
$gene_name_arr = array(
'ENSG00000004848' => 'ARX',
'ENSG00000101868' => 'POLA1',
'ENSG00000176812' => 'RP11-629O4.1',
'ENSG00000212075' => 'AC112778.1',
'ENSG00000214111' => 'RP1-258N20.3',
'ENSG00000228519' => 'RP11-298C3.2',
'ENSG00000229310' => 'RPP40P1',
'ENSG00000240439' => 'RN7SL91P',
'ENSMUSG00000006678' => 'Pola1',
'ENSMUSG00000035277' => 'Arx',
'ENSMUSG00000065266' => 'Gm23454',
'ENSMUSG00000067649' => 'Mageb18',
'ENSMUSG00000077294' => 'Gm24123',
'ENSMUSG00000080737' => 'Gm6982',
'ENSMUSG00000088663' => 'Gm25332',
'ENSMUSG00000093329' => 'Gm24973',
'ENSMUSG00000095110' => '1700003E24Rik',
'ENSMUSG00000096153' => 'BC061195',
'ENSDARG00000045308' => 'pola1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0001',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '24805232',
'seq_end' => '25650665',
'region_length' => '845433',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0002',
'tax_id' => '10090',
'chromosome' => 'X',
'seq_start' => '92514784',
'seq_end' => '93497939',
'region_length' => '983155',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0003',
'tax_id' => '7955',
'chromosome' => '24',
'seq_start' => '24487345',
'seq_end' => '24541379',
'region_length' => '54034',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_scaffold3460',
'seq_start' => '16340',
'seq_end' => '16890',
'region_length' => '550',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 10 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 22 => 'Brain',
(int) 35 => 'Breast',
(int) 42 => 'Colon',
(int) 50 => 'Heart',
(int) 56 => 'Kidney',
(int) 68 => 'Liver',
(int) 78 => 'Lung',
(int) 83 => 'Muscle',
(int) 96 => 'Ovary',
(int) 111 => 'Placenta',
(int) 119 => '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) 32
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000379044' => array(
'start' => '25003694',
'end' => '25015948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ARX-001'
),
'ENST00000379059' => array(
'start' => '24693947',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-001'
),
'ENST00000379068' => array(
'start' => '24693919',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-005'
),
'ENST00000480125' => array(
'start' => '24745503',
'end' => '24810781',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-002'
),
'ENST00000493342' => array(
'start' => '24726933',
'end' => '24734353',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-003'
),
'ENST00000494204' => array(
'start' => '24812830',
'end' => '24841983',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-004'
),
'ENST00000611764' => array(
'start' => '24693947',
'end' => '24996983',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-201'
),
'ENST00000433306' => array(
'start' => '25194381',
'end' => '25195207',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-629O4.1-001'
),
'ENST00000390786' => array(
'start' => '25206370',
'end' => '25206460',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC112778.1-201'
),
'ENST00000438281' => array(
'start' => '25029545',
'end' => '25030235',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-258N20.3-001'
),
'ENST00000496795' => array(
'start' => '25645722',
'end' => '25646327',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-298C3.2-001'
),
'ENST00000426762' => array(
'start' => '25591353',
'end' => '25591808',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPP40P1-001'
),
'ENST00000469313' => array(
'start' => '25060649',
'end' => '25060939',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL91P-201'
),
'ENSMUST00000006856' => array(
'start' => '93304767',
'end' => '93632155',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Pola1-001'
),
'ENSMUST00000124236' => array(
'start' => '93623298',
'end' => '93632115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-002'
),
'ENSMUST00000127718' => array(
'start' => '93623076',
'end' => '93632143',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Pola1-003'
),
'ENSMUST00000142479' => array(
'start' => '93480490',
'end' => '93490946',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-004'
),
'ENSMUST00000046565' => array(
'start' => '93286529',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-001'
),
'ENSMUST00000113947' => array(
'start' => '93286522',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-002'
),
'ENSMUST00000187010' => array(
'start' => '93286445',
'end' => '93288382',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Arx-003'
),
'ENSMUST00000083332' => array(
'start' => '93251474',
'end' => '93251606',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23454-201'
),
'ENSMUST00000088137' => array(
'start' => '92119201',
'end' => '92120771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-201'
),
'ENSMUST00000113955' => array(
'start' => '92118879',
'end' => '92599572',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-001'
),
'ENSMUST00000104106' => array(
'start' => '93164902',
'end' => '93164984',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24123-201'
),
'ENSMUST00000118752' => array(
'start' => '92593809',
'end' => '92595368',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6982-001'
),
'ENSMUST00000158038' => array(
'start' => '92882451',
'end' => '92882555',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm25332-201'
),
'ENSMUST00000175588' => array(
'start' => '92989095',
'end' => '92989195',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm24973-201'
),
'ENSMUST00000088134' => array(
'start' => '93156154',
'end' => '93156873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700003E24Rik-001'
),
'ENSMUST00000088133' => array(
'start' => '93183227',
'end' => '93183946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BC061195-001'
),
'ENSDART00000127188' => array(
'start' => '24448797',
'end' => '24540473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-001'
),
'ENSDART00000128595' => array(
'start' => '24448900',
'end' => '24540472',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-201'
),
'ENSDART00000138097' => array(
'start' => '24449632',
'end' => '24540473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'pola1-002'
)
)
$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_0007PA_0001' => array(
'genes_in_region' => array(
'ENSG00000004848' => array(
[maximum depth reached]
),
'ENSG00000101868' => array(
[maximum depth reached]
),
'ENSG00000176812' => array(
[maximum depth reached]
),
'ENSG00000214111' => array(
[maximum depth reached]
),
'ENSG00000228519' => array(
[maximum depth reached]
),
'ENSG00000240439' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Brain',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Colon',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Kidney',
(int) 45 => 'Ovary',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Kidney',
(int) 51 => 'Lung',
(int) 52 => 'Muscle'
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000006678' => array(
[maximum depth reached]
),
'ENSMUSG00000035277' => array(
[maximum depth reached]
),
'ENSMUSG00000067649' => array(
[maximum depth reached]
),
'ENSMUSG00000080737' => array(
[maximum depth reached]
),
'ENSMUSG00000095110' => array(
[maximum depth reached]
),
'ENSMUSG00000096153' => 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 => 'Adrenal',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Ovary',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Testis',
(int) 29 => 'Adipose',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Adipose',
(int) 43 => 'Brain',
(int) 44 => 'Kidney',
(int) 45 => 'Muscle',
(int) 46 => 'Adipose',
(int) 47 => 'Brain',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Testis',
(int) 52 => 'Adipose',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Muscle',
(int) 57 => 'Ovary',
(int) 58 => 'Testis',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Brain',
(int) 62 => 'Liver',
(int) 63 => 'Ovary',
(int) 64 => 'Testis',
(int) 65 => 'Kidney',
(int) 66 => 'Liver',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000045308' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Heart',
(int) 9 => 'Liver'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_scaffold3460',
'seq_start' => '16340',
'seq_end' => '16890',
'region_length' => '550',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
)
$gene_el = array(
'ENSDART00000127188' => array(
'Brain' => array(
'average_FPKM' => '0.794',
'stddev_FPKM' => '0.41'
),
'Heart' => array(
'average_FPKM' => '0.773',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1.872',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.232',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000128595' => array(
'Brain' => array(
'average_FPKM' => '0.870',
'stddev_FPKM' => '0.25'
),
'Heart' => array(
'average_FPKM' => '0.262',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '2.024',
'stddev_FPKM' => '2.62'
),
'Muscle' => array(
'average_FPKM' => '0.345',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000138097' => array(
'Heart' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.242',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000045308'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.242',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000138097'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0007PA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000004848' => 'aristaless related homeobox',
'ENSG00000101868' => 'polymerase (DNA directed), alpha 1, catalytic subunit',
'ENSG00000176812' => null,
'ENSG00000212075' => null,
'ENSG00000214111' => null,
'ENSG00000228519' => null,
'ENSG00000229310' => 'ribonuclease P/MRP 40kDa subunit pseudogene 1',
'ENSG00000240439' => 'RNA, 7SL, cytoplasmic 91, pseudogene',
'ENSMUSG00000006678' => 'polymerase (DNA directed), alpha 1',
'ENSMUSG00000035277' => 'aristaless related homeobox',
'ENSMUSG00000065266' => 'predicted gene, 23454',
'ENSMUSG00000067649' => 'melanoma antigen family B, 18',
'ENSMUSG00000077294' => 'predicted gene, 24123',
'ENSMUSG00000080737' => 'predicted gene 6982',
'ENSMUSG00000088663' => 'predicted gene, 25332',
'ENSMUSG00000093329' => 'predicted gene, 24973',
'ENSMUSG00000095110' => 'RIKEN cDNA 1700003E24 gene',
'ENSMUSG00000096153' => 'cDNA sequence BC061195',
'ENSDARG00000045308' => 'polymerase (DNA directed), alpha 1'
),
'gene_name_arr' => array(
'ENSG00000004848' => 'ARX',
'ENSG00000101868' => 'POLA1',
'ENSG00000176812' => 'RP11-629O4.1',
'ENSG00000212075' => 'AC112778.1',
'ENSG00000214111' => 'RP1-258N20.3',
'ENSG00000228519' => 'RP11-298C3.2',
'ENSG00000229310' => 'RPP40P1',
'ENSG00000240439' => 'RN7SL91P',
'ENSMUSG00000006678' => 'Pola1',
'ENSMUSG00000035277' => 'Arx',
'ENSMUSG00000065266' => 'Gm23454',
'ENSMUSG00000067649' => 'Mageb18',
'ENSMUSG00000077294' => 'Gm24123',
'ENSMUSG00000080737' => 'Gm6982',
'ENSMUSG00000088663' => 'Gm25332',
'ENSMUSG00000093329' => 'Gm24973',
'ENSMUSG00000095110' => '1700003E24Rik',
'ENSMUSG00000096153' => 'BC061195',
'ENSDARG00000045308' => 'pola1'
),
'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) 10 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 22 => 'Brain',
(int) 35 => 'Breast',
(int) 42 => 'Colon',
(int) 50 => 'Heart',
(int) 56 => 'Kidney',
(int) 68 => 'Liver',
(int) 78 => 'Lung',
(int) 83 => 'Muscle',
(int) 96 => 'Ovary',
(int) 111 => 'Placenta',
(int) 119 => '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) 32,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000379044' => array(
'start' => '25003694',
'end' => '25015948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ARX-001'
),
'ENST00000379059' => array(
'start' => '24693947',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-001'
),
'ENST00000379068' => array(
'start' => '24693919',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-005'
),
'ENST00000480125' => array(
'start' => '24745503',
'end' => '24810781',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-002'
),
'ENST00000493342' => array(
'start' => '24726933',
'end' => '24734353',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-003'
),
'ENST00000494204' => array(
'start' => '24812830',
'end' => '24841983',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-004'
),
'ENST00000611764' => array(
'start' => '24693947',
'end' => '24996983',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-201'
),
'ENST00000433306' => array(
'start' => '25194381',
'end' => '25195207',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-629O4.1-001'
),
'ENST00000390786' => array(
'start' => '25206370',
'end' => '25206460',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC112778.1-201'
),
'ENST00000438281' => array(
'start' => '25029545',
'end' => '25030235',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-258N20.3-001'
),
'ENST00000496795' => array(
'start' => '25645722',
'end' => '25646327',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-298C3.2-001'
),
'ENST00000426762' => array(
'start' => '25591353',
'end' => '25591808',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPP40P1-001'
),
'ENST00000469313' => array(
'start' => '25060649',
'end' => '25060939',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL91P-201'
),
'ENSMUST00000006856' => array(
'start' => '93304767',
'end' => '93632155',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Pola1-001'
),
'ENSMUST00000124236' => array(
'start' => '93623298',
'end' => '93632115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-002'
),
'ENSMUST00000127718' => array(
'start' => '93623076',
'end' => '93632143',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Pola1-003'
),
'ENSMUST00000142479' => array(
'start' => '93480490',
'end' => '93490946',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-004'
),
'ENSMUST00000046565' => array(
'start' => '93286529',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-001'
),
'ENSMUST00000113947' => array(
'start' => '93286522',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-002'
),
'ENSMUST00000187010' => array(
'start' => '93286445',
'end' => '93288382',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Arx-003'
),
'ENSMUST00000083332' => array(
'start' => '93251474',
'end' => '93251606',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23454-201'
),
'ENSMUST00000088137' => array(
'start' => '92119201',
'end' => '92120771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-201'
),
'ENSMUST00000113955' => array(
'start' => '92118879',
'end' => '92599572',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-001'
),
'ENSMUST00000104106' => array(
'start' => '93164902',
'end' => '93164984',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24123-201'
),
'ENSMUST00000118752' => array(
'start' => '92593809',
'end' => '92595368',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6982-001'
),
'ENSMUST00000158038' => array(
'start' => '92882451',
'end' => '92882555',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm25332-201'
),
'ENSMUST00000175588' => array(
'start' => '92989095',
'end' => '92989195',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm24973-201'
),
'ENSMUST00000088134' => array(
'start' => '93156154',
'end' => '93156873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700003E24Rik-001'
),
'ENSMUST00000088133' => array(
'start' => '93183227',
'end' => '93183946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BC061195-001'
),
'ENSDART00000127188' => array(
'start' => '24448797',
'end' => '24540473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-001'
),
'ENSDART00000128595' => array(
'start' => '24448900',
'end' => '24540472',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-201'
),
'ENSDART00000138097' => array(
'start' => '24449632',
'end' => '24540473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'pola1-002'
)
),
'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_0007PA_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0007PA_0001' => array(
'genes_in_region' => array(
'ENSG00000004848' => array(
[maximum depth reached]
),
'ENSG00000101868' => array(
[maximum depth reached]
),
'ENSG00000176812' => array(
[maximum depth reached]
),
'ENSG00000214111' => array(
[maximum depth reached]
),
'ENSG00000228519' => array(
[maximum depth reached]
),
'ENSG00000240439' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Brain',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Colon',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Kidney',
(int) 45 => 'Ovary',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Kidney',
(int) 51 => 'Lung',
(int) 52 => 'Muscle'
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000006678' => array(
[maximum depth reached]
),
'ENSMUSG00000035277' => array(
[maximum depth reached]
),
'ENSMUSG00000067649' => array(
[maximum depth reached]
),
'ENSMUSG00000080737' => array(
[maximum depth reached]
),
'ENSMUSG00000095110' => array(
[maximum depth reached]
),
'ENSMUSG00000096153' => 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 => 'Adrenal',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Ovary',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Testis',
(int) 29 => 'Adipose',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Adipose',
(int) 43 => 'Brain',
(int) 44 => 'Kidney',
(int) 45 => 'Muscle',
(int) 46 => 'Adipose',
(int) 47 => 'Brain',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Testis',
(int) 52 => 'Adipose',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Muscle',
(int) 57 => 'Ovary',
(int) 58 => 'Testis',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Brain',
(int) 62 => 'Liver',
(int) 63 => 'Ovary',
(int) 64 => 'Testis',
(int) 65 => 'Kidney',
(int) 66 => 'Liver',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000045308' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Heart',
(int) 9 => 'Liver'
)
)
)
$gene_desc_arr = array(
'ENSG00000004848' => 'aristaless related homeobox',
'ENSG00000101868' => 'polymerase (DNA directed), alpha 1, catalytic subunit',
'ENSG00000176812' => null,
'ENSG00000212075' => null,
'ENSG00000214111' => null,
'ENSG00000228519' => null,
'ENSG00000229310' => 'ribonuclease P/MRP 40kDa subunit pseudogene 1',
'ENSG00000240439' => 'RNA, 7SL, cytoplasmic 91, pseudogene',
'ENSMUSG00000006678' => 'polymerase (DNA directed), alpha 1',
'ENSMUSG00000035277' => 'aristaless related homeobox',
'ENSMUSG00000065266' => 'predicted gene, 23454',
'ENSMUSG00000067649' => 'melanoma antigen family B, 18',
'ENSMUSG00000077294' => 'predicted gene, 24123',
'ENSMUSG00000080737' => 'predicted gene 6982',
'ENSMUSG00000088663' => 'predicted gene, 25332',
'ENSMUSG00000093329' => 'predicted gene, 24973',
'ENSMUSG00000095110' => 'RIKEN cDNA 1700003E24 gene',
'ENSMUSG00000096153' => 'cDNA sequence BC061195',
'ENSDARG00000045308' => 'polymerase (DNA directed), alpha 1'
)
$gene_name_arr = array(
'ENSG00000004848' => 'ARX',
'ENSG00000101868' => 'POLA1',
'ENSG00000176812' => 'RP11-629O4.1',
'ENSG00000212075' => 'AC112778.1',
'ENSG00000214111' => 'RP1-258N20.3',
'ENSG00000228519' => 'RP11-298C3.2',
'ENSG00000229310' => 'RPP40P1',
'ENSG00000240439' => 'RN7SL91P',
'ENSMUSG00000006678' => 'Pola1',
'ENSMUSG00000035277' => 'Arx',
'ENSMUSG00000065266' => 'Gm23454',
'ENSMUSG00000067649' => 'Mageb18',
'ENSMUSG00000077294' => 'Gm24123',
'ENSMUSG00000080737' => 'Gm6982',
'ENSMUSG00000088663' => 'Gm25332',
'ENSMUSG00000093329' => 'Gm24973',
'ENSMUSG00000095110' => '1700003E24Rik',
'ENSMUSG00000096153' => 'BC061195',
'ENSDARG00000045308' => 'pola1'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0001',
'tax_id' => '9606',
'chromosome' => 'X',
'seq_start' => '24805232',
'seq_end' => '25650665',
'region_length' => '845433',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0002',
'tax_id' => '10090',
'chromosome' => 'X',
'seq_start' => '92514784',
'seq_end' => '93497939',
'region_length' => '983155',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0003',
'tax_id' => '7955',
'chromosome' => '24',
'seq_start' => '24487345',
'seq_end' => '24541379',
'region_length' => '54034',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
),
(int) 3 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_scaffold3460',
'seq_start' => '16340',
'seq_end' => '16890',
'region_length' => '550',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 10 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 22 => 'Brain',
(int) 35 => 'Breast',
(int) 42 => 'Colon',
(int) 50 => 'Heart',
(int) 56 => 'Kidney',
(int) 68 => 'Liver',
(int) 78 => 'Lung',
(int) 83 => 'Muscle',
(int) 96 => 'Ovary',
(int) 111 => 'Placenta',
(int) 119 => '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) 32
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000379044' => array(
'start' => '25003694',
'end' => '25015948',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ARX-001'
),
'ENST00000379059' => array(
'start' => '24693947',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-001'
),
'ENST00000379068' => array(
'start' => '24693919',
'end' => '24996986',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-005'
),
'ENST00000480125' => array(
'start' => '24745503',
'end' => '24810781',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-002'
),
'ENST00000493342' => array(
'start' => '24726933',
'end' => '24734353',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-003'
),
'ENST00000494204' => array(
'start' => '24812830',
'end' => '24841983',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'POLA1-004'
),
'ENST00000611764' => array(
'start' => '24693947',
'end' => '24996983',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'POLA1-201'
),
'ENST00000433306' => array(
'start' => '25194381',
'end' => '25195207',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-629O4.1-001'
),
'ENST00000390786' => array(
'start' => '25206370',
'end' => '25206460',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'AC112778.1-201'
),
'ENST00000438281' => array(
'start' => '25029545',
'end' => '25030235',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP1-258N20.3-001'
),
'ENST00000496795' => array(
'start' => '25645722',
'end' => '25646327',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RP11-298C3.2-001'
),
'ENST00000426762' => array(
'start' => '25591353',
'end' => '25591808',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'RPP40P1-001'
),
'ENST00000469313' => array(
'start' => '25060649',
'end' => '25060939',
'transcript_biotype' => 'misc_RNA',
'transcript_name' => 'RN7SL91P-201'
),
'ENSMUST00000006856' => array(
'start' => '93304767',
'end' => '93632155',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Pola1-001'
),
'ENSMUST00000124236' => array(
'start' => '93623298',
'end' => '93632115',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-002'
),
'ENSMUST00000127718' => array(
'start' => '93623076',
'end' => '93632143',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Pola1-003'
),
'ENSMUST00000142479' => array(
'start' => '93480490',
'end' => '93490946',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Pola1-004'
),
'ENSMUST00000046565' => array(
'start' => '93286529',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-001'
),
'ENSMUST00000113947' => array(
'start' => '93286522',
'end' => '93298357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Arx-002'
),
'ENSMUST00000187010' => array(
'start' => '93286445',
'end' => '93288382',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Arx-003'
),
'ENSMUST00000083332' => array(
'start' => '93251474',
'end' => '93251606',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm23454-201'
),
'ENSMUST00000088137' => array(
'start' => '92119201',
'end' => '92120771',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-201'
),
'ENSMUST00000113955' => array(
'start' => '92118879',
'end' => '92599572',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mageb18-001'
),
'ENSMUST00000104106' => array(
'start' => '93164902',
'end' => '93164984',
'transcript_biotype' => 'snoRNA',
'transcript_name' => 'Gm24123-201'
),
'ENSMUST00000118752' => array(
'start' => '92593809',
'end' => '92595368',
'transcript_biotype' => 'processed_pseudogene',
'transcript_name' => 'Gm6982-001'
),
'ENSMUST00000158038' => array(
'start' => '92882451',
'end' => '92882555',
'transcript_biotype' => 'snRNA',
'transcript_name' => 'Gm25332-201'
),
'ENSMUST00000175588' => array(
'start' => '92989095',
'end' => '92989195',
'transcript_biotype' => 'miRNA',
'transcript_name' => 'Gm24973-201'
),
'ENSMUST00000088134' => array(
'start' => '93156154',
'end' => '93156873',
'transcript_biotype' => 'protein_coding',
'transcript_name' => '1700003E24Rik-001'
),
'ENSMUST00000088133' => array(
'start' => '93183227',
'end' => '93183946',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'BC061195-001'
),
'ENSDART00000127188' => array(
'start' => '24448797',
'end' => '24540473',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-001'
),
'ENSDART00000128595' => array(
'start' => '24448900',
'end' => '24540472',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'pola1-201'
),
'ENSDART00000138097' => array(
'start' => '24449632',
'end' => '24540473',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'pola1-002'
)
)
$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_0007PA_0001' => array(
'genes_in_region' => array(
'ENSG00000004848' => array(
[maximum depth reached]
),
'ENSG00000101868' => array(
[maximum depth reached]
),
'ENSG00000176812' => array(
[maximum depth reached]
),
'ENSG00000214111' => array(
[maximum depth reached]
),
'ENSG00000228519' => array(
[maximum depth reached]
),
'ENSG00000240439' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Kidney',
(int) 6 => 'Lung',
(int) 7 => 'Muscle',
(int) 8 => 'Ovary',
(int) 9 => 'Placenta',
(int) 10 => 'Testis',
(int) 11 => 'Adipose',
(int) 12 => 'Adrenal',
(int) 13 => 'Brain',
(int) 14 => 'Breast',
(int) 15 => 'Colon',
(int) 16 => 'Kidney',
(int) 17 => 'Liver',
(int) 18 => 'Ovary',
(int) 19 => 'Placenta',
(int) 20 => 'Testis',
(int) 21 => 'Adrenal',
(int) 22 => 'Bladder',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Liver',
(int) 27 => 'Lung',
(int) 28 => 'Muscle',
(int) 29 => 'Ovary',
(int) 30 => 'Placenta',
(int) 31 => 'Testis',
(int) 32 => 'Muscle',
(int) 33 => 'Brain',
(int) 34 => 'Kidney',
(int) 35 => 'Liver',
(int) 36 => 'Muscle',
(int) 37 => 'Ovary',
(int) 38 => 'Adipose',
(int) 39 => 'Adrenal',
(int) 40 => 'Colon',
(int) 41 => 'Ovary',
(int) 42 => 'Placenta',
(int) 43 => 'Testis',
(int) 44 => 'Kidney',
(int) 45 => 'Ovary',
(int) 46 => 'Adipose',
(int) 47 => 'Adrenal',
(int) 48 => 'Breast',
(int) 49 => 'Colon',
(int) 50 => 'Kidney',
(int) 51 => 'Lung',
(int) 52 => 'Muscle'
)
),
'CIL_0007PA_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000006678' => array(
[maximum depth reached]
),
'ENSMUSG00000035277' => array(
[maximum depth reached]
),
'ENSMUSG00000067649' => array(
[maximum depth reached]
),
'ENSMUSG00000080737' => array(
[maximum depth reached]
),
'ENSMUSG00000095110' => array(
[maximum depth reached]
),
'ENSMUSG00000096153' => 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 => 'Adrenal',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Breast',
(int) 19 => 'Kidney',
(int) 20 => 'Ovary',
(int) 21 => 'Adipose',
(int) 22 => 'Adrenal',
(int) 23 => 'Brain',
(int) 24 => 'Colon',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Testis',
(int) 29 => 'Adipose',
(int) 30 => 'Adrenal',
(int) 31 => 'Brain',
(int) 32 => 'Breast',
(int) 33 => 'Colon',
(int) 34 => 'Heart',
(int) 35 => 'Kidney',
(int) 36 => 'Liver',
(int) 37 => 'Lung',
(int) 38 => 'Muscle',
(int) 39 => 'Ovary',
(int) 40 => 'Placenta',
(int) 41 => 'Testis',
(int) 42 => 'Adipose',
(int) 43 => 'Brain',
(int) 44 => 'Kidney',
(int) 45 => 'Muscle',
(int) 46 => 'Adipose',
(int) 47 => 'Brain',
(int) 48 => 'Muscle',
(int) 49 => 'Ovary',
(int) 50 => 'Placenta',
(int) 51 => 'Testis',
(int) 52 => 'Adipose',
(int) 53 => 'Adrenal',
(int) 54 => 'Brain',
(int) 55 => 'Breast',
(int) 56 => 'Muscle',
(int) 57 => 'Ovary',
(int) 58 => 'Testis',
(int) 59 => 'Placenta',
(int) 60 => 'Testis',
(int) 61 => 'Brain',
(int) 62 => 'Liver',
(int) 63 => 'Ovary',
(int) 64 => 'Testis',
(int) 65 => 'Kidney',
(int) 66 => 'Liver',
(int) 67 => 'Ovary',
(int) 68 => 'Testis'
)
),
'CIL_0007PA_0003' => array(
'genes_in_region' => array(
'ENSDARG00000045308' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Heart',
(int) 2 => 'Kidney',
(int) 3 => 'Liver',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Heart',
(int) 9 => 'Liver'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0007PA_0004',
'tax_id' => '7955',
'chromosome' => 'Zv9_scaffold3460',
'seq_start' => '16340',
'seq_end' => '16890',
'region_length' => '550',
'region_type' => 'UCNEbase',
'el_id' => 'ARX'
)
)
$gene_el = array(
'ENSDART00000127188' => array(
'Brain' => array(
'average_FPKM' => '0.794',
'stddev_FPKM' => '0.41'
),
'Heart' => array(
'average_FPKM' => '0.773',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1.872',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.232',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000128595' => array(
'Brain' => array(
'average_FPKM' => '0.870',
'stddev_FPKM' => '0.25'
),
'Heart' => array(
'average_FPKM' => '0.262',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '2.024',
'stddev_FPKM' => '2.62'
),
'Muscle' => array(
'average_FPKM' => '0.345',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000138097' => array(
'Heart' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.242',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000045308'
$is_first = false
$tran_el = array(
'Heart' => array(
'average_FPKM' => '0.223',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.242',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000138097'
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
(ARX)