| Source ID |
Type |
Tax ID |
Position |
| ENSG00000174442-ENSG00000188501 |
CGP |
9606 |
15:66504959-66565979  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_000477_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_000477_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000016337' => 'lactase-like b',
'ENSDARG00000057100' => 'Zwilch, kinetochore associated, homolog (Drosophila)',
'ENSG00000174442' => 'zwilch kinetochore protein',
'ENSG00000174444' => 'ribosomal protein L4',
'ENSG00000188501' => 'lactase-like'
),
'gene_name_arr' => array(
'ENSDARG00000016337' => 'lctlb',
'ENSDARG00000057100' => 'zwilch',
'ENSG00000174442' => 'ZWILCH',
'ENSG00000174444' => 'RPL4',
'ENSG00000188501' => 'LCTL'
),
'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) 2 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 15 => 'Colon',
(int) 17 => 'Heart',
(int) 22 => 'Kidney',
(int) 27 => 'Liver',
(int) 31 => 'Lung',
(int) 33 => 'Muscle',
(int) 37 => 'Ovary',
(int) 41 => 'Placenta',
(int) 44 => '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) 40,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000100557' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-201'
),
'ENSDART00000130329' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-202'
),
'ENSDART00000079695' => array(
'start' => '19237359',
'end' => '19253357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'zwilch-001'
),
'ENSDART00000134503' => array(
'start' => '19237547',
'end' => '19243454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'zwilch-002'
),
'ENST00000307897' => array(
'start' => '66504959',
'end' => '66550128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-001'
),
'ENST00000446801' => array(
'start' => '66505117',
'end' => '66549487',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-002'
),
'ENST00000535141' => array(
'start' => '66504959',
'end' => '66548426',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-004'
),
'ENST00000561583' => array(
'start' => '66520508',
'end' => '66528933',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-013'
),
'ENST00000562645' => array(
'start' => '66523511',
'end' => '66528909',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-012'
),
'ENST00000563698' => array(
'start' => '66505295',
'end' => '66519082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-011'
),
'ENST00000564179' => array(
'start' => '66505300',
'end' => '66520664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-008'
),
'ENST00000564309' => array(
'start' => '66505300',
'end' => '66514522',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-005'
),
'ENST00000565627' => array(
'start' => '66505295',
'end' => '66546705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-003'
),
'ENST00000565960' => array(
'start' => '66505326',
'end' => '66520657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-006'
),
'ENST00000567816' => array(
'start' => '66537169',
'end' => '66547292',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-009'
),
'ENST00000567926' => array(
'start' => '66505300',
'end' => '66519129',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-007'
),
'ENST00000569489' => array(
'start' => '66540153',
'end' => '66546887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-010'
),
'ENST00000613446' => array(
'start' => '66505083',
'end' => '66549474',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-201'
),
'ENST00000307961' => array(
'start' => '66498015',
'end' => '66504883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-001'
),
'ENST00000561554' => array(
'start' => '66502702',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-014'
),
'ENST00000561775' => array(
'start' => '66499346',
'end' => '66504827',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-006'
),
'ENST00000563473' => array(
'start' => '66500131',
'end' => '66501381',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-016'
),
'ENST00000564439' => array(
'start' => '66501399',
'end' => '66504845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-011'
),
'ENST00000564517' => array(
'start' => '66505243',
'end' => '66523411',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-019'
),
'ENST00000564647' => array(
'start' => '66500058',
'end' => '66502407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-015'
),
'ENST00000564744' => array(
'start' => '66500056',
'end' => '66500842',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-017'
),
'ENST00000565723' => array(
'start' => '66499323',
'end' => '66499818',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-018'
),
'ENST00000566039' => array(
'start' => '66501008',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-007'
),
'ENST00000566491' => array(
'start' => '66502996',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-008'
),
'ENST00000566622' => array(
'start' => '66501560',
'end' => '66504833',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-013'
),
'ENST00000566624' => array(
'start' => '66502270',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-009'
),
'ENST00000567229' => array(
'start' => '66499320',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-005'
),
'ENST00000568588' => array(
'start' => '66499323',
'end' => '66524532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-020'
),
'ENST00000569438' => array(
'start' => '66501785',
'end' => '66504845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-012'
),
'ENST00000569696' => array(
'start' => '66499575',
'end' => '66504846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-010'
),
'ENST00000341509' => array(
'start' => '66547179',
'end' => '66565497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-001'
),
'ENST00000537670' => array(
'start' => '66547468',
'end' => '66565964',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-003'
),
'ENST00000562179' => array(
'start' => '66564278',
'end' => '66565893',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-004'
),
'ENST00000563438' => array(
'start' => '66563567',
'end' => '66565974',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-005'
),
'ENST00000565875' => array(
'start' => '66548333',
'end' => '66565979',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LCTL-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_000477_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000477_0001' => array(
'genes_in_region' => array(
'ENSDARG00000016337' => array(
[maximum depth reached]
),
'ENSDARG00000057100' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Kidney',
(int) 2 => 'Liver',
(int) 3 => 'Heart',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000016337' => 'lactase-like b',
'ENSDARG00000057100' => 'Zwilch, kinetochore associated, homolog (Drosophila)',
'ENSG00000174442' => 'zwilch kinetochore protein',
'ENSG00000174444' => 'ribosomal protein L4',
'ENSG00000188501' => 'lactase-like'
)
$gene_name_arr = array(
'ENSDARG00000016337' => 'lctlb',
'ENSDARG00000057100' => 'zwilch',
'ENSG00000174442' => 'ZWILCH',
'ENSG00000174444' => 'RPL4',
'ENSG00000188501' => 'LCTL'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000477_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '19237359',
'seq_end' => '19264154',
'region_length' => '26795',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000057100-ENSDARG00000016337'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000477_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '66504959',
'seq_end' => '66565979',
'region_length' => '61020',
'region_type' => 'CGP',
'el_id' => 'ENSG00000174442-ENSG00000188501'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 15 => 'Colon',
(int) 17 => 'Heart',
(int) 22 => 'Kidney',
(int) 27 => 'Liver',
(int) 31 => 'Lung',
(int) 33 => 'Muscle',
(int) 37 => 'Ovary',
(int) 41 => 'Placenta',
(int) 44 => '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) 40
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000100557' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-201'
),
'ENSDART00000130329' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-202'
),
'ENSDART00000079695' => array(
'start' => '19237359',
'end' => '19253357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'zwilch-001'
),
'ENSDART00000134503' => array(
'start' => '19237547',
'end' => '19243454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'zwilch-002'
),
'ENST00000307897' => array(
'start' => '66504959',
'end' => '66550128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-001'
),
'ENST00000446801' => array(
'start' => '66505117',
'end' => '66549487',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-002'
),
'ENST00000535141' => array(
'start' => '66504959',
'end' => '66548426',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-004'
),
'ENST00000561583' => array(
'start' => '66520508',
'end' => '66528933',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-013'
),
'ENST00000562645' => array(
'start' => '66523511',
'end' => '66528909',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-012'
),
'ENST00000563698' => array(
'start' => '66505295',
'end' => '66519082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-011'
),
'ENST00000564179' => array(
'start' => '66505300',
'end' => '66520664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-008'
),
'ENST00000564309' => array(
'start' => '66505300',
'end' => '66514522',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-005'
),
'ENST00000565627' => array(
'start' => '66505295',
'end' => '66546705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-003'
),
'ENST00000565960' => array(
'start' => '66505326',
'end' => '66520657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-006'
),
'ENST00000567816' => array(
'start' => '66537169',
'end' => '66547292',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-009'
),
'ENST00000567926' => array(
'start' => '66505300',
'end' => '66519129',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-007'
),
'ENST00000569489' => array(
'start' => '66540153',
'end' => '66546887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-010'
),
'ENST00000613446' => array(
'start' => '66505083',
'end' => '66549474',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-201'
),
'ENST00000307961' => array(
'start' => '66498015',
'end' => '66504883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-001'
),
'ENST00000561554' => array(
'start' => '66502702',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-014'
),
'ENST00000561775' => array(
'start' => '66499346',
'end' => '66504827',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-006'
),
'ENST00000563473' => array(
'start' => '66500131',
'end' => '66501381',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-016'
),
'ENST00000564439' => array(
'start' => '66501399',
'end' => '66504845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-011'
),
'ENST00000564517' => array(
'start' => '66505243',
'end' => '66523411',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-019'
),
'ENST00000564647' => array(
'start' => '66500058',
'end' => '66502407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-015'
),
'ENST00000564744' => array(
'start' => '66500056',
'end' => '66500842',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-017'
),
'ENST00000565723' => array(
'start' => '66499323',
'end' => '66499818',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-018'
),
'ENST00000566039' => array(
'start' => '66501008',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-007'
),
'ENST00000566491' => array(
'start' => '66502996',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-008'
),
'ENST00000566622' => array(
'start' => '66501560',
'end' => '66504833',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-013'
),
'ENST00000566624' => array(
'start' => '66502270',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-009'
),
'ENST00000567229' => array(
'start' => '66499320',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-005'
),
'ENST00000568588' => array(
'start' => '66499323',
'end' => '66524532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-020'
),
'ENST00000569438' => array(
'start' => '66501785',
'end' => '66504845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-012'
),
'ENST00000569696' => array(
'start' => '66499575',
'end' => '66504846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-010'
),
'ENST00000341509' => array(
'start' => '66547179',
'end' => '66565497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-001'
),
'ENST00000537670' => array(
'start' => '66547468',
'end' => '66565964',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-003'
),
'ENST00000562179' => array(
'start' => '66564278',
'end' => '66565893',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-004'
),
'ENST00000563438' => array(
'start' => '66563567',
'end' => '66565974',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-005'
),
'ENST00000565875' => array(
'start' => '66548333',
'end' => '66565979',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LCTL-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_000477_0001' => array(
'genes_in_region' => array(
'ENSDARG00000016337' => array(
[maximum depth reached]
),
'ENSDARG00000057100' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Kidney',
(int) 2 => 'Liver',
(int) 3 => 'Heart',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000477_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '66504959',
'seq_end' => '66565979',
'region_length' => '61020',
'region_type' => 'CGP',
'el_id' => 'ENSG00000174442-ENSG00000188501'
)
)
$gene_el = array(
'ENSDART00000079695' => array(
'Brain' => array(
'average_FPKM' => '0.770',
'stddev_FPKM' => '0.34'
),
'Heart' => array(
'average_FPKM' => '0.601',
'stddev_FPKM' => '0.34'
),
'Kidney' => array(
'average_FPKM' => '5.125',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.169',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000134503' => array(
'Brain' => array(
'average_FPKM' => '0.447',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000057100'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.447',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000134503'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_000477_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSDARG00000016337' => 'lactase-like b',
'ENSDARG00000057100' => 'Zwilch, kinetochore associated, homolog (Drosophila)',
'ENSG00000174442' => 'zwilch kinetochore protein',
'ENSG00000174444' => 'ribosomal protein L4',
'ENSG00000188501' => 'lactase-like'
),
'gene_name_arr' => array(
'ENSDARG00000016337' => 'lctlb',
'ENSDARG00000057100' => 'zwilch',
'ENSG00000174442' => 'ZWILCH',
'ENSG00000174444' => 'RPL4',
'ENSG00000188501' => 'LCTL'
),
'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) 2 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 15 => 'Colon',
(int) 17 => 'Heart',
(int) 22 => 'Kidney',
(int) 27 => 'Liver',
(int) 31 => 'Lung',
(int) 33 => 'Muscle',
(int) 37 => 'Ovary',
(int) 41 => 'Placenta',
(int) 44 => '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) 40,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENSDART00000100557' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-201'
),
'ENSDART00000130329' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-202'
),
'ENSDART00000079695' => array(
'start' => '19237359',
'end' => '19253357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'zwilch-001'
),
'ENSDART00000134503' => array(
'start' => '19237547',
'end' => '19243454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'zwilch-002'
),
'ENST00000307897' => array(
'start' => '66504959',
'end' => '66550128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-001'
),
'ENST00000446801' => array(
'start' => '66505117',
'end' => '66549487',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-002'
),
'ENST00000535141' => array(
'start' => '66504959',
'end' => '66548426',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-004'
),
'ENST00000561583' => array(
'start' => '66520508',
'end' => '66528933',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-013'
),
'ENST00000562645' => array(
'start' => '66523511',
'end' => '66528909',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-012'
),
'ENST00000563698' => array(
'start' => '66505295',
'end' => '66519082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-011'
),
'ENST00000564179' => array(
'start' => '66505300',
'end' => '66520664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-008'
),
'ENST00000564309' => array(
'start' => '66505300',
'end' => '66514522',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-005'
),
'ENST00000565627' => array(
'start' => '66505295',
'end' => '66546705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-003'
),
'ENST00000565960' => array(
'start' => '66505326',
'end' => '66520657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-006'
),
'ENST00000567816' => array(
'start' => '66537169',
'end' => '66547292',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-009'
),
'ENST00000567926' => array(
'start' => '66505300',
'end' => '66519129',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-007'
),
'ENST00000569489' => array(
'start' => '66540153',
'end' => '66546887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-010'
),
'ENST00000613446' => array(
'start' => '66505083',
'end' => '66549474',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-201'
),
'ENST00000307961' => array(
'start' => '66498015',
'end' => '66504883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-001'
),
'ENST00000561554' => array(
'start' => '66502702',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-014'
),
'ENST00000561775' => array(
'start' => '66499346',
'end' => '66504827',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-006'
),
'ENST00000563473' => array(
'start' => '66500131',
'end' => '66501381',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-016'
),
'ENST00000564439' => array(
'start' => '66501399',
'end' => '66504845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-011'
),
'ENST00000564517' => array(
'start' => '66505243',
'end' => '66523411',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-019'
),
'ENST00000564647' => array(
'start' => '66500058',
'end' => '66502407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-015'
),
'ENST00000564744' => array(
'start' => '66500056',
'end' => '66500842',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-017'
),
'ENST00000565723' => array(
'start' => '66499323',
'end' => '66499818',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-018'
),
'ENST00000566039' => array(
'start' => '66501008',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-007'
),
'ENST00000566491' => array(
'start' => '66502996',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-008'
),
'ENST00000566622' => array(
'start' => '66501560',
'end' => '66504833',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-013'
),
'ENST00000566624' => array(
'start' => '66502270',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-009'
),
'ENST00000567229' => array(
'start' => '66499320',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-005'
),
'ENST00000568588' => array(
'start' => '66499323',
'end' => '66524532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-020'
),
'ENST00000569438' => array(
'start' => '66501785',
'end' => '66504845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-012'
),
'ENST00000569696' => array(
'start' => '66499575',
'end' => '66504846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-010'
),
'ENST00000341509' => array(
'start' => '66547179',
'end' => '66565497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-001'
),
'ENST00000537670' => array(
'start' => '66547468',
'end' => '66565964',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-003'
),
'ENST00000562179' => array(
'start' => '66564278',
'end' => '66565893',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-004'
),
'ENST00000563438' => array(
'start' => '66563567',
'end' => '66565974',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-005'
),
'ENST00000565875' => array(
'start' => '66548333',
'end' => '66565979',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LCTL-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_000477_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_000477_0001' => array(
'genes_in_region' => array(
'ENSDARG00000016337' => array(
[maximum depth reached]
),
'ENSDARG00000057100' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Kidney',
(int) 2 => 'Liver',
(int) 3 => 'Heart',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain'
)
)
)
$gene_desc_arr = array(
'ENSDARG00000016337' => 'lactase-like b',
'ENSDARG00000057100' => 'Zwilch, kinetochore associated, homolog (Drosophila)',
'ENSG00000174442' => 'zwilch kinetochore protein',
'ENSG00000174444' => 'ribosomal protein L4',
'ENSG00000188501' => 'lactase-like'
)
$gene_name_arr = array(
'ENSDARG00000016337' => 'lctlb',
'ENSDARG00000057100' => 'zwilch',
'ENSG00000174442' => 'ZWILCH',
'ENSG00000174444' => 'RPL4',
'ENSG00000188501' => 'LCTL'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000477_0001',
'tax_id' => '7955',
'chromosome' => '18',
'seq_start' => '19237359',
'seq_end' => '19264154',
'region_length' => '26795',
'region_type' => 'CGP',
'el_id' => 'ENSDARG00000057100-ENSDARG00000016337'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_000477_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '66504959',
'seq_end' => '66565979',
'region_length' => '61020',
'region_type' => 'CGP',
'el_id' => 'ENSG00000174442-ENSG00000188501'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 7 => 'Brain',
(int) 13 => 'Breast',
(int) 15 => 'Colon',
(int) 17 => 'Heart',
(int) 22 => 'Kidney',
(int) 27 => 'Liver',
(int) 31 => 'Lung',
(int) 33 => 'Muscle',
(int) 37 => 'Ovary',
(int) 41 => 'Placenta',
(int) 44 => '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) 40
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENSDART00000100557' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-201'
),
'ENSDART00000130329' => array(
'start' => '19248922',
'end' => '19264154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'lctlb-202'
),
'ENSDART00000079695' => array(
'start' => '19237359',
'end' => '19253357',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'zwilch-001'
),
'ENSDART00000134503' => array(
'start' => '19237547',
'end' => '19243454',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'zwilch-002'
),
'ENST00000307897' => array(
'start' => '66504959',
'end' => '66550128',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-001'
),
'ENST00000446801' => array(
'start' => '66505117',
'end' => '66549487',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-002'
),
'ENST00000535141' => array(
'start' => '66504959',
'end' => '66548426',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-004'
),
'ENST00000561583' => array(
'start' => '66520508',
'end' => '66528933',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-013'
),
'ENST00000562645' => array(
'start' => '66523511',
'end' => '66528909',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-012'
),
'ENST00000563698' => array(
'start' => '66505295',
'end' => '66519082',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-011'
),
'ENST00000564179' => array(
'start' => '66505300',
'end' => '66520664',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-008'
),
'ENST00000564309' => array(
'start' => '66505300',
'end' => '66514522',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-005'
),
'ENST00000565627' => array(
'start' => '66505295',
'end' => '66546705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-003'
),
'ENST00000565960' => array(
'start' => '66505326',
'end' => '66520657',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'ZWILCH-006'
),
'ENST00000567816' => array(
'start' => '66537169',
'end' => '66547292',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-009'
),
'ENST00000567926' => array(
'start' => '66505300',
'end' => '66519129',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'ZWILCH-007'
),
'ENST00000569489' => array(
'start' => '66540153',
'end' => '66546887',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-010'
),
'ENST00000613446' => array(
'start' => '66505083',
'end' => '66549474',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'ZWILCH-201'
),
'ENST00000307961' => array(
'start' => '66498015',
'end' => '66504883',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-001'
),
'ENST00000561554' => array(
'start' => '66502702',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-014'
),
'ENST00000561775' => array(
'start' => '66499346',
'end' => '66504827',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-006'
),
'ENST00000563473' => array(
'start' => '66500131',
'end' => '66501381',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-016'
),
'ENST00000564439' => array(
'start' => '66501399',
'end' => '66504845',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-011'
),
'ENST00000564517' => array(
'start' => '66505243',
'end' => '66523411',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-019'
),
'ENST00000564647' => array(
'start' => '66500058',
'end' => '66502407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-015'
),
'ENST00000564744' => array(
'start' => '66500056',
'end' => '66500842',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-017'
),
'ENST00000565723' => array(
'start' => '66499323',
'end' => '66499818',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'RPL4-018'
),
'ENST00000566039' => array(
'start' => '66501008',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-007'
),
'ENST00000566491' => array(
'start' => '66502996',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-008'
),
'ENST00000566622' => array(
'start' => '66501560',
'end' => '66504833',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-013'
),
'ENST00000566624' => array(
'start' => '66502270',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-009'
),
'ENST00000567229' => array(
'start' => '66499320',
'end' => '66504846',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RPL4-005'
),
'ENST00000568588' => array(
'start' => '66499323',
'end' => '66524532',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-020'
),
'ENST00000569438' => array(
'start' => '66501785',
'end' => '66504845',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-012'
),
'ENST00000569696' => array(
'start' => '66499575',
'end' => '66504846',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'RPL4-010'
),
'ENST00000341509' => array(
'start' => '66547179',
'end' => '66565497',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-001'
),
'ENST00000537670' => array(
'start' => '66547468',
'end' => '66565964',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LCTL-003'
),
'ENST00000562179' => array(
'start' => '66564278',
'end' => '66565893',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-004'
),
'ENST00000563438' => array(
'start' => '66563567',
'end' => '66565974',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LCTL-005'
),
'ENST00000565875' => array(
'start' => '66548333',
'end' => '66565979',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LCTL-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_000477_0001' => array(
'genes_in_region' => array(
'ENSDARG00000016337' => array(
[maximum depth reached]
),
'ENSDARG00000057100' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Kidney',
(int) 2 => 'Liver',
(int) 3 => 'Heart',
(int) 4 => 'Brain',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Muscle',
(int) 8 => 'Brain'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_000477_0002',
'tax_id' => '9606',
'chromosome' => '15',
'seq_start' => '66504959',
'seq_end' => '66565979',
'region_length' => '61020',
'region_type' => 'CGP',
'el_id' => 'ENSG00000174442-ENSG00000188501'
)
)
$gene_el = array(
'ENSDART00000079695' => array(
'Brain' => array(
'average_FPKM' => '0.770',
'stddev_FPKM' => '0.34'
),
'Heart' => array(
'average_FPKM' => '0.601',
'stddev_FPKM' => '0.34'
),
'Kidney' => array(
'average_FPKM' => '5.125',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.169',
'stddev_FPKM' => '0.00'
)
),
'ENSDART00000134503' => array(
'Brain' => array(
'average_FPKM' => '0.447',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSDARG00000057100'
$is_first = false
$tran_el = array(
'Brain' => array(
'average_FPKM' => '0.447',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENSDART00000134503'
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
(lctlb)