| Source ID |
Type |
Tax ID |
Position |
| ENSG00000130332-ENSG00000005206 |
CGP |
9606 |
19:2321517-2354806  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0001IB_0001 [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_0001IB_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000005206' => 'signal peptide peptidase like 2B',
'ENSG00000130332' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)',
'ENSG00000273734' => null,
'ENSMUSG00000035206' => 'signal peptide peptidase like 2B',
'ENSMUSG00000035215' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)'
),
'gene_name_arr' => array(
'ENSG00000005206' => 'SPPL2B',
'ENSG00000130332' => 'LSM7',
'ENSG00000273734' => 'LLfos-48D6.2',
'ENSMUSG00000035206' => 'Sppl2b',
'ENSMUSG00000035215' => 'Lsm7'
),
'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) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 21 => 'Muscle',
(int) 23 => 'Ovary',
(int) 25 => 'Placenta',
(int) 27 => '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) 24,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000585725' => array(
'start' => '2328615',
'end' => '2338526',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-009'
),
'ENST00000586111' => array(
'start' => '2330297',
'end' => '2330759',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-015'
),
'ENST00000586332' => array(
'start' => '2328659',
'end' => '2337482',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-008'
),
'ENST00000587851' => array(
'start' => '2334629',
'end' => '2337935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-011'
),
'ENST00000589515' => array(
'start' => '2342722',
'end' => '2353567',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-012'
),
'ENST00000593243' => array(
'start' => '2337111',
'end' => '2339877',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-010'
),
'ENST00000610743' => array(
'start' => '2328693',
'end' => '2353933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-013'
),
'ENST00000612623' => array(
'start' => '2339158',
'end' => '2343972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-014'
),
'ENST00000613503' => array(
'start' => '2328630',
'end' => '2354806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-002'
),
'ENST00000614784' => array(
'start' => '2339678',
'end' => '2341956',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-006'
),
'ENST00000614794' => array(
'start' => '2328684',
'end' => '2341468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-004'
),
'ENST00000618220' => array(
'start' => '2328696',
'end' => '2342503',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-005'
),
'ENST00000621568' => array(
'start' => '2328673',
'end' => '2343292',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-001'
),
'ENST00000622308' => array(
'start' => '2338760',
'end' => '2341187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-007'
),
'ENST00000252622' => array(
'start' => '2321517',
'end' => '2328620',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-001'
),
'ENST00000585395' => array(
'start' => '2321521',
'end' => '2328477',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LSM7-003'
),
'ENST00000585409' => array(
'start' => '2321521',
'end' => '2328611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-007'
),
'ENST00000587502' => array(
'start' => '2321520',
'end' => '2328586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-002'
),
'ENST00000589532' => array(
'start' => '2321521',
'end' => '2324906',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LSM7-004'
),
'ENST00000591515' => array(
'start' => '2321521',
'end' => '2324532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-005'
),
'ENST00000591745' => array(
'start' => '2327962',
'end' => '2328587',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-006'
),
'ENST00000621615' => array(
'start' => '2269525',
'end' => '2341172',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LLfos-48D6.2-001'
),
'ENSMUST00000035597' => array(
'start' => '80855275',
'end' => '80868705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sppl2b-201'
),
'ENSMUST00000035775' => array(
'start' => '80852825',
'end' => '80855209',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lsm7-201'
)
),
'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_0001IB_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0001IB_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000035206' => array(
[maximum depth reached]
),
'ENSMUSG00000035215' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000005206' => 'signal peptide peptidase like 2B',
'ENSG00000130332' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)',
'ENSG00000273734' => null,
'ENSMUSG00000035206' => 'signal peptide peptidase like 2B',
'ENSMUSG00000035215' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)'
)
$gene_name_arr = array(
'ENSG00000005206' => 'SPPL2B',
'ENSG00000130332' => 'LSM7',
'ENSG00000273734' => 'LLfos-48D6.2',
'ENSMUSG00000035206' => 'Sppl2b',
'ENSMUSG00000035215' => 'Lsm7'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001IB_0001',
'tax_id' => '9606',
'chromosome' => '19',
'seq_start' => '2321517',
'seq_end' => '2354806',
'region_length' => '33289',
'region_type' => 'CGP',
'el_id' => 'ENSG00000130332-ENSG00000005206'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001IB_0002',
'tax_id' => '10090',
'chromosome' => '10',
'seq_start' => '80852825',
'seq_end' => '80868705',
'region_length' => '15880',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000035215-ENSMUSG00000035206'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 7 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 21 => 'Muscle',
(int) 23 => 'Ovary',
(int) 25 => 'Placenta',
(int) 27 => '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) 24
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000585725' => array(
'start' => '2328615',
'end' => '2338526',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-009'
),
'ENST00000586111' => array(
'start' => '2330297',
'end' => '2330759',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-015'
),
'ENST00000586332' => array(
'start' => '2328659',
'end' => '2337482',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-008'
),
'ENST00000587851' => array(
'start' => '2334629',
'end' => '2337935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-011'
),
'ENST00000589515' => array(
'start' => '2342722',
'end' => '2353567',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-012'
),
'ENST00000593243' => array(
'start' => '2337111',
'end' => '2339877',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-010'
),
'ENST00000610743' => array(
'start' => '2328693',
'end' => '2353933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-013'
),
'ENST00000612623' => array(
'start' => '2339158',
'end' => '2343972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-014'
),
'ENST00000613503' => array(
'start' => '2328630',
'end' => '2354806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-002'
),
'ENST00000614784' => array(
'start' => '2339678',
'end' => '2341956',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-006'
),
'ENST00000614794' => array(
'start' => '2328684',
'end' => '2341468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-004'
),
'ENST00000618220' => array(
'start' => '2328696',
'end' => '2342503',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-005'
),
'ENST00000621568' => array(
'start' => '2328673',
'end' => '2343292',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-001'
),
'ENST00000622308' => array(
'start' => '2338760',
'end' => '2341187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-007'
),
'ENST00000252622' => array(
'start' => '2321517',
'end' => '2328620',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-001'
),
'ENST00000585395' => array(
'start' => '2321521',
'end' => '2328477',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LSM7-003'
),
'ENST00000585409' => array(
'start' => '2321521',
'end' => '2328611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-007'
),
'ENST00000587502' => array(
'start' => '2321520',
'end' => '2328586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-002'
),
'ENST00000589532' => array(
'start' => '2321521',
'end' => '2324906',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LSM7-004'
),
'ENST00000591515' => array(
'start' => '2321521',
'end' => '2324532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-005'
),
'ENST00000591745' => array(
'start' => '2327962',
'end' => '2328587',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-006'
),
'ENST00000621615' => array(
'start' => '2269525',
'end' => '2341172',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LLfos-48D6.2-001'
),
'ENSMUST00000035597' => array(
'start' => '80855275',
'end' => '80868705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sppl2b-201'
),
'ENSMUST00000035775' => array(
'start' => '80852825',
'end' => '80855209',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lsm7-201'
)
)
$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_0001IB_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000035206' => array(
[maximum depth reached]
),
'ENSMUSG00000035215' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0001IB_0001',
'tax_id' => '9606',
'chromosome' => '19',
'seq_start' => '2321517',
'seq_end' => '2354806',
'region_length' => '33289',
'region_type' => 'CGP',
'el_id' => 'ENSG00000130332-ENSG00000005206'
)
)
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0001IB_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000005206' => 'signal peptide peptidase like 2B',
'ENSG00000130332' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)',
'ENSG00000273734' => null,
'ENSMUSG00000035206' => 'signal peptide peptidase like 2B',
'ENSMUSG00000035215' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)'
),
'gene_name_arr' => array(
'ENSG00000005206' => 'SPPL2B',
'ENSG00000130332' => 'LSM7',
'ENSG00000273734' => 'LLfos-48D6.2',
'ENSMUSG00000035206' => 'Sppl2b',
'ENSMUSG00000035215' => 'Lsm7'
),
'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) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 21 => 'Muscle',
(int) 23 => 'Ovary',
(int) 25 => 'Placenta',
(int) 27 => '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) 24,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000585725' => array(
'start' => '2328615',
'end' => '2338526',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-009'
),
'ENST00000586111' => array(
'start' => '2330297',
'end' => '2330759',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-015'
),
'ENST00000586332' => array(
'start' => '2328659',
'end' => '2337482',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-008'
),
'ENST00000587851' => array(
'start' => '2334629',
'end' => '2337935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-011'
),
'ENST00000589515' => array(
'start' => '2342722',
'end' => '2353567',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-012'
),
'ENST00000593243' => array(
'start' => '2337111',
'end' => '2339877',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-010'
),
'ENST00000610743' => array(
'start' => '2328693',
'end' => '2353933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-013'
),
'ENST00000612623' => array(
'start' => '2339158',
'end' => '2343972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-014'
),
'ENST00000613503' => array(
'start' => '2328630',
'end' => '2354806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-002'
),
'ENST00000614784' => array(
'start' => '2339678',
'end' => '2341956',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-006'
),
'ENST00000614794' => array(
'start' => '2328684',
'end' => '2341468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-004'
),
'ENST00000618220' => array(
'start' => '2328696',
'end' => '2342503',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-005'
),
'ENST00000621568' => array(
'start' => '2328673',
'end' => '2343292',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-001'
),
'ENST00000622308' => array(
'start' => '2338760',
'end' => '2341187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-007'
),
'ENST00000252622' => array(
'start' => '2321517',
'end' => '2328620',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-001'
),
'ENST00000585395' => array(
'start' => '2321521',
'end' => '2328477',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LSM7-003'
),
'ENST00000585409' => array(
'start' => '2321521',
'end' => '2328611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-007'
),
'ENST00000587502' => array(
'start' => '2321520',
'end' => '2328586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-002'
),
'ENST00000589532' => array(
'start' => '2321521',
'end' => '2324906',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LSM7-004'
),
'ENST00000591515' => array(
'start' => '2321521',
'end' => '2324532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-005'
),
'ENST00000591745' => array(
'start' => '2327962',
'end' => '2328587',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-006'
),
'ENST00000621615' => array(
'start' => '2269525',
'end' => '2341172',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LLfos-48D6.2-001'
),
'ENSMUST00000035597' => array(
'start' => '80855275',
'end' => '80868705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sppl2b-201'
),
'ENSMUST00000035775' => array(
'start' => '80852825',
'end' => '80855209',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lsm7-201'
)
),
'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_0001IB_0002' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0001IB_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000035206' => array(
[maximum depth reached]
),
'ENSMUSG00000035215' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000005206' => 'signal peptide peptidase like 2B',
'ENSG00000130332' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)',
'ENSG00000273734' => null,
'ENSMUSG00000035206' => 'signal peptide peptidase like 2B',
'ENSMUSG00000035215' => 'LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)'
)
$gene_name_arr = array(
'ENSG00000005206' => 'SPPL2B',
'ENSG00000130332' => 'LSM7',
'ENSG00000273734' => 'LLfos-48D6.2',
'ENSMUSG00000035206' => 'Sppl2b',
'ENSMUSG00000035215' => 'Lsm7'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001IB_0001',
'tax_id' => '9606',
'chromosome' => '19',
'seq_start' => '2321517',
'seq_end' => '2354806',
'region_length' => '33289',
'region_type' => 'CGP',
'el_id' => 'ENSG00000130332-ENSG00000005206'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0001IB_0002',
'tax_id' => '10090',
'chromosome' => '10',
'seq_start' => '80852825',
'seq_end' => '80868705',
'region_length' => '15880',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000035215-ENSMUSG00000035206'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 2 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 7 => 'Brain',
(int) 9 => 'Breast',
(int) 11 => 'Colon',
(int) 13 => 'Heart',
(int) 15 => 'Kidney',
(int) 17 => 'Liver',
(int) 19 => 'Lung',
(int) 21 => 'Muscle',
(int) 23 => 'Ovary',
(int) 25 => 'Placenta',
(int) 27 => '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) 24
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000585725' => array(
'start' => '2328615',
'end' => '2338526',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-009'
),
'ENST00000586111' => array(
'start' => '2330297',
'end' => '2330759',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-015'
),
'ENST00000586332' => array(
'start' => '2328659',
'end' => '2337482',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-008'
),
'ENST00000587851' => array(
'start' => '2334629',
'end' => '2337935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-011'
),
'ENST00000589515' => array(
'start' => '2342722',
'end' => '2353567',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-012'
),
'ENST00000593243' => array(
'start' => '2337111',
'end' => '2339877',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPPL2B-010'
),
'ENST00000610743' => array(
'start' => '2328693',
'end' => '2353933',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-013'
),
'ENST00000612623' => array(
'start' => '2339158',
'end' => '2343972',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-014'
),
'ENST00000613503' => array(
'start' => '2328630',
'end' => '2354806',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-002'
),
'ENST00000614784' => array(
'start' => '2339678',
'end' => '2341956',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-006'
),
'ENST00000614794' => array(
'start' => '2328684',
'end' => '2341468',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-004'
),
'ENST00000618220' => array(
'start' => '2328696',
'end' => '2342503',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPPL2B-005'
),
'ENST00000621568' => array(
'start' => '2328673',
'end' => '2343292',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPPL2B-001'
),
'ENST00000622308' => array(
'start' => '2338760',
'end' => '2341187',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPPL2B-007'
),
'ENST00000252622' => array(
'start' => '2321517',
'end' => '2328620',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-001'
),
'ENST00000585395' => array(
'start' => '2321521',
'end' => '2328477',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LSM7-003'
),
'ENST00000585409' => array(
'start' => '2321521',
'end' => '2328611',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-007'
),
'ENST00000587502' => array(
'start' => '2321520',
'end' => '2328586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'LSM7-002'
),
'ENST00000589532' => array(
'start' => '2321521',
'end' => '2324906',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'LSM7-004'
),
'ENST00000591515' => array(
'start' => '2321521',
'end' => '2324532',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-005'
),
'ENST00000591745' => array(
'start' => '2327962',
'end' => '2328587',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'LSM7-006'
),
'ENST00000621615' => array(
'start' => '2269525',
'end' => '2341172',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'LLfos-48D6.2-001'
),
'ENSMUST00000035597' => array(
'start' => '80855275',
'end' => '80868705',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Sppl2b-201'
),
'ENSMUST00000035775' => array(
'start' => '80852825',
'end' => '80855209',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Lsm7-201'
)
)
$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_0001IB_0002' => array(
'genes_in_region' => array(
'ENSMUSG00000035206' => array(
[maximum depth reached]
),
'ENSMUSG00000035215' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Bladder',
(int) 3 => 'Brain',
(int) 4 => 'Breast',
(int) 5 => 'Colon',
(int) 6 => 'Heart',
(int) 7 => 'Kidney',
(int) 8 => 'Liver',
(int) 9 => 'Lung',
(int) 10 => 'Muscle',
(int) 11 => 'Ovary',
(int) 12 => 'Placenta',
(int) 13 => 'Testis',
(int) 14 => 'Adipose',
(int) 15 => 'Adrenal',
(int) 16 => 'Bladder',
(int) 17 => 'Brain',
(int) 18 => 'Breast',
(int) 19 => 'Colon',
(int) 20 => 'Heart',
(int) 21 => 'Kidney',
(int) 22 => 'Liver',
(int) 23 => 'Lung',
(int) 24 => 'Muscle',
(int) 25 => 'Ovary',
(int) 26 => 'Placenta',
(int) 27 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0001IB_0001',
'tax_id' => '9606',
'chromosome' => '19',
'seq_start' => '2321517',
'seq_end' => '2354806',
'region_length' => '33289',
'region_type' => 'CGP',
'el_id' => 'ENSG00000130332-ENSG00000005206'
)
)
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
(Sppl2b)