Notice (8): Undefined index: CIL_00005J_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_00005J_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000204991' => 'spire-type actin nucleation factor 2',
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000010154' => 'spire homolog 2 (Drosophila)'
),
'gene_name_arr' => array(
'ENSG00000141002' => 'TCF25',
'ENSG00000204991' => 'SPIRE2',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000010154' => 'Spire2'
),
'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) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 22 => 'Colon',
(int) 28 => 'Heart',
(int) 35 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 55 => 'Muscle',
(int) 58 => 'Ovary',
(int) 66 => 'Placenta',
(int) 70 => 'Testis'
),
'column_titles' => array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
),
'geneviewer' => array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
),
'transcript_count' => (int) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000378247' => array(
'start' => '89828508',
'end' => '89871319',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-001'
),
'ENST00000393062' => array(
'start' => '89828499',
'end' => '89870391',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-002'
),
'ENST00000561883' => array(
'start' => '89854322',
'end' => '89856061',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-007'
),
'ENST00000562029' => array(
'start' => '89861966',
'end' => '89870407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-006'
),
'ENST00000563972' => array(
'start' => '89828547',
'end' => '89847156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-004'
),
'ENST00000564878' => array(
'start' => '89818179',
'end' => '89850562',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-009'
),
'ENST00000565103' => array(
'start' => '89818250',
'end' => '89822530',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-010'
),
'ENST00000565628' => array(
'start' => '89863442',
'end' => '89870201',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-008'
),
'ENST00000566337' => array(
'start' => '89828698',
'end' => '89859189',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPIRE2-005'
),
'ENST00000569108' => array(
'start' => '89849866',
'end' => '89870386',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-003'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000010298' => array(
'start' => '123332713',
'end' => '123369515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spire2-201'
)
),
'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_00005J_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00005J_0001' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
),
'ENSG00000204991' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Ovary',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Breast',
(int) 61 => 'Heart',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Breast',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Lung',
(int) 73 => 'Ovary'
)
)
)
$gene_desc_arr = array(
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000204991' => 'spire-type actin nucleation factor 2',
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000010154' => 'spire homolog 2 (Drosophila)'
)
$gene_name_arr = array(
'ENSG00000141002' => 'TCF25',
'ENSG00000204991' => 'SPIRE2',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000010154' => 'Spire2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005J_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89818179',
'seq_end' => '89911384',
'region_length' => '93205',
'region_type' => 'CGP',
'el_id' => 'ENSG00000204991-ENSG00000141002'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005J_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123332713',
'seq_end' => '123404173',
'region_length' => '71460',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000010154-ENSMUSG00000001472'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 22 => 'Colon',
(int) 28 => 'Heart',
(int) 35 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 55 => 'Muscle',
(int) 58 => 'Ovary',
(int) 66 => 'Placenta',
(int) 70 => 'Testis'
)
$column_titles = array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
)
$geneviewer = array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
)
$transcript_count = (int) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000378247' => array(
'start' => '89828508',
'end' => '89871319',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-001'
),
'ENST00000393062' => array(
'start' => '89828499',
'end' => '89870391',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-002'
),
'ENST00000561883' => array(
'start' => '89854322',
'end' => '89856061',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-007'
),
'ENST00000562029' => array(
'start' => '89861966',
'end' => '89870407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-006'
),
'ENST00000563972' => array(
'start' => '89828547',
'end' => '89847156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-004'
),
'ENST00000564878' => array(
'start' => '89818179',
'end' => '89850562',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-009'
),
'ENST00000565103' => array(
'start' => '89818250',
'end' => '89822530',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-010'
),
'ENST00000565628' => array(
'start' => '89863442',
'end' => '89870201',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-008'
),
'ENST00000566337' => array(
'start' => '89828698',
'end' => '89859189',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPIRE2-005'
),
'ENST00000569108' => array(
'start' => '89849866',
'end' => '89870386',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-003'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000010298' => array(
'start' => '123332713',
'end' => '123369515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spire2-201'
)
)
$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_00005J_0001' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
),
'ENSG00000204991' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Ovary',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Breast',
(int) 61 => 'Heart',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Breast',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Lung',
(int) 73 => 'Ovary'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00005J_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123332713',
'seq_end' => '123404173',
'region_length' => '71460',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000010154-ENSMUSG00000001472'
)
)
$gene_el = array(
'ENST00000378247' => array(
'Adipose' => array(
'average_FPKM' => '0.368',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.619',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.568',
'stddev_FPKM' => '0.88'
),
'Breast' => array(
'average_FPKM' => '0.340',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '3.252',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.109',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1.118',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.690',
'stddev_FPKM' => '0.11'
),
'Placenta' => array(
'average_FPKM' => '4.593',
'stddev_FPKM' => '0.58'
),
'Testis' => array(
'average_FPKM' => '0.872',
'stddev_FPKM' => '0.00'
)
),
'ENST00000393062' => array(
'Colon' => array(
'average_FPKM' => '1.308',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.318',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.418',
'stddev_FPKM' => '0.20'
),
'Testis' => array(
'average_FPKM' => '1.864',
'stddev_FPKM' => '0.00'
)
),
'ENST00000561883' => array(),
'ENST00000562029' => array(
'Adipose' => array(
'average_FPKM' => '0.291',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.395',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.892',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.327',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '1.694',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.506',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.333',
'stddev_FPKM' => '0.27'
)
),
'ENST00000563972' => array(
'Adipose' => array(
'average_FPKM' => '0.187',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.713',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.402',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.216',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.181',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.299',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564878' => array(
'Liver' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.00'
)
),
'ENST00000565103' => array(),
'ENST00000565628' => array(),
'ENST00000566337' => array(
'Ovary' => array(
'average_FPKM' => '0.316',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569108' => array(
'Adipose' => array(
'average_FPKM' => '0.699',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.306',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.635',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.233',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.738',
'stddev_FPKM' => '0.39'
),
'Lung' => array(
'average_FPKM' => '3.051',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.591',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000204991'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.699',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.306',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.635',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.233',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.738',
'stddev_FPKM' => '0.39'
),
'Lung' => array(
'average_FPKM' => '3.051',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.591',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000569108'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00005J_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000204991' => 'spire-type actin nucleation factor 2',
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000010154' => 'spire homolog 2 (Drosophila)'
),
'gene_name_arr' => array(
'ENSG00000141002' => 'TCF25',
'ENSG00000204991' => 'SPIRE2',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000010154' => 'Spire2'
),
'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) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 22 => 'Colon',
(int) 28 => 'Heart',
(int) 35 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 55 => 'Muscle',
(int) 58 => 'Ovary',
(int) 66 => 'Placenta',
(int) 70 => 'Testis'
),
'column_titles' => array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
),
'geneviewer' => array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
),
'transcript_count' => (int) 39,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000378247' => array(
'start' => '89828508',
'end' => '89871319',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-001'
),
'ENST00000393062' => array(
'start' => '89828499',
'end' => '89870391',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-002'
),
'ENST00000561883' => array(
'start' => '89854322',
'end' => '89856061',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-007'
),
'ENST00000562029' => array(
'start' => '89861966',
'end' => '89870407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-006'
),
'ENST00000563972' => array(
'start' => '89828547',
'end' => '89847156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-004'
),
'ENST00000564878' => array(
'start' => '89818179',
'end' => '89850562',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-009'
),
'ENST00000565103' => array(
'start' => '89818250',
'end' => '89822530',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-010'
),
'ENST00000565628' => array(
'start' => '89863442',
'end' => '89870201',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-008'
),
'ENST00000566337' => array(
'start' => '89828698',
'end' => '89859189',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPIRE2-005'
),
'ENST00000569108' => array(
'start' => '89849866',
'end' => '89870386',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-003'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000010298' => array(
'start' => '123332713',
'end' => '123369515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spire2-201'
)
),
'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_00005J_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00005J_0001' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
),
'ENSG00000204991' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Ovary',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Breast',
(int) 61 => 'Heart',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Breast',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Lung',
(int) 73 => 'Ovary'
)
)
)
$gene_desc_arr = array(
'ENSG00000141002' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSG00000204991' => 'spire-type actin nucleation factor 2',
'ENSG00000267048' => null,
'ENSMUSG00000001472' => 'transcription factor 25 (basic helix-loop-helix)',
'ENSMUSG00000010154' => 'spire homolog 2 (Drosophila)'
)
$gene_name_arr = array(
'ENSG00000141002' => 'TCF25',
'ENSG00000204991' => 'SPIRE2',
'ENSG00000267048' => 'RP11-566K11.7',
'ENSMUSG00000001472' => 'Tcf25',
'ENSMUSG00000010154' => 'Spire2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005J_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '89818179',
'seq_end' => '89911384',
'region_length' => '93205',
'region_type' => 'CGP',
'el_id' => 'ENSG00000204991-ENSG00000141002'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00005J_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123332713',
'seq_end' => '123404173',
'region_length' => '71460',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000010154-ENSMUSG00000001472'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 5 => 'Adrenal',
(int) 10 => 'Bladder',
(int) 11 => 'Brain',
(int) 15 => 'Breast',
(int) 22 => 'Colon',
(int) 28 => 'Heart',
(int) 35 => 'Kidney',
(int) 42 => 'Liver',
(int) 49 => 'Lung',
(int) 55 => 'Muscle',
(int) 58 => 'Ovary',
(int) 66 => 'Placenta',
(int) 70 => 'Testis'
)
$column_titles = array(
(int) 0 => 'Region Sub-Accession',
(int) 1 => 'Tax ID',
(int) 2 => 'Position',
(int) 3 => 'Region Length'
)
$geneviewer = array(
(int) 9606 => array(
'version' => 'GRCh38',
'coord_key' => 'Homo sapiens',
'reference_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.reference',
'gene_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Homo_sapiens.GRCh38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCh38.2bit',
'bwgURI' => '/static/files/GRCh38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 10090 => array(
'version' => 'GRCm38',
'coord_key' => 'Mus musculus',
'reference_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.reference',
'gene_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.gene',
'transcript_url' => 'http://www.ensembl.org/das/Mus_musculus.GRCm38.transcript',
'desc' => 'Gene structures from GENCODE 19',
'twoBitURI' => '/static/files/GRCm38.2bit',
'bwgURI' => '/static/files/GRCm38.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
),
(int) 7955 => array(
'version' => 'Zv9',
'coord_key' => 'Danio rerio',
'reference_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.reference',
'gene_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.gene',
'transcript_url' => 'http://www.ensembl.org/das/Danio_rerio.Zv9.transcript',
'twoBitURI' => '/static/files/Zv9.2bit',
'bwgURI' => '/static/files/Zv9.77.bb',
'stylesheet_uri' => '/static/files/gencode.xml',
'collapseSuperGroups' => 'true',
'trixURI' => '//www.biodalliance.org/datasets/geneIndex.ix'
)
)
$transcript_count = (int) 39
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000263346' => array(
'start' => '89873612',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-001'
),
'ENST00000263347' => array(
'start' => '89873586',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-201'
),
'ENST00000561585' => array(
'start' => '89873592',
'end' => '89884063',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-002'
),
'ENST00000561958' => array(
'start' => '89873606',
'end' => '89893767',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-012'
),
'ENST00000562184' => array(
'start' => '89894956',
'end' => '89900793',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-017'
),
'ENST00000562193' => array(
'start' => '89898601',
'end' => '89904975',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-023'
),
'ENST00000562256' => array(
'start' => '89884644',
'end' => '89911384',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-004'
),
'ENST00000563032' => array(
'start' => '89873643',
'end' => '89874855',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-009'
),
'ENST00000563406' => array(
'start' => '89874550',
'end' => '89884613',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-010'
),
'ENST00000563484' => array(
'start' => '89905009',
'end' => '89909174',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-021'
),
'ENST00000563636' => array(
'start' => '89895115',
'end' => '89901039',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-018'
),
'ENST00000564652' => array(
'start' => '89873644',
'end' => '89892247',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'TCF25-008'
),
'ENST00000564957' => array(
'start' => '89909840',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-024'
),
'ENST00000565196' => array(
'start' => '89873644',
'end' => '89892275',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-011'
),
'ENST00000565404' => array(
'start' => '89883394',
'end' => '89886130',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-013'
),
'ENST00000565860' => array(
'start' => '89910293',
'end' => '89911379',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-026'
),
'ENST00000566158' => array(
'start' => '89895990',
'end' => '89898835',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-019'
),
'ENST00000566283' => array(
'start' => '89908966',
'end' => '89911379',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-025'
),
'ENST00000566751' => array(
'start' => '89884642',
'end' => '89895137',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'TCF25-015'
),
'ENST00000567171' => array(
'start' => '89909428',
'end' => '89911378',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-007'
),
'ENST00000568409' => array(
'start' => '89887649',
'end' => '89904183',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-016'
),
'ENST00000568412' => array(
'start' => '89873668',
'end' => '89896083',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-014'
),
'ENST00000568870' => array(
'start' => '89892193',
'end' => '89893907',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-020'
),
'ENST00000570116' => array(
'start' => '89895990',
'end' => '89911350',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'TCF25-005'
),
'ENST00000614813' => array(
'start' => '89873641',
'end' => '89890633',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'TCF25-027'
),
'ENST00000378247' => array(
'start' => '89828508',
'end' => '89871319',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-001'
),
'ENST00000393062' => array(
'start' => '89828499',
'end' => '89870391',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-002'
),
'ENST00000561883' => array(
'start' => '89854322',
'end' => '89856061',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-007'
),
'ENST00000562029' => array(
'start' => '89861966',
'end' => '89870407',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-006'
),
'ENST00000563972' => array(
'start' => '89828547',
'end' => '89847156',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SPIRE2-004'
),
'ENST00000564878' => array(
'start' => '89818179',
'end' => '89850562',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-009'
),
'ENST00000565103' => array(
'start' => '89818250',
'end' => '89822530',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SPIRE2-010'
),
'ENST00000565628' => array(
'start' => '89863442',
'end' => '89870201',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-008'
),
'ENST00000566337' => array(
'start' => '89828698',
'end' => '89859189',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SPIRE2-005'
),
'ENST00000569108' => array(
'start' => '89849866',
'end' => '89870386',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SPIRE2-003'
),
'ENST00000570217' => array(
'start' => '89906157',
'end' => '89918233',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'RP11-566K11.7-001'
),
'ENSMUST00000057934' => array(
'start' => '123373824',
'end' => '123401892',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-201'
),
'ENSMUST00000108840' => array(
'start' => '123373835',
'end' => '123404173',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Tcf25-202'
),
'ENSMUST00000010298' => array(
'start' => '123332713',
'end' => '123369515',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Spire2-201'
)
)
$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_00005J_0001' => array(
'genes_in_region' => array(
'ENSG00000141002' => array(
[maximum depth reached]
),
'ENSG00000204991' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Adipose',
(int) 1 => 'Adrenal',
(int) 2 => 'Brain',
(int) 3 => 'Breast',
(int) 4 => 'Colon',
(int) 5 => 'Heart',
(int) 6 => 'Kidney',
(int) 7 => 'Liver',
(int) 8 => 'Lung',
(int) 9 => 'Muscle',
(int) 10 => 'Ovary',
(int) 11 => 'Placenta',
(int) 12 => 'Testis',
(int) 13 => 'Heart',
(int) 14 => 'Lung',
(int) 15 => 'Heart',
(int) 16 => 'Liver',
(int) 17 => 'Lung',
(int) 18 => 'Ovary',
(int) 19 => 'Colon',
(int) 20 => 'Kidney',
(int) 21 => 'Bladder',
(int) 22 => 'Brain',
(int) 23 => 'Breast',
(int) 24 => 'Colon',
(int) 25 => 'Heart',
(int) 26 => 'Kidney',
(int) 27 => 'Liver',
(int) 28 => 'Lung',
(int) 29 => 'Muscle',
(int) 30 => 'Ovary',
(int) 31 => 'Placenta',
(int) 32 => 'Testis',
(int) 33 => 'Placenta',
(int) 34 => 'Breast',
(int) 35 => 'Adipose',
(int) 36 => 'Adrenal',
(int) 37 => 'Brain',
(int) 38 => 'Breast',
(int) 39 => 'Colon',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Ovary',
(int) 43 => 'Placenta',
(int) 44 => 'Testis',
(int) 45 => 'Colon',
(int) 46 => 'Kidney',
(int) 47 => 'Liver',
(int) 48 => 'Ovary',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Kidney',
(int) 56 => 'Liver',
(int) 57 => 'Ovary',
(int) 58 => 'Adipose',
(int) 59 => 'Adrenal',
(int) 60 => 'Breast',
(int) 61 => 'Heart',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Liver',
(int) 66 => 'Ovary',
(int) 67 => 'Adipose',
(int) 68 => 'Adrenal',
(int) 69 => 'Breast',
(int) 70 => 'Heart',
(int) 71 => 'Kidney',
(int) 72 => 'Lung',
(int) 73 => 'Ovary'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00005J_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '123332713',
'seq_end' => '123404173',
'region_length' => '71460',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000010154-ENSMUSG00000001472'
)
)
$gene_el = array(
'ENST00000378247' => array(
'Adipose' => array(
'average_FPKM' => '0.368',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.619',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '2.568',
'stddev_FPKM' => '0.88'
),
'Breast' => array(
'average_FPKM' => '0.340',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '3.252',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.109',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '1.118',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.690',
'stddev_FPKM' => '0.11'
),
'Placenta' => array(
'average_FPKM' => '4.593',
'stddev_FPKM' => '0.58'
),
'Testis' => array(
'average_FPKM' => '0.872',
'stddev_FPKM' => '0.00'
)
),
'ENST00000393062' => array(
'Colon' => array(
'average_FPKM' => '1.308',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.213',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.318',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '1.418',
'stddev_FPKM' => '0.20'
),
'Testis' => array(
'average_FPKM' => '1.864',
'stddev_FPKM' => '0.00'
)
),
'ENST00000561883' => array(),
'ENST00000562029' => array(
'Adipose' => array(
'average_FPKM' => '0.291',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.395',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.892',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.327',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '1.694',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.506',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.333',
'stddev_FPKM' => '0.27'
)
),
'ENST00000563972' => array(
'Adipose' => array(
'average_FPKM' => '0.187',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.713',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.402',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.216',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.181',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.299',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
)
),
'ENST00000564878' => array(
'Liver' => array(
'average_FPKM' => '0.192',
'stddev_FPKM' => '0.00'
)
),
'ENST00000565103' => array(),
'ENST00000565628' => array(),
'ENST00000566337' => array(
'Ovary' => array(
'average_FPKM' => '0.316',
'stddev_FPKM' => '0.00'
)
),
'ENST00000569108' => array(
'Adipose' => array(
'average_FPKM' => '0.699',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.306',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.635',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.233',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.738',
'stddev_FPKM' => '0.39'
),
'Lung' => array(
'average_FPKM' => '3.051',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.591',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000204991'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.699',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.306',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.635',
'stddev_FPKM' => '0.15'
),
'Heart' => array(
'average_FPKM' => '0.233',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.738',
'stddev_FPKM' => '0.39'
),
'Lung' => array(
'average_FPKM' => '3.051',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.591',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000569108'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000010154-ENSMUSG00000001472 |
CGP |
10090 |
8:123332713-123404173  |
| Gene | Transcript | Position | Biotype |
|---|
(TCF25)