| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000089837-ENSMUSG00000089715 |
CGP |
10090 |
15:79789675-79834688  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0005NH_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_0005NH_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000183741' => 'chromobox homolog 6',
'ENSG00000221890' => 'neuronal pentraxin receptor',
'ENSMUSG00000022421' => 'neuronal pentraxin receptor',
'ENSMUSG00000089715' => 'chromobox 6',
'ENSMUSG00000089837' => 'neuronal pentraxin chromo domain'
),
'gene_name_arr' => array(
'ENSG00000183741' => 'CBX6',
'ENSG00000221890' => 'NPTXR',
'ENSMUSG00000022421' => 'Nptxr',
'ENSMUSG00000089715' => 'Cbx6',
'ENSMUSG00000089837' => 'Npcd'
),
'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) 4 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 34 => 'Liver',
(int) 38 => 'Lung',
(int) 42 => 'Muscle',
(int) 46 => 'Ovary',
(int) 51 => 'Placenta',
(int) 57 => '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) 16,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000216083' => array(
'start' => '38864229',
'end' => '38872216',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-003'
),
'ENST00000407418' => array(
'start' => '38861450',
'end' => '38872314',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-001'
),
'ENST00000469420' => array(
'start' => '38869572',
'end' => '38872249',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBX6-002'
),
'ENST00000333039' => array(
'start' => '38818452',
'end' => '38843982',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NPTXR-001'
),
'ENSMUST00000023057' => array(
'start' => '79786353',
'end' => '79804766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-001'
),
'ENSMUST00000125283' => array(
'start' => '79789262',
'end' => '79790981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nptxr-002'
),
'ENSMUST00000175858' => array(
'start' => '79786352',
'end' => '79804709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-201'
),
'ENSMUST00000109623' => array(
'start' => '79827837',
'end' => '79834226',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-003'
),
'ENSMUST00000109625' => array(
'start' => '79826141',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-002'
),
'ENSMUST00000109627' => array(
'start' => '79823896',
'end' => '79834688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-001'
),
'ENSMUST00000127721' => array(
'start' => '79832572',
'end' => '79834325',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-004'
),
'ENSMUST00000129614' => array(
'start' => '79833245',
'end' => '79834274',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-005'
),
'ENSMUST00000141345' => array(
'start' => '79828636',
'end' => '79833798',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-007'
),
'ENSMUST00000148358' => array(
'start' => '79828777',
'end' => '79834280',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-006'
),
'ENSMUST00000023060' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-002'
),
'ENSMUST00000089299' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-001'
)
),
'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_0005NH_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0005NH_0001' => array(
'genes_in_region' => array(
'ENSG00000183741' => array(
[maximum depth reached]
),
'ENSG00000221890' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Heart',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Breast',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000183741' => 'chromobox homolog 6',
'ENSG00000221890' => 'neuronal pentraxin receptor',
'ENSMUSG00000022421' => 'neuronal pentraxin receptor',
'ENSMUSG00000089715' => 'chromobox 6',
'ENSMUSG00000089837' => 'neuronal pentraxin chromo domain'
)
$gene_name_arr = array(
'ENSG00000183741' => 'CBX6',
'ENSG00000221890' => 'NPTXR',
'ENSMUSG00000022421' => 'Nptxr',
'ENSMUSG00000089715' => 'Cbx6',
'ENSMUSG00000089837' => 'Npcd'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005NH_0001',
'tax_id' => '9606',
'chromosome' => '22',
'seq_start' => '38818452',
'seq_end' => '38872314',
'region_length' => '53862',
'region_type' => 'CGP',
'el_id' => 'ENSG00000221890-ENSG00000183741'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005NH_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '79789675',
'seq_end' => '79834688',
'region_length' => '45013',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000089837-ENSMUSG00000089715'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 34 => 'Liver',
(int) 38 => 'Lung',
(int) 42 => 'Muscle',
(int) 46 => 'Ovary',
(int) 51 => 'Placenta',
(int) 57 => '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) 16
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000216083' => array(
'start' => '38864229',
'end' => '38872216',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-003'
),
'ENST00000407418' => array(
'start' => '38861450',
'end' => '38872314',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-001'
),
'ENST00000469420' => array(
'start' => '38869572',
'end' => '38872249',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBX6-002'
),
'ENST00000333039' => array(
'start' => '38818452',
'end' => '38843982',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NPTXR-001'
),
'ENSMUST00000023057' => array(
'start' => '79786353',
'end' => '79804766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-001'
),
'ENSMUST00000125283' => array(
'start' => '79789262',
'end' => '79790981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nptxr-002'
),
'ENSMUST00000175858' => array(
'start' => '79786352',
'end' => '79804709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-201'
),
'ENSMUST00000109623' => array(
'start' => '79827837',
'end' => '79834226',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-003'
),
'ENSMUST00000109625' => array(
'start' => '79826141',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-002'
),
'ENSMUST00000109627' => array(
'start' => '79823896',
'end' => '79834688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-001'
),
'ENSMUST00000127721' => array(
'start' => '79832572',
'end' => '79834325',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-004'
),
'ENSMUST00000129614' => array(
'start' => '79833245',
'end' => '79834274',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-005'
),
'ENSMUST00000141345' => array(
'start' => '79828636',
'end' => '79833798',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-007'
),
'ENSMUST00000148358' => array(
'start' => '79828777',
'end' => '79834280',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-006'
),
'ENSMUST00000023060' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-002'
),
'ENSMUST00000089299' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-001'
)
)
$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_0005NH_0001' => array(
'genes_in_region' => array(
'ENSG00000183741' => array(
[maximum depth reached]
),
'ENSG00000221890' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Heart',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Breast',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0005NH_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '79789675',
'seq_end' => '79834688',
'region_length' => '45013',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000089837-ENSMUSG00000089715'
)
)
$gene_el = array(
'ENST00000333039' => array(
'Adipose' => array(
'average_FPKM' => '1.147',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '3.508',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '30.696',
'stddev_FPKM' => '22.30'
),
'Breast' => array(
'average_FPKM' => '1.622',
'stddev_FPKM' => '1.45'
),
'Colon' => array(
'average_FPKM' => '5.531',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3.279',
'stddev_FPKM' => '2.83'
),
'Kidney' => array(
'average_FPKM' => '0.969',
'stddev_FPKM' => '0.93'
),
'Liver' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.10'
),
'Lung' => array(
'average_FPKM' => '0.995',
'stddev_FPKM' => '0.73'
),
'Muscle' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.14'
),
'Ovary' => array(
'average_FPKM' => '2.616',
'stddev_FPKM' => '3.01'
),
'Placenta' => array(
'average_FPKM' => '0.313',
'stddev_FPKM' => '0.08'
),
'Testis' => array(
'average_FPKM' => '1.456',
'stddev_FPKM' => '1.05'
)
)
)
$gene_key = 'ENSG00000221890'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '1.147',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '3.508',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '30.696',
'stddev_FPKM' => '22.30'
),
'Breast' => array(
'average_FPKM' => '1.622',
'stddev_FPKM' => '1.45'
),
'Colon' => array(
'average_FPKM' => '5.531',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3.279',
'stddev_FPKM' => '2.83'
),
'Kidney' => array(
'average_FPKM' => '0.969',
'stddev_FPKM' => '0.93'
),
'Liver' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.10'
),
'Lung' => array(
'average_FPKM' => '0.995',
'stddev_FPKM' => '0.73'
),
'Muscle' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.14'
),
'Ovary' => array(
'average_FPKM' => '2.616',
'stddev_FPKM' => '3.01'
),
'Placenta' => array(
'average_FPKM' => '0.313',
'stddev_FPKM' => '0.08'
),
'Testis' => array(
'average_FPKM' => '1.456',
'stddev_FPKM' => '1.05'
)
)
$tran_key = 'ENST00000333039'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0005NH_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000183741' => 'chromobox homolog 6',
'ENSG00000221890' => 'neuronal pentraxin receptor',
'ENSMUSG00000022421' => 'neuronal pentraxin receptor',
'ENSMUSG00000089715' => 'chromobox 6',
'ENSMUSG00000089837' => 'neuronal pentraxin chromo domain'
),
'gene_name_arr' => array(
'ENSG00000183741' => 'CBX6',
'ENSG00000221890' => 'NPTXR',
'ENSMUSG00000022421' => 'Nptxr',
'ENSMUSG00000089715' => 'Cbx6',
'ENSMUSG00000089837' => 'Npcd'
),
'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) 4 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 34 => 'Liver',
(int) 38 => 'Lung',
(int) 42 => 'Muscle',
(int) 46 => 'Ovary',
(int) 51 => 'Placenta',
(int) 57 => '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) 16,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000216083' => array(
'start' => '38864229',
'end' => '38872216',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-003'
),
'ENST00000407418' => array(
'start' => '38861450',
'end' => '38872314',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-001'
),
'ENST00000469420' => array(
'start' => '38869572',
'end' => '38872249',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBX6-002'
),
'ENST00000333039' => array(
'start' => '38818452',
'end' => '38843982',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NPTXR-001'
),
'ENSMUST00000023057' => array(
'start' => '79786353',
'end' => '79804766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-001'
),
'ENSMUST00000125283' => array(
'start' => '79789262',
'end' => '79790981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nptxr-002'
),
'ENSMUST00000175858' => array(
'start' => '79786352',
'end' => '79804709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-201'
),
'ENSMUST00000109623' => array(
'start' => '79827837',
'end' => '79834226',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-003'
),
'ENSMUST00000109625' => array(
'start' => '79826141',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-002'
),
'ENSMUST00000109627' => array(
'start' => '79823896',
'end' => '79834688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-001'
),
'ENSMUST00000127721' => array(
'start' => '79832572',
'end' => '79834325',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-004'
),
'ENSMUST00000129614' => array(
'start' => '79833245',
'end' => '79834274',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-005'
),
'ENSMUST00000141345' => array(
'start' => '79828636',
'end' => '79833798',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-007'
),
'ENSMUST00000148358' => array(
'start' => '79828777',
'end' => '79834280',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-006'
),
'ENSMUST00000023060' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-002'
),
'ENSMUST00000089299' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-001'
)
),
'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_0005NH_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0005NH_0001' => array(
'genes_in_region' => array(
'ENSG00000183741' => array(
[maximum depth reached]
),
'ENSG00000221890' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Heart',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Breast',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000183741' => 'chromobox homolog 6',
'ENSG00000221890' => 'neuronal pentraxin receptor',
'ENSMUSG00000022421' => 'neuronal pentraxin receptor',
'ENSMUSG00000089715' => 'chromobox 6',
'ENSMUSG00000089837' => 'neuronal pentraxin chromo domain'
)
$gene_name_arr = array(
'ENSG00000183741' => 'CBX6',
'ENSG00000221890' => 'NPTXR',
'ENSMUSG00000022421' => 'Nptxr',
'ENSMUSG00000089715' => 'Cbx6',
'ENSMUSG00000089837' => 'Npcd'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005NH_0001',
'tax_id' => '9606',
'chromosome' => '22',
'seq_start' => '38818452',
'seq_end' => '38872314',
'region_length' => '53862',
'region_type' => 'CGP',
'el_id' => 'ENSG00000221890-ENSG00000183741'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0005NH_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '79789675',
'seq_end' => '79834688',
'region_length' => '45013',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000089837-ENSMUSG00000089715'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 4 => 'Adrenal',
(int) 8 => 'Bladder',
(int) 11 => 'Brain',
(int) 16 => 'Breast',
(int) 21 => 'Colon',
(int) 25 => 'Heart',
(int) 30 => 'Kidney',
(int) 34 => 'Liver',
(int) 38 => 'Lung',
(int) 42 => 'Muscle',
(int) 46 => 'Ovary',
(int) 51 => 'Placenta',
(int) 57 => '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) 16
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000216083' => array(
'start' => '38864229',
'end' => '38872216',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-003'
),
'ENST00000407418' => array(
'start' => '38861450',
'end' => '38872314',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'CBX6-001'
),
'ENST00000469420' => array(
'start' => '38869572',
'end' => '38872249',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'CBX6-002'
),
'ENST00000333039' => array(
'start' => '38818452',
'end' => '38843982',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'NPTXR-001'
),
'ENSMUST00000023057' => array(
'start' => '79786353',
'end' => '79804766',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-001'
),
'ENSMUST00000125283' => array(
'start' => '79789262',
'end' => '79790981',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Nptxr-002'
),
'ENSMUST00000175858' => array(
'start' => '79786352',
'end' => '79804709',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Nptxr-201'
),
'ENSMUST00000109623' => array(
'start' => '79827837',
'end' => '79834226',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-003'
),
'ENSMUST00000109625' => array(
'start' => '79826141',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-002'
),
'ENSMUST00000109627' => array(
'start' => '79823896',
'end' => '79834688',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-001'
),
'ENSMUST00000127721' => array(
'start' => '79832572',
'end' => '79834325',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-004'
),
'ENSMUST00000129614' => array(
'start' => '79833245',
'end' => '79834274',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-005'
),
'ENSMUST00000141345' => array(
'start' => '79828636',
'end' => '79833798',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Cbx6-007'
),
'ENSMUST00000148358' => array(
'start' => '79828777',
'end' => '79834280',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Cbx6-006'
),
'ENSMUST00000023060' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-002'
),
'ENSMUST00000089299' => array(
'start' => '79789675',
'end' => '79834237',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Npcd-001'
)
)
$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_0005NH_0001' => array(
'genes_in_region' => array(
'ENSG00000183741' => array(
[maximum depth reached]
),
'ENSG00000221890' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Breast',
(int) 1 => 'Placenta',
(int) 2 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 4 => 'Bladder',
(int) 5 => 'Brain',
(int) 6 => 'Breast',
(int) 7 => 'Colon',
(int) 8 => 'Heart',
(int) 9 => 'Kidney',
(int) 10 => 'Liver',
(int) 11 => 'Lung',
(int) 12 => 'Muscle',
(int) 13 => 'Ovary',
(int) 14 => 'Placenta',
(int) 15 => 'Testis',
(int) 16 => 'Heart',
(int) 17 => 'Adipose',
(int) 18 => 'Adrenal',
(int) 19 => 'Bladder',
(int) 20 => 'Brain',
(int) 21 => 'Breast',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Lung',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Placenta',
(int) 30 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0005NH_0002',
'tax_id' => '10090',
'chromosome' => '15',
'seq_start' => '79789675',
'seq_end' => '79834688',
'region_length' => '45013',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000089837-ENSMUSG00000089715'
)
)
$gene_el = array(
'ENST00000333039' => array(
'Adipose' => array(
'average_FPKM' => '1.147',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '3.508',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '30.696',
'stddev_FPKM' => '22.30'
),
'Breast' => array(
'average_FPKM' => '1.622',
'stddev_FPKM' => '1.45'
),
'Colon' => array(
'average_FPKM' => '5.531',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3.279',
'stddev_FPKM' => '2.83'
),
'Kidney' => array(
'average_FPKM' => '0.969',
'stddev_FPKM' => '0.93'
),
'Liver' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.10'
),
'Lung' => array(
'average_FPKM' => '0.995',
'stddev_FPKM' => '0.73'
),
'Muscle' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.14'
),
'Ovary' => array(
'average_FPKM' => '2.616',
'stddev_FPKM' => '3.01'
),
'Placenta' => array(
'average_FPKM' => '0.313',
'stddev_FPKM' => '0.08'
),
'Testis' => array(
'average_FPKM' => '1.456',
'stddev_FPKM' => '1.05'
)
)
)
$gene_key = 'ENSG00000221890'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '1.147',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '3.508',
'stddev_FPKM' => '0.00'
),
'Bladder' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '30.696',
'stddev_FPKM' => '22.30'
),
'Breast' => array(
'average_FPKM' => '1.622',
'stddev_FPKM' => '1.45'
),
'Colon' => array(
'average_FPKM' => '5.531',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '3.279',
'stddev_FPKM' => '2.83'
),
'Kidney' => array(
'average_FPKM' => '0.969',
'stddev_FPKM' => '0.93'
),
'Liver' => array(
'average_FPKM' => '0.300',
'stddev_FPKM' => '0.10'
),
'Lung' => array(
'average_FPKM' => '0.995',
'stddev_FPKM' => '0.73'
),
'Muscle' => array(
'average_FPKM' => '0.164',
'stddev_FPKM' => '0.14'
),
'Ovary' => array(
'average_FPKM' => '2.616',
'stddev_FPKM' => '3.01'
),
'Placenta' => array(
'average_FPKM' => '0.313',
'stddev_FPKM' => '0.08'
),
'Testis' => array(
'average_FPKM' => '1.456',
'stddev_FPKM' => '1.05'
)
)
$tran_key = 'ENST00000333039'
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
(CBX6)