| Source ID |
Type |
Tax ID |
Position |
| ENSG00000205572-ENSG00000205571 |
CGP |
9606 |
5:70025247-70078522  |
| Gene | Transcript | Position | Biotype |
|---|
Notice (8): Undefined index: CIL_0004ZD_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_0004ZD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000172058' => 'small EDRK-rich factor 1A (telomeric)',
'ENSG00000172062' => 'survival of motor neuron 1, telomeric',
'ENSG00000205571' => 'survival of motor neuron 2, centromeric',
'ENSG00000205572' => 'small EDRK-rich factor 1B (centromeric)',
'ENSMUSG00000021643' => 'small EDRK-rich factor 1',
'ENSMUSG00000021645' => 'survival motor neuron 1',
'ENSMUSG00000097022' => 'cDNA sequence BC001981'
),
'gene_name_arr' => array(
'ENSG00000172058' => 'SERF1A',
'ENSG00000172062' => 'SMN1',
'ENSG00000205571' => 'SMN2',
'ENSG00000205572' => 'SERF1B',
'ENSMUSG00000021643' => 'Serf1',
'ENSMUSG00000021645' => 'Smn1',
'ENSMUSG00000097022' => 'BC001981'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 10 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 27 => 'Brain',
(int) 43 => 'Breast',
(int) 58 => 'Colon',
(int) 72 => 'Heart',
(int) 88 => 'Kidney',
(int) 101 => 'Liver',
(int) 112 => 'Lung',
(int) 126 => 'Muscle',
(int) 139 => 'Ovary',
(int) 158 => 'Placenta',
(int) 174 => '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) 57,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000317633' => array(
'start' => '70900665',
'end' => '70908375',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-001'
),
'ENST00000354833' => array(
'start' => '70900687',
'end' => '70918530',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-002'
),
'ENST00000503509' => array(
'start' => '70901682',
'end' => '70908113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1A-004'
),
'ENST00000504458' => array(
'start' => '70900774',
'end' => '70905541',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-003'
),
'ENST00000507348' => array(
'start' => '70900978',
'end' => '70908115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-007'
),
'ENST00000511162' => array(
'start' => '70900669',
'end' => '70901921',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-009'
),
'ENST00000512649' => array(
'start' => '70900994',
'end' => '70917521',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-006'
),
'ENST00000512868' => array(
'start' => '70900981',
'end' => '70917134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-005'
),
'ENST00000513436' => array(
'start' => '70900764',
'end' => '70918520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-008'
),
'ENST00000351205' => array(
'start' => '70925104',
'end' => '70952006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-201'
),
'ENST00000380707' => array(
'start' => '70925030',
'end' => '70953012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-001'
),
'ENST00000503079' => array(
'start' => '70925030',
'end' => '70952347',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-008'
),
'ENST00000506163' => array(
'start' => '70925095',
'end' => '70953040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-007'
),
'ENST00000506239' => array(
'start' => '70925075',
'end' => '70953016',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-003'
),
'ENST00000507905' => array(
'start' => '70942508',
'end' => '70946079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-005'
),
'ENST00000510679' => array(
'start' => '70946089',
'end' => '70953942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SMN1-004'
),
'ENST00000513228' => array(
'start' => '70942518',
'end' => '70946274',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-009'
),
'ENST00000514951' => array(
'start' => '70925056',
'end' => '70952567',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-002'
),
'ENST00000518504' => array(
'start' => '70942472',
'end' => '70946278',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-010'
),
'ENST00000380741' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-201'
),
'ENST00000380742' => array(
'start' => '70049664',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-002'
),
'ENST00000380743' => array(
'start' => '70049612',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-001'
),
'ENST00000503678' => array(
'start' => '70063411',
'end' => '70070755',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-006'
),
'ENST00000505346' => array(
'start' => '70067099',
'end' => '70076927',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-007'
),
'ENST00000506734' => array(
'start' => '70049657',
'end' => '70077596',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-003'
),
'ENST00000507458' => array(
'start' => '70070664',
'end' => '70078522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-005'
),
'ENST00000508258' => array(
'start' => '70069233',
'end' => '70070753',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-014'
),
'ENST00000509805' => array(
'start' => '70067094',
'end' => '70070849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-011'
),
'ENST00000511812' => array(
'start' => '70049638',
'end' => '70076706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-004'
),
'ENST00000511873' => array(
'start' => '70067084',
'end' => '70070654',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-012'
),
'ENST00000514914' => array(
'start' => '70067279',
'end' => '70077251',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-013'
),
'ENST00000614240' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-202'
),
'ENST00000380750' => array(
'start' => '70025269',
'end' => '70043113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-001'
),
'ENST00000380751' => array(
'start' => '70025247',
'end' => '70032696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-004'
),
'ENST00000503931' => array(
'start' => '70025356',
'end' => '70030122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-008'
),
'ENST00000506542' => array(
'start' => '70025373',
'end' => '70043103',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-002'
),
'ENST00000507177' => array(
'start' => '70025563',
'end' => '70026515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-005'
),
'ENST00000513144' => array(
'start' => '70026264',
'end' => '70032694',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1B-009'
),
'ENST00000514285' => array(
'start' => '70025587',
'end' => '70032493',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-006'
),
'ENST00000515588' => array(
'start' => '70025534',
'end' => '70042008',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-007'
),
'ENSMUST00000022145' => array(
'start' => '100108012',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-001'
),
'ENSMUST00000129014' => array(
'start' => '100108155',
'end' => '100114571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-006'
),
'ENSMUST00000132053' => array(
'start' => '100108085',
'end' => '100111009',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-002'
),
'ENSMUST00000142155' => array(
'start' => '100107997',
'end' => '100114233',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-003'
),
'ENSMUST00000151821' => array(
'start' => '100108341',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-004'
),
'ENSMUST00000152286' => array(
'start' => '100108396',
'end' => '100114231',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-005'
),
'ENSMUST00000022147' => array(
'start' => '100124852',
'end' => '100137690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-001'
),
'ENSMUST00000091321' => array(
'start' => '100124894',
'end' => '100137480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-003'
),
'ENSMUST00000125572' => array(
'start' => '100126125',
'end' => '100126935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-007'
),
'ENSMUST00000134514' => array(
'start' => '100124858',
'end' => '100127142',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-002'
),
'ENSMUST00000135355' => array(
'start' => '100135393',
'end' => '100137450',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-010'
),
'ENSMUST00000140745' => array(
'start' => '100124858',
'end' => '100127812',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Smn1-006'
),
'ENSMUST00000143937' => array(
'start' => '100124924',
'end' => '100131174',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-008'
),
'ENSMUST00000147306' => array(
'start' => '100131003',
'end' => '100137690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-005'
),
'ENSMUST00000151389' => array(
'start' => '100127875',
'end' => '100128630',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-009'
),
'ENSMUST00000180822' => array(
'start' => '100108035',
'end' => '100108337',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-201'
),
'ENSMUST00000191393' => array(
'start' => '100106795',
'end' => '100108339',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-001'
)
),
'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_0004ZD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004ZD_0001' => array(
'genes_in_region' => array(
'ENSG00000172058' => 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 => 'Adipose',
(int) 14 => 'Lung',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Bladder',
(int) 44 => 'Brain',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Colon',
(int) 60 => 'Heart',
(int) 61 => 'Kidney',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Ovary',
(int) 66 => 'Placenta',
(int) 67 => 'Testis'
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000021643' => array(
[maximum depth reached]
),
'ENSMUSG00000021645' => 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 => 'Heart',
(int) 15 => 'Brain',
(int) 16 => 'Muscle',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Testis',
(int) 20 => 'Breast',
(int) 21 => 'Ovary',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Placenta',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adrenal',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary'
)
)
)
$gene_desc_arr = array(
'ENSG00000172058' => 'small EDRK-rich factor 1A (telomeric)',
'ENSG00000172062' => 'survival of motor neuron 1, telomeric',
'ENSG00000205571' => 'survival of motor neuron 2, centromeric',
'ENSG00000205572' => 'small EDRK-rich factor 1B (centromeric)',
'ENSMUSG00000021643' => 'small EDRK-rich factor 1',
'ENSMUSG00000021645' => 'survival motor neuron 1',
'ENSMUSG00000097022' => 'cDNA sequence BC001981'
)
$gene_name_arr = array(
'ENSG00000172058' => 'SERF1A',
'ENSG00000172062' => 'SMN1',
'ENSG00000205571' => 'SMN2',
'ENSG00000205572' => 'SERF1B',
'ENSMUSG00000021643' => 'Serf1',
'ENSMUSG00000021645' => 'Smn1',
'ENSMUSG00000097022' => 'BC001981'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0001',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '70900665',
'seq_end' => '70953942',
'region_length' => '53277',
'region_type' => 'CGP',
'el_id' => 'ENSG00000172058-ENSG00000172062'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0002',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '70025247',
'seq_end' => '70078522',
'region_length' => '53275',
'region_type' => 'CGP',
'el_id' => 'ENSG00000205572-ENSG00000205571'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0003',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '100107997',
'seq_end' => '100137690',
'region_length' => '29693',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000021643-ENSMUSG00000021645'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 10 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 27 => 'Brain',
(int) 43 => 'Breast',
(int) 58 => 'Colon',
(int) 72 => 'Heart',
(int) 88 => 'Kidney',
(int) 101 => 'Liver',
(int) 112 => 'Lung',
(int) 126 => 'Muscle',
(int) 139 => 'Ovary',
(int) 158 => 'Placenta',
(int) 174 => '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) 57
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000317633' => array(
'start' => '70900665',
'end' => '70908375',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-001'
),
'ENST00000354833' => array(
'start' => '70900687',
'end' => '70918530',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-002'
),
'ENST00000503509' => array(
'start' => '70901682',
'end' => '70908113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1A-004'
),
'ENST00000504458' => array(
'start' => '70900774',
'end' => '70905541',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-003'
),
'ENST00000507348' => array(
'start' => '70900978',
'end' => '70908115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-007'
),
'ENST00000511162' => array(
'start' => '70900669',
'end' => '70901921',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-009'
),
'ENST00000512649' => array(
'start' => '70900994',
'end' => '70917521',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-006'
),
'ENST00000512868' => array(
'start' => '70900981',
'end' => '70917134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-005'
),
'ENST00000513436' => array(
'start' => '70900764',
'end' => '70918520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-008'
),
'ENST00000351205' => array(
'start' => '70925104',
'end' => '70952006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-201'
),
'ENST00000380707' => array(
'start' => '70925030',
'end' => '70953012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-001'
),
'ENST00000503079' => array(
'start' => '70925030',
'end' => '70952347',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-008'
),
'ENST00000506163' => array(
'start' => '70925095',
'end' => '70953040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-007'
),
'ENST00000506239' => array(
'start' => '70925075',
'end' => '70953016',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-003'
),
'ENST00000507905' => array(
'start' => '70942508',
'end' => '70946079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-005'
),
'ENST00000510679' => array(
'start' => '70946089',
'end' => '70953942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SMN1-004'
),
'ENST00000513228' => array(
'start' => '70942518',
'end' => '70946274',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-009'
),
'ENST00000514951' => array(
'start' => '70925056',
'end' => '70952567',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-002'
),
'ENST00000518504' => array(
'start' => '70942472',
'end' => '70946278',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-010'
),
'ENST00000380741' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-201'
),
'ENST00000380742' => array(
'start' => '70049664',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-002'
),
'ENST00000380743' => array(
'start' => '70049612',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-001'
),
'ENST00000503678' => array(
'start' => '70063411',
'end' => '70070755',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-006'
),
'ENST00000505346' => array(
'start' => '70067099',
'end' => '70076927',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-007'
),
'ENST00000506734' => array(
'start' => '70049657',
'end' => '70077596',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-003'
),
'ENST00000507458' => array(
'start' => '70070664',
'end' => '70078522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-005'
),
'ENST00000508258' => array(
'start' => '70069233',
'end' => '70070753',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-014'
),
'ENST00000509805' => array(
'start' => '70067094',
'end' => '70070849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-011'
),
'ENST00000511812' => array(
'start' => '70049638',
'end' => '70076706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-004'
),
'ENST00000511873' => array(
'start' => '70067084',
'end' => '70070654',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-012'
),
'ENST00000514914' => array(
'start' => '70067279',
'end' => '70077251',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-013'
),
'ENST00000614240' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-202'
),
'ENST00000380750' => array(
'start' => '70025269',
'end' => '70043113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-001'
),
'ENST00000380751' => array(
'start' => '70025247',
'end' => '70032696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-004'
),
'ENST00000503931' => array(
'start' => '70025356',
'end' => '70030122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-008'
),
'ENST00000506542' => array(
'start' => '70025373',
'end' => '70043103',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-002'
),
'ENST00000507177' => array(
'start' => '70025563',
'end' => '70026515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-005'
),
'ENST00000513144' => array(
'start' => '70026264',
'end' => '70032694',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1B-009'
),
'ENST00000514285' => array(
'start' => '70025587',
'end' => '70032493',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-006'
),
'ENST00000515588' => array(
'start' => '70025534',
'end' => '70042008',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-007'
),
'ENSMUST00000022145' => array(
'start' => '100108012',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-001'
),
'ENSMUST00000129014' => array(
'start' => '100108155',
'end' => '100114571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-006'
),
'ENSMUST00000132053' => array(
'start' => '100108085',
'end' => '100111009',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-002'
),
'ENSMUST00000142155' => array(
'start' => '100107997',
'end' => '100114233',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-003'
),
'ENSMUST00000151821' => array(
'start' => '100108341',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-004'
),
'ENSMUST00000152286' => array(
'start' => '100108396',
'end' => '100114231',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-005'
),
'ENSMUST00000022147' => array(
'start' => '100124852',
'end' => '100137690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-001'
),
'ENSMUST00000091321' => array(
'start' => '100124894',
'end' => '100137480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-003'
),
'ENSMUST00000125572' => array(
'start' => '100126125',
'end' => '100126935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-007'
),
'ENSMUST00000134514' => array(
'start' => '100124858',
'end' => '100127142',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-002'
),
'ENSMUST00000135355' => array(
'start' => '100135393',
'end' => '100137450',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-010'
),
'ENSMUST00000140745' => array(
'start' => '100124858',
'end' => '100127812',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Smn1-006'
),
'ENSMUST00000143937' => array(
'start' => '100124924',
'end' => '100131174',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-008'
),
'ENSMUST00000147306' => array(
'start' => '100131003',
'end' => '100137690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-005'
),
'ENSMUST00000151389' => array(
'start' => '100127875',
'end' => '100128630',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-009'
),
'ENSMUST00000180822' => array(
'start' => '100108035',
'end' => '100108337',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-201'
),
'ENSMUST00000191393' => array(
'start' => '100106795',
'end' => '100108339',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-001'
)
)
$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_0004ZD_0001' => array(
'genes_in_region' => array(
'ENSG00000172058' => 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 => 'Adipose',
(int) 14 => 'Lung',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Bladder',
(int) 44 => 'Brain',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Colon',
(int) 60 => 'Heart',
(int) 61 => 'Kidney',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Ovary',
(int) 66 => 'Placenta',
(int) 67 => 'Testis'
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000021643' => array(
[maximum depth reached]
),
'ENSMUSG00000021645' => 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 => 'Heart',
(int) 15 => 'Brain',
(int) 16 => 'Muscle',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Testis',
(int) 20 => 'Breast',
(int) 21 => 'Ovary',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Placenta',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adrenal',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0002',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '70025247',
'seq_end' => '70078522',
'region_length' => '53275',
'region_type' => 'CGP',
'el_id' => 'ENSG00000205572-ENSG00000205571'
)
)
$gene_el = array(
'ENST00000317633' => array(
'Adipose' => array(
'average_FPKM' => '0.012',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.146',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.186',
'stddev_FPKM' => '0.04'
),
'Breast' => array(
'average_FPKM' => '0.206',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.206',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.176',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.029',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.208',
'stddev_FPKM' => '0.09'
),
'Muscle' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.059',
'stddev_FPKM' => '0.02'
),
'Placenta' => array(
'average_FPKM' => '0.073',
'stddev_FPKM' => '0.02'
),
'Testis' => array(
'average_FPKM' => '0.257',
'stddev_FPKM' => '0.19'
)
),
'ENST00000354833' => array(),
'ENST00000503509' => array(),
'ENST00000504458' => array(),
'ENST00000507348' => array(),
'ENST00000511162' => array(),
'ENST00000512649' => array(
'Adipose' => array(
'average_FPKM' => '0.017',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.293',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.046',
'stddev_FPKM' => '0.00'
)
),
'ENST00000512868' => array(),
'ENST00000513436' => array()
)
$gene_key = 'ENSG00000172058'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000513436'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_0004ZD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000172058' => 'small EDRK-rich factor 1A (telomeric)',
'ENSG00000172062' => 'survival of motor neuron 1, telomeric',
'ENSG00000205571' => 'survival of motor neuron 2, centromeric',
'ENSG00000205572' => 'small EDRK-rich factor 1B (centromeric)',
'ENSMUSG00000021643' => 'small EDRK-rich factor 1',
'ENSMUSG00000021645' => 'survival motor neuron 1',
'ENSMUSG00000097022' => 'cDNA sequence BC001981'
),
'gene_name_arr' => array(
'ENSG00000172058' => 'SERF1A',
'ENSG00000172062' => 'SMN1',
'ENSG00000205571' => 'SMN2',
'ENSG00000205572' => 'SERF1B',
'ENSMUSG00000021643' => 'Serf1',
'ENSMUSG00000021645' => 'Smn1',
'ENSMUSG00000097022' => 'BC001981'
),
'accession_table' => array(
(int) 0 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 1 => array(
'region_elements' => array(
[maximum depth reached]
)
),
(int) 2 => array(
'region_elements' => array(
[maximum depth reached]
)
)
),
'all_tissues' => array(
(int) 0 => 'Adipose',
(int) 10 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 27 => 'Brain',
(int) 43 => 'Breast',
(int) 58 => 'Colon',
(int) 72 => 'Heart',
(int) 88 => 'Kidney',
(int) 101 => 'Liver',
(int) 112 => 'Lung',
(int) 126 => 'Muscle',
(int) 139 => 'Ovary',
(int) 158 => 'Placenta',
(int) 174 => '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) 57,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000317633' => array(
'start' => '70900665',
'end' => '70908375',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-001'
),
'ENST00000354833' => array(
'start' => '70900687',
'end' => '70918530',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-002'
),
'ENST00000503509' => array(
'start' => '70901682',
'end' => '70908113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1A-004'
),
'ENST00000504458' => array(
'start' => '70900774',
'end' => '70905541',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-003'
),
'ENST00000507348' => array(
'start' => '70900978',
'end' => '70908115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-007'
),
'ENST00000511162' => array(
'start' => '70900669',
'end' => '70901921',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-009'
),
'ENST00000512649' => array(
'start' => '70900994',
'end' => '70917521',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-006'
),
'ENST00000512868' => array(
'start' => '70900981',
'end' => '70917134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-005'
),
'ENST00000513436' => array(
'start' => '70900764',
'end' => '70918520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-008'
),
'ENST00000351205' => array(
'start' => '70925104',
'end' => '70952006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-201'
),
'ENST00000380707' => array(
'start' => '70925030',
'end' => '70953012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-001'
),
'ENST00000503079' => array(
'start' => '70925030',
'end' => '70952347',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-008'
),
'ENST00000506163' => array(
'start' => '70925095',
'end' => '70953040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-007'
),
'ENST00000506239' => array(
'start' => '70925075',
'end' => '70953016',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-003'
),
'ENST00000507905' => array(
'start' => '70942508',
'end' => '70946079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-005'
),
'ENST00000510679' => array(
'start' => '70946089',
'end' => '70953942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SMN1-004'
),
'ENST00000513228' => array(
'start' => '70942518',
'end' => '70946274',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-009'
),
'ENST00000514951' => array(
'start' => '70925056',
'end' => '70952567',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-002'
),
'ENST00000518504' => array(
'start' => '70942472',
'end' => '70946278',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-010'
),
'ENST00000380741' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-201'
),
'ENST00000380742' => array(
'start' => '70049664',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-002'
),
'ENST00000380743' => array(
'start' => '70049612',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-001'
),
'ENST00000503678' => array(
'start' => '70063411',
'end' => '70070755',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-006'
),
'ENST00000505346' => array(
'start' => '70067099',
'end' => '70076927',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-007'
),
'ENST00000506734' => array(
'start' => '70049657',
'end' => '70077596',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-003'
),
'ENST00000507458' => array(
'start' => '70070664',
'end' => '70078522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-005'
),
'ENST00000508258' => array(
'start' => '70069233',
'end' => '70070753',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-014'
),
'ENST00000509805' => array(
'start' => '70067094',
'end' => '70070849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-011'
),
'ENST00000511812' => array(
'start' => '70049638',
'end' => '70076706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-004'
),
'ENST00000511873' => array(
'start' => '70067084',
'end' => '70070654',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-012'
),
'ENST00000514914' => array(
'start' => '70067279',
'end' => '70077251',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-013'
),
'ENST00000614240' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-202'
),
'ENST00000380750' => array(
'start' => '70025269',
'end' => '70043113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-001'
),
'ENST00000380751' => array(
'start' => '70025247',
'end' => '70032696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-004'
),
'ENST00000503931' => array(
'start' => '70025356',
'end' => '70030122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-008'
),
'ENST00000506542' => array(
'start' => '70025373',
'end' => '70043103',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-002'
),
'ENST00000507177' => array(
'start' => '70025563',
'end' => '70026515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-005'
),
'ENST00000513144' => array(
'start' => '70026264',
'end' => '70032694',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1B-009'
),
'ENST00000514285' => array(
'start' => '70025587',
'end' => '70032493',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-006'
),
'ENST00000515588' => array(
'start' => '70025534',
'end' => '70042008',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-007'
),
'ENSMUST00000022145' => array(
'start' => '100108012',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-001'
),
'ENSMUST00000129014' => array(
'start' => '100108155',
'end' => '100114571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-006'
),
'ENSMUST00000132053' => array(
'start' => '100108085',
'end' => '100111009',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-002'
),
'ENSMUST00000142155' => array(
'start' => '100107997',
'end' => '100114233',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-003'
),
'ENSMUST00000151821' => array(
'start' => '100108341',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-004'
),
'ENSMUST00000152286' => array(
'start' => '100108396',
'end' => '100114231',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-005'
),
'ENSMUST00000022147' => array(
'start' => '100124852',
'end' => '100137690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-001'
),
'ENSMUST00000091321' => array(
'start' => '100124894',
'end' => '100137480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-003'
),
'ENSMUST00000125572' => array(
'start' => '100126125',
'end' => '100126935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-007'
),
'ENSMUST00000134514' => array(
'start' => '100124858',
'end' => '100127142',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-002'
),
'ENSMUST00000135355' => array(
'start' => '100135393',
'end' => '100137450',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-010'
),
'ENSMUST00000140745' => array(
'start' => '100124858',
'end' => '100127812',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Smn1-006'
),
'ENSMUST00000143937' => array(
'start' => '100124924',
'end' => '100131174',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-008'
),
'ENSMUST00000147306' => array(
'start' => '100131003',
'end' => '100137690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-005'
),
'ENSMUST00000151389' => array(
'start' => '100127875',
'end' => '100128630',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-009'
),
'ENSMUST00000180822' => array(
'start' => '100108035',
'end' => '100108337',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-201'
),
'ENSMUST00000191393' => array(
'start' => '100106795',
'end' => '100108339',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-001'
)
),
'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_0004ZD_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_0004ZD_0001' => array(
'genes_in_region' => array(
'ENSG00000172058' => 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 => 'Adipose',
(int) 14 => 'Lung',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Bladder',
(int) 44 => 'Brain',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Colon',
(int) 60 => 'Heart',
(int) 61 => 'Kidney',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Ovary',
(int) 66 => 'Placenta',
(int) 67 => 'Testis'
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000021643' => array(
[maximum depth reached]
),
'ENSMUSG00000021645' => 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 => 'Heart',
(int) 15 => 'Brain',
(int) 16 => 'Muscle',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Testis',
(int) 20 => 'Breast',
(int) 21 => 'Ovary',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Placenta',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adrenal',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary'
)
)
)
$gene_desc_arr = array(
'ENSG00000172058' => 'small EDRK-rich factor 1A (telomeric)',
'ENSG00000172062' => 'survival of motor neuron 1, telomeric',
'ENSG00000205571' => 'survival of motor neuron 2, centromeric',
'ENSG00000205572' => 'small EDRK-rich factor 1B (centromeric)',
'ENSMUSG00000021643' => 'small EDRK-rich factor 1',
'ENSMUSG00000021645' => 'survival motor neuron 1',
'ENSMUSG00000097022' => 'cDNA sequence BC001981'
)
$gene_name_arr = array(
'ENSG00000172058' => 'SERF1A',
'ENSG00000172062' => 'SMN1',
'ENSG00000205571' => 'SMN2',
'ENSG00000205572' => 'SERF1B',
'ENSMUSG00000021643' => 'Serf1',
'ENSMUSG00000021645' => 'Smn1',
'ENSMUSG00000097022' => 'BC001981'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0001',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '70900665',
'seq_end' => '70953942',
'region_length' => '53277',
'region_type' => 'CGP',
'el_id' => 'ENSG00000172058-ENSG00000172062'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0002',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '70025247',
'seq_end' => '70078522',
'region_length' => '53275',
'region_type' => 'CGP',
'el_id' => 'ENSG00000205572-ENSG00000205571'
)
),
(int) 2 => array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0003',
'tax_id' => '10090',
'chromosome' => '13',
'seq_start' => '100107997',
'seq_end' => '100137690',
'region_length' => '29693',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000021643-ENSMUSG00000021645'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 10 => 'Adrenal',
(int) 21 => 'Bladder',
(int) 27 => 'Brain',
(int) 43 => 'Breast',
(int) 58 => 'Colon',
(int) 72 => 'Heart',
(int) 88 => 'Kidney',
(int) 101 => 'Liver',
(int) 112 => 'Lung',
(int) 126 => 'Muscle',
(int) 139 => 'Ovary',
(int) 158 => 'Placenta',
(int) 174 => '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) 57
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000317633' => array(
'start' => '70900665',
'end' => '70908375',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-001'
),
'ENST00000354833' => array(
'start' => '70900687',
'end' => '70918530',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-002'
),
'ENST00000503509' => array(
'start' => '70901682',
'end' => '70908113',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1A-004'
),
'ENST00000504458' => array(
'start' => '70900774',
'end' => '70905541',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-003'
),
'ENST00000507348' => array(
'start' => '70900978',
'end' => '70908115',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-007'
),
'ENST00000511162' => array(
'start' => '70900669',
'end' => '70901921',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-009'
),
'ENST00000512649' => array(
'start' => '70900994',
'end' => '70917521',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-006'
),
'ENST00000512868' => array(
'start' => '70900981',
'end' => '70917134',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-005'
),
'ENST00000513436' => array(
'start' => '70900764',
'end' => '70918520',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1A-008'
),
'ENST00000351205' => array(
'start' => '70925104',
'end' => '70952006',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-201'
),
'ENST00000380707' => array(
'start' => '70925030',
'end' => '70953012',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-001'
),
'ENST00000503079' => array(
'start' => '70925030',
'end' => '70952347',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-008'
),
'ENST00000506163' => array(
'start' => '70925095',
'end' => '70953040',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-007'
),
'ENST00000506239' => array(
'start' => '70925075',
'end' => '70953016',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-003'
),
'ENST00000507905' => array(
'start' => '70942508',
'end' => '70946079',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN1-005'
),
'ENST00000510679' => array(
'start' => '70946089',
'end' => '70953942',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SMN1-004'
),
'ENST00000513228' => array(
'start' => '70942518',
'end' => '70946274',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-009'
),
'ENST00000514951' => array(
'start' => '70925056',
'end' => '70952567',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN1-002'
),
'ENST00000518504' => array(
'start' => '70942472',
'end' => '70946278',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN1-010'
),
'ENST00000380741' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-201'
),
'ENST00000380742' => array(
'start' => '70049664',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-002'
),
'ENST00000380743' => array(
'start' => '70049612',
'end' => '70077592',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-001'
),
'ENST00000503678' => array(
'start' => '70063411',
'end' => '70070755',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-006'
),
'ENST00000505346' => array(
'start' => '70067099',
'end' => '70076927',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-007'
),
'ENST00000506734' => array(
'start' => '70049657',
'end' => '70077596',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-003'
),
'ENST00000507458' => array(
'start' => '70070664',
'end' => '70078522',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-005'
),
'ENST00000508258' => array(
'start' => '70069233',
'end' => '70070753',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-014'
),
'ENST00000509805' => array(
'start' => '70067094',
'end' => '70070849',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-011'
),
'ENST00000511812' => array(
'start' => '70049638',
'end' => '70076706',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-004'
),
'ENST00000511873' => array(
'start' => '70067084',
'end' => '70070654',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'SMN2-012'
),
'ENST00000514914' => array(
'start' => '70067279',
'end' => '70077251',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SMN2-013'
),
'ENST00000614240' => array(
'start' => '70049686',
'end' => '70076586',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SMN2-202'
),
'ENST00000380750' => array(
'start' => '70025269',
'end' => '70043113',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-001'
),
'ENST00000380751' => array(
'start' => '70025247',
'end' => '70032696',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-004'
),
'ENST00000503931' => array(
'start' => '70025356',
'end' => '70030122',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-008'
),
'ENST00000506542' => array(
'start' => '70025373',
'end' => '70043103',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-002'
),
'ENST00000507177' => array(
'start' => '70025563',
'end' => '70026515',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-005'
),
'ENST00000513144' => array(
'start' => '70026264',
'end' => '70032694',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'SERF1B-009'
),
'ENST00000514285' => array(
'start' => '70025587',
'end' => '70032493',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'SERF1B-006'
),
'ENST00000515588' => array(
'start' => '70025534',
'end' => '70042008',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'SERF1B-007'
),
'ENSMUST00000022145' => array(
'start' => '100108012',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-001'
),
'ENSMUST00000129014' => array(
'start' => '100108155',
'end' => '100114571',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-006'
),
'ENSMUST00000132053' => array(
'start' => '100108085',
'end' => '100111009',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-002'
),
'ENSMUST00000142155' => array(
'start' => '100107997',
'end' => '100114233',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-003'
),
'ENSMUST00000151821' => array(
'start' => '100108341',
'end' => '100114238',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-004'
),
'ENSMUST00000152286' => array(
'start' => '100108396',
'end' => '100114231',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Serf1-005'
),
'ENSMUST00000022147' => array(
'start' => '100124852',
'end' => '100137690',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-001'
),
'ENSMUST00000091321' => array(
'start' => '100124894',
'end' => '100137480',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-003'
),
'ENSMUST00000125572' => array(
'start' => '100126125',
'end' => '100126935',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-007'
),
'ENSMUST00000134514' => array(
'start' => '100124858',
'end' => '100127142',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-002'
),
'ENSMUST00000135355' => array(
'start' => '100135393',
'end' => '100137450',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-010'
),
'ENSMUST00000140745' => array(
'start' => '100124858',
'end' => '100127812',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'Smn1-006'
),
'ENSMUST00000143937' => array(
'start' => '100124924',
'end' => '100131174',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Smn1-008'
),
'ENSMUST00000147306' => array(
'start' => '100131003',
'end' => '100137690',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-005'
),
'ENSMUST00000151389' => array(
'start' => '100127875',
'end' => '100128630',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Smn1-009'
),
'ENSMUST00000180822' => array(
'start' => '100108035',
'end' => '100108337',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-201'
),
'ENSMUST00000191393' => array(
'start' => '100106795',
'end' => '100108339',
'transcript_biotype' => 'antisense',
'transcript_name' => 'BC001981-001'
)
)
$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_0004ZD_0001' => array(
'genes_in_region' => array(
'ENSG00000172058' => 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 => 'Adipose',
(int) 14 => 'Lung',
(int) 15 => 'Muscle',
(int) 16 => 'Ovary',
(int) 17 => 'Testis',
(int) 18 => 'Adipose',
(int) 19 => 'Adrenal',
(int) 20 => 'Bladder',
(int) 21 => 'Brain',
(int) 22 => 'Colon',
(int) 23 => 'Heart',
(int) 24 => 'Kidney',
(int) 25 => 'Liver',
(int) 26 => 'Muscle',
(int) 27 => 'Ovary',
(int) 28 => 'Placenta',
(int) 29 => 'Testis',
(int) 30 => 'Adipose',
(int) 31 => 'Adrenal',
(int) 32 => 'Brain',
(int) 33 => 'Breast',
(int) 34 => 'Colon',
(int) 35 => 'Heart',
(int) 36 => 'Kidney',
(int) 37 => 'Liver',
(int) 38 => 'Lung',
(int) 39 => 'Muscle',
(int) 40 => 'Ovary',
(int) 41 => 'Placenta',
(int) 42 => 'Testis',
(int) 43 => 'Bladder',
(int) 44 => 'Brain',
(int) 45 => 'Breast',
(int) 46 => 'Colon',
(int) 47 => 'Heart',
(int) 48 => 'Kidney',
(int) 49 => 'Liver',
(int) 50 => 'Lung',
(int) 51 => 'Muscle',
(int) 52 => 'Ovary',
(int) 53 => 'Placenta',
(int) 54 => 'Adipose',
(int) 55 => 'Adrenal',
(int) 56 => 'Bladder',
(int) 57 => 'Brain',
(int) 58 => 'Breast',
(int) 59 => 'Colon',
(int) 60 => 'Heart',
(int) 61 => 'Kidney',
(int) 62 => 'Liver',
(int) 63 => 'Lung',
(int) 64 => 'Muscle',
(int) 65 => 'Ovary',
(int) 66 => 'Placenta',
(int) 67 => 'Testis'
)
),
'CIL_0004ZD_0003' => array(
'genes_in_region' => array(
'ENSMUSG00000021643' => array(
[maximum depth reached]
),
'ENSMUSG00000021645' => 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 => 'Heart',
(int) 15 => 'Brain',
(int) 16 => 'Muscle',
(int) 17 => 'Ovary',
(int) 18 => 'Placenta',
(int) 19 => 'Testis',
(int) 20 => 'Breast',
(int) 21 => 'Ovary',
(int) 22 => 'Ovary',
(int) 23 => 'Placenta',
(int) 24 => 'Adipose',
(int) 25 => 'Adrenal',
(int) 26 => 'Bladder',
(int) 27 => 'Brain',
(int) 28 => 'Breast',
(int) 29 => 'Colon',
(int) 30 => 'Heart',
(int) 31 => 'Kidney',
(int) 32 => 'Liver',
(int) 33 => 'Lung',
(int) 34 => 'Muscle',
(int) 35 => 'Ovary',
(int) 36 => 'Placenta',
(int) 37 => 'Testis',
(int) 38 => 'Brain',
(int) 39 => 'Breast',
(int) 40 => 'Heart',
(int) 41 => 'Kidney',
(int) 42 => 'Liver',
(int) 43 => 'Lung',
(int) 44 => 'Placenta',
(int) 45 => 'Brain',
(int) 46 => 'Heart',
(int) 47 => 'Muscle',
(int) 48 => 'Ovary',
(int) 49 => 'Placenta',
(int) 50 => 'Testis',
(int) 51 => 'Adrenal',
(int) 52 => 'Breast',
(int) 53 => 'Colon',
(int) 54 => 'Lung',
(int) 55 => 'Ovary'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_0004ZD_0002',
'tax_id' => '9606',
'chromosome' => '5',
'seq_start' => '70025247',
'seq_end' => '70078522',
'region_length' => '53275',
'region_type' => 'CGP',
'el_id' => 'ENSG00000205572-ENSG00000205571'
)
)
$gene_el = array(
'ENST00000317633' => array(
'Adipose' => array(
'average_FPKM' => '0.012',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.146',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.186',
'stddev_FPKM' => '0.04'
),
'Breast' => array(
'average_FPKM' => '0.206',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.206',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.078',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.176',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.029',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.208',
'stddev_FPKM' => '0.09'
),
'Muscle' => array(
'average_FPKM' => '0.094',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.059',
'stddev_FPKM' => '0.02'
),
'Placenta' => array(
'average_FPKM' => '0.073',
'stddev_FPKM' => '0.02'
),
'Testis' => array(
'average_FPKM' => '0.257',
'stddev_FPKM' => '0.19'
)
),
'ENST00000354833' => array(),
'ENST00000503509' => array(),
'ENST00000504458' => array(),
'ENST00000507348' => array(),
'ENST00000511162' => array(),
'ENST00000512649' => array(
'Adipose' => array(
'average_FPKM' => '0.017',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.293',
'stddev_FPKM' => '0.00'
),
'Muscle' => array(
'average_FPKM' => '0.072',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.037',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.046',
'stddev_FPKM' => '0.00'
)
),
'ENST00000512868' => array(),
'ENST00000513436' => array()
)
$gene_key = 'ENSG00000172058'
$is_first = false
$tran_el = array()
$tran_key = 'ENST00000513436'
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
(SERF1A)