Notice (8): Undefined index: CIL_00023B_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_00023B_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000103248' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSG00000176692' => 'forkhead box C2 (MFH-1, mesenchyme forkhead 1)',
'ENSG00000260944' => 'FOXC2 antisense RNA 1',
'ENSG00000280278' => 'uncharacterized protein FLJ30679',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000046714' => 'forkhead box C2'
),
'gene_name_arr' => array(
'ENSG00000103248' => 'MTHFSD',
'ENSG00000176692' => 'FOXC2',
'ENSG00000260944' => 'FOXC2-AS1',
'ENSG00000280278' => 'FLJ30679',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000046714' => 'Foxc2'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 14 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 33 => 'Kidney',
(int) 37 => 'Liver',
(int) 42 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 56 => '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) 38,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000360900' => array(
'start' => '86530176',
'end' => '86555210',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-001'
),
'ENST00000381214' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-003'
),
'ENST00000543303' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-002'
),
'ENST00000546093' => array(
'start' => '86530833',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-004'
),
'ENST00000561522' => array(
'start' => '86542117',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-010'
),
'ENST00000561848' => array(
'start' => '86552038',
'end' => '86553721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MTHFSD-016'
),
'ENST00000561989' => array(
'start' => '86548067',
'end' => '86555169',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-012'
),
'ENST00000562096' => array(
'start' => '86532362',
'end' => '86542545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MTHFSD-019'
),
'ENST00000562940' => array(
'start' => '86540720',
'end' => '86554749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-005'
),
'ENST00000562994' => array(
'start' => '86542112',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-009'
),
'ENST00000564364' => array(
'start' => '86546605',
'end' => '86555154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-014'
),
'ENST00000565482' => array(
'start' => '86548488',
'end' => '86555021',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-015'
),
'ENST00000566050' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-007'
),
'ENST00000566469' => array(
'start' => '86541535',
'end' => '86554748',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-018'
),
'ENST00000567539' => array(
'start' => '86532336',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-013'
),
'ENST00000568037' => array(
'start' => '86547146',
'end' => '86555178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-017'
),
'ENST00000568798' => array(
'start' => '86542110',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-008'
),
'ENST00000569000' => array(
'start' => '86541739',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-011'
),
'ENST00000625049' => array(
'start' => '86530178',
'end' => '86533800',
'transcript_biotype' => 'TEC',
'transcript_name' => 'MTHFSD-006'
),
'ENST00000320354' => array(
'start' => '86567251',
'end' => '86569728',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXC2-001'
),
'ENST00000563280' => array(
'start' => '86565145',
'end' => '86567761',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXC2-AS1-001'
),
'ENST00000624773' => array(
'start' => '86555320',
'end' => '86557299',
'transcript_biotype' => 'TEC',
'transcript_name' => 'FLJ30679-001'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
)
),
'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_00023B_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00023B_0001' => array(
'genes_in_region' => array(
'ENSG00000103248' => array(
[maximum depth reached]
),
'ENSG00000176692' => array(
[maximum depth reached]
),
'ENSG00000280278' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Adipose',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Kidney',
(int) 23 => 'Muscle',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Colon',
(int) 30 => 'Breast',
(int) 31 => 'Liver',
(int) 32 => 'Adrenal',
(int) 33 => 'Bladder',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Ovary',
(int) 37 => 'Adipose',
(int) 38 => 'Adrenal',
(int) 39 => 'Bladder',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Ovary',
(int) 60 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000103248' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSG00000176692' => 'forkhead box C2 (MFH-1, mesenchyme forkhead 1)',
'ENSG00000260944' => 'FOXC2 antisense RNA 1',
'ENSG00000280278' => 'uncharacterized protein FLJ30679',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000046714' => 'forkhead box C2'
)
$gene_name_arr = array(
'ENSG00000103248' => 'MTHFSD',
'ENSG00000176692' => 'FOXC2',
'ENSG00000260944' => 'FOXC2-AS1',
'ENSG00000280278' => 'FLJ30679',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000046714' => 'Foxc2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00023B_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '86530176',
'seq_end' => '86569728',
'region_length' => '39552',
'region_type' => 'CGP',
'el_id' => 'ENSG00000103248-ENSG00000176692'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00023B_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121095012',
'seq_end' => '121118895',
'region_length' => '23883',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031816-ENSMUSG00000046714'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 14 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 33 => 'Kidney',
(int) 37 => 'Liver',
(int) 42 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 56 => '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) 38
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000360900' => array(
'start' => '86530176',
'end' => '86555210',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-001'
),
'ENST00000381214' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-003'
),
'ENST00000543303' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-002'
),
'ENST00000546093' => array(
'start' => '86530833',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-004'
),
'ENST00000561522' => array(
'start' => '86542117',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-010'
),
'ENST00000561848' => array(
'start' => '86552038',
'end' => '86553721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MTHFSD-016'
),
'ENST00000561989' => array(
'start' => '86548067',
'end' => '86555169',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-012'
),
'ENST00000562096' => array(
'start' => '86532362',
'end' => '86542545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MTHFSD-019'
),
'ENST00000562940' => array(
'start' => '86540720',
'end' => '86554749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-005'
),
'ENST00000562994' => array(
'start' => '86542112',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-009'
),
'ENST00000564364' => array(
'start' => '86546605',
'end' => '86555154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-014'
),
'ENST00000565482' => array(
'start' => '86548488',
'end' => '86555021',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-015'
),
'ENST00000566050' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-007'
),
'ENST00000566469' => array(
'start' => '86541535',
'end' => '86554748',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-018'
),
'ENST00000567539' => array(
'start' => '86532336',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-013'
),
'ENST00000568037' => array(
'start' => '86547146',
'end' => '86555178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-017'
),
'ENST00000568798' => array(
'start' => '86542110',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-008'
),
'ENST00000569000' => array(
'start' => '86541739',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-011'
),
'ENST00000625049' => array(
'start' => '86530178',
'end' => '86533800',
'transcript_biotype' => 'TEC',
'transcript_name' => 'MTHFSD-006'
),
'ENST00000320354' => array(
'start' => '86567251',
'end' => '86569728',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXC2-001'
),
'ENST00000563280' => array(
'start' => '86565145',
'end' => '86567761',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXC2-AS1-001'
),
'ENST00000624773' => array(
'start' => '86555320',
'end' => '86557299',
'transcript_biotype' => 'TEC',
'transcript_name' => 'FLJ30679-001'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
)
)
$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_00023B_0001' => array(
'genes_in_region' => array(
'ENSG00000103248' => array(
[maximum depth reached]
),
'ENSG00000176692' => array(
[maximum depth reached]
),
'ENSG00000280278' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Adipose',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Kidney',
(int) 23 => 'Muscle',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Colon',
(int) 30 => 'Breast',
(int) 31 => 'Liver',
(int) 32 => 'Adrenal',
(int) 33 => 'Bladder',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Ovary',
(int) 37 => 'Adipose',
(int) 38 => 'Adrenal',
(int) 39 => 'Bladder',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Ovary',
(int) 60 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00023B_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121095012',
'seq_end' => '121118895',
'region_length' => '23883',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031816-ENSMUSG00000046714'
)
)
$gene_el = array(
'ENST00000624773' => array(
'Adipose' => array(
'average_FPKM' => '0.187',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.129',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.379',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.111',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.546',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000280278'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.187',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.129',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.379',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.111',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.546',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000624773'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
Warning (2): Invalid argument supplied for foreach() [APP/View/Region/show.ctp, line 46]Code Context <tr><th colspan="2">Gene</th><th>Transcript</th><th>Position</th><th>Biotype</th></tr>
<?php foreach ($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_00023B_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
),
'gene_desc_arr' => array(
'ENSG00000103248' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSG00000176692' => 'forkhead box C2 (MFH-1, mesenchyme forkhead 1)',
'ENSG00000260944' => 'FOXC2 antisense RNA 1',
'ENSG00000280278' => 'uncharacterized protein FLJ30679',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000046714' => 'forkhead box C2'
),
'gene_name_arr' => array(
'ENSG00000103248' => 'MTHFSD',
'ENSG00000176692' => 'FOXC2',
'ENSG00000260944' => 'FOXC2-AS1',
'ENSG00000280278' => 'FLJ30679',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000046714' => 'Foxc2'
),
'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) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 14 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 33 => 'Kidney',
(int) 37 => 'Liver',
(int) 42 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 56 => '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) 38,
'longest_tissue_len' => (int) 8,
'transcript_data' => array(
'ENST00000360900' => array(
'start' => '86530176',
'end' => '86555210',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-001'
),
'ENST00000381214' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-003'
),
'ENST00000543303' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-002'
),
'ENST00000546093' => array(
'start' => '86530833',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-004'
),
'ENST00000561522' => array(
'start' => '86542117',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-010'
),
'ENST00000561848' => array(
'start' => '86552038',
'end' => '86553721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MTHFSD-016'
),
'ENST00000561989' => array(
'start' => '86548067',
'end' => '86555169',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-012'
),
'ENST00000562096' => array(
'start' => '86532362',
'end' => '86542545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MTHFSD-019'
),
'ENST00000562940' => array(
'start' => '86540720',
'end' => '86554749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-005'
),
'ENST00000562994' => array(
'start' => '86542112',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-009'
),
'ENST00000564364' => array(
'start' => '86546605',
'end' => '86555154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-014'
),
'ENST00000565482' => array(
'start' => '86548488',
'end' => '86555021',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-015'
),
'ENST00000566050' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-007'
),
'ENST00000566469' => array(
'start' => '86541535',
'end' => '86554748',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-018'
),
'ENST00000567539' => array(
'start' => '86532336',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-013'
),
'ENST00000568037' => array(
'start' => '86547146',
'end' => '86555178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-017'
),
'ENST00000568798' => array(
'start' => '86542110',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-008'
),
'ENST00000569000' => array(
'start' => '86541739',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-011'
),
'ENST00000625049' => array(
'start' => '86530178',
'end' => '86533800',
'transcript_biotype' => 'TEC',
'transcript_name' => 'MTHFSD-006'
),
'ENST00000320354' => array(
'start' => '86567251',
'end' => '86569728',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXC2-001'
),
'ENST00000563280' => array(
'start' => '86565145',
'end' => '86567761',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXC2-AS1-001'
),
'ENST00000624773' => array(
'start' => '86555320',
'end' => '86557299',
'transcript_biotype' => 'TEC',
'transcript_name' => 'FLJ30679-001'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
)
),
'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_00023B_0001' => array(
'genes_in_region' => array(
[maximum depth reached]
),
'tissues_title' => array(
[maximum depth reached]
)
)
)
)
$region_arr = array(
'CIL_00023B_0001' => array(
'genes_in_region' => array(
'ENSG00000103248' => array(
[maximum depth reached]
),
'ENSG00000176692' => array(
[maximum depth reached]
),
'ENSG00000280278' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Adipose',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Kidney',
(int) 23 => 'Muscle',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Colon',
(int) 30 => 'Breast',
(int) 31 => 'Liver',
(int) 32 => 'Adrenal',
(int) 33 => 'Bladder',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Ovary',
(int) 37 => 'Adipose',
(int) 38 => 'Adrenal',
(int) 39 => 'Bladder',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Ovary',
(int) 60 => 'Testis'
)
)
)
$gene_desc_arr = array(
'ENSG00000103248' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSG00000176692' => 'forkhead box C2 (MFH-1, mesenchyme forkhead 1)',
'ENSG00000260944' => 'FOXC2 antisense RNA 1',
'ENSG00000280278' => 'uncharacterized protein FLJ30679',
'ENSMUSG00000031816' => 'methenyltetrahydrofolate synthetase domain containing',
'ENSMUSG00000046714' => 'forkhead box C2'
)
$gene_name_arr = array(
'ENSG00000103248' => 'MTHFSD',
'ENSG00000176692' => 'FOXC2',
'ENSG00000260944' => 'FOXC2-AS1',
'ENSG00000280278' => 'FLJ30679',
'ENSMUSG00000031816' => 'Mthfsd',
'ENSMUSG00000046714' => 'Foxc2'
)
$accession_table = array(
(int) 0 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00023B_0001',
'tax_id' => '9606',
'chromosome' => '16',
'seq_start' => '86530176',
'seq_end' => '86569728',
'region_length' => '39552',
'region_type' => 'CGP',
'el_id' => 'ENSG00000103248-ENSG00000176692'
)
),
(int) 1 => array(
'region_elements' => array(
'region_element_id' => 'CIL_00023B_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121095012',
'seq_end' => '121118895',
'region_length' => '23883',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031816-ENSMUSG00000046714'
)
)
)
$all_tissues = array(
(int) 0 => 'Adipose',
(int) 3 => 'Adrenal',
(int) 6 => 'Bladder',
(int) 9 => 'Brain',
(int) 14 => 'Breast',
(int) 21 => 'Colon',
(int) 27 => 'Heart',
(int) 33 => 'Kidney',
(int) 37 => 'Liver',
(int) 42 => 'Lung',
(int) 45 => 'Muscle',
(int) 50 => 'Ovary',
(int) 56 => '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) 38
$longest_tissue_len = (int) 8
$transcript_data = array(
'ENST00000360900' => array(
'start' => '86530176',
'end' => '86555210',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-001'
),
'ENST00000381214' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-003'
),
'ENST00000543303' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-002'
),
'ENST00000546093' => array(
'start' => '86530833',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-004'
),
'ENST00000561522' => array(
'start' => '86542117',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-010'
),
'ENST00000561848' => array(
'start' => '86552038',
'end' => '86553721',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'MTHFSD-016'
),
'ENST00000561989' => array(
'start' => '86548067',
'end' => '86555169',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-012'
),
'ENST00000562096' => array(
'start' => '86532362',
'end' => '86542545',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'MTHFSD-019'
),
'ENST00000562940' => array(
'start' => '86540720',
'end' => '86554749',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-005'
),
'ENST00000562994' => array(
'start' => '86542112',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-009'
),
'ENST00000564364' => array(
'start' => '86546605',
'end' => '86555154',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-014'
),
'ENST00000565482' => array(
'start' => '86548488',
'end' => '86555021',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-015'
),
'ENST00000566050' => array(
'start' => '86531972',
'end' => '86555203',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-007'
),
'ENST00000566469' => array(
'start' => '86541535',
'end' => '86554748',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-018'
),
'ENST00000567539' => array(
'start' => '86532336',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-013'
),
'ENST00000568037' => array(
'start' => '86547146',
'end' => '86555178',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-017'
),
'ENST00000568798' => array(
'start' => '86542110',
'end' => '86555235',
'transcript_biotype' => 'nonsense_mediated_decay',
'transcript_name' => 'MTHFSD-008'
),
'ENST00000569000' => array(
'start' => '86541739',
'end' => '86555235',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'MTHFSD-011'
),
'ENST00000625049' => array(
'start' => '86530178',
'end' => '86533800',
'transcript_biotype' => 'TEC',
'transcript_name' => 'MTHFSD-006'
),
'ENST00000320354' => array(
'start' => '86567251',
'end' => '86569728',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'FOXC2-001'
),
'ENST00000563280' => array(
'start' => '86565145',
'end' => '86567761',
'transcript_biotype' => 'antisense',
'transcript_name' => 'FOXC2-AS1-001'
),
'ENST00000624773' => array(
'start' => '86555320',
'end' => '86557299',
'transcript_biotype' => 'TEC',
'transcript_name' => 'FLJ30679-001'
),
'ENSMUST00000047282' => array(
'start' => '121097940',
'end' => '121108318',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-002'
),
'ENSMUST00000116415' => array(
'start' => '121097557',
'end' => '121108327',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-001'
),
'ENSMUST00000126431' => array(
'start' => '121101176',
'end' => '121108298',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-010'
),
'ENSMUST00000128052' => array(
'start' => '121097555',
'end' => '121108295',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-003'
),
'ENSMUST00000128503' => array(
'start' => '121104475',
'end' => '121108343',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-006'
),
'ENSMUST00000133037' => array(
'start' => '121097851',
'end' => '121108392',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-005'
),
'ENSMUST00000133058' => array(
'start' => '121095012',
'end' => '121101185',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-015'
),
'ENSMUST00000134758' => array(
'start' => '121098708',
'end' => '121108288',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-011'
),
'ENSMUST00000138908' => array(
'start' => '121099008',
'end' => '121105632',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-012'
),
'ENSMUST00000139782' => array(
'start' => '121097557',
'end' => '121108310',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Mthfsd-008'
),
'ENSMUST00000140260' => array(
'start' => '121097767',
'end' => '121101593',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-013'
),
'ENSMUST00000145991' => array(
'start' => '121103852',
'end' => '121105689',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-014'
),
'ENSMUST00000149718' => array(
'start' => '121097937',
'end' => '121108379',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-004'
),
'ENSMUST00000151576' => array(
'start' => '121104099',
'end' => '121108313',
'transcript_biotype' => 'processed_transcript',
'transcript_name' => 'Mthfsd-007'
),
'ENSMUST00000156606' => array(
'start' => '121102723',
'end' => '121107643',
'transcript_biotype' => 'retained_intron',
'transcript_name' => 'Mthfsd-009'
),
'ENSMUST00000054691' => array(
'start' => '121116171',
'end' => '121118895',
'transcript_biotype' => 'protein_coding',
'transcript_name' => 'Foxc2-001'
)
)
$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_00023B_0001' => array(
'genes_in_region' => array(
'ENSG00000103248' => array(
[maximum depth reached]
),
'ENSG00000176692' => array(
[maximum depth reached]
),
'ENSG00000280278' => array(
[maximum depth reached]
)
),
'tissues_title' => array(
(int) 0 => 'Brain',
(int) 1 => 'Breast',
(int) 2 => 'Colon',
(int) 3 => 'Heart',
(int) 4 => 'Kidney',
(int) 5 => 'Liver',
(int) 6 => 'Muscle',
(int) 7 => 'Ovary',
(int) 8 => 'Testis',
(int) 9 => 'Heart',
(int) 10 => 'Adipose',
(int) 11 => 'Breast',
(int) 12 => 'Colon',
(int) 13 => 'Heart',
(int) 14 => 'Kidney',
(int) 15 => 'Liver',
(int) 16 => 'Lung',
(int) 17 => 'Ovary',
(int) 18 => 'Testis',
(int) 19 => 'Brain',
(int) 20 => 'Muscle',
(int) 21 => 'Breast',
(int) 22 => 'Kidney',
(int) 23 => 'Muscle',
(int) 24 => 'Bladder',
(int) 25 => 'Brain',
(int) 26 => 'Heart',
(int) 27 => 'Muscle',
(int) 28 => 'Ovary',
(int) 29 => 'Colon',
(int) 30 => 'Breast',
(int) 31 => 'Liver',
(int) 32 => 'Adrenal',
(int) 33 => 'Bladder',
(int) 34 => 'Breast',
(int) 35 => 'Colon',
(int) 36 => 'Ovary',
(int) 37 => 'Adipose',
(int) 38 => 'Adrenal',
(int) 39 => 'Bladder',
(int) 40 => 'Brain',
(int) 41 => 'Breast',
(int) 42 => 'Colon',
(int) 43 => 'Heart',
(int) 44 => 'Liver',
(int) 45 => 'Lung',
(int) 46 => 'Muscle',
(int) 47 => 'Ovary',
(int) 48 => 'Placenta',
(int) 49 => 'Testis',
(int) 50 => 'Adipose',
(int) 51 => 'Adrenal',
(int) 52 => 'Brain',
(int) 53 => 'Breast',
(int) 54 => 'Colon',
(int) 55 => 'Heart',
(int) 56 => 'Kidney',
(int) 57 => 'Liver',
(int) 58 => 'Lung',
(int) 59 => 'Ovary',
(int) 60 => 'Testis'
)
)
)
$accession = array(
'region_elements' => array(
'region_element_id' => 'CIL_00023B_0002',
'tax_id' => '10090',
'chromosome' => '8',
'seq_start' => '121095012',
'seq_end' => '121118895',
'region_length' => '23883',
'region_type' => 'CGP',
'el_id' => 'ENSMUSG00000031816-ENSMUSG00000046714'
)
)
$gene_el = array(
'ENST00000624773' => array(
'Adipose' => array(
'average_FPKM' => '0.187',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.129',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.379',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.111',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.546',
'stddev_FPKM' => '0.00'
)
)
)
$gene_key = 'ENSG00000280278'
$is_first = false
$tran_el = array(
'Adipose' => array(
'average_FPKM' => '0.187',
'stddev_FPKM' => '0.00'
),
'Adrenal' => array(
'average_FPKM' => '0.399',
'stddev_FPKM' => '0.00'
),
'Brain' => array(
'average_FPKM' => '0.129',
'stddev_FPKM' => '0.00'
),
'Breast' => array(
'average_FPKM' => '0.161',
'stddev_FPKM' => '0.00'
),
'Colon' => array(
'average_FPKM' => '0.379',
'stddev_FPKM' => '0.00'
),
'Heart' => array(
'average_FPKM' => '0.113',
'stddev_FPKM' => '0.00'
),
'Kidney' => array(
'average_FPKM' => '0.111',
'stddev_FPKM' => '0.00'
),
'Liver' => array(
'average_FPKM' => '0.077',
'stddev_FPKM' => '0.00'
),
'Lung' => array(
'average_FPKM' => '0.092',
'stddev_FPKM' => '0.00'
),
'Ovary' => array(
'average_FPKM' => '0.027',
'stddev_FPKM' => '0.00'
),
'Testis' => array(
'average_FPKM' => '0.546',
'stddev_FPKM' => '0.00'
)
)
$tran_key = 'ENST00000624773'
include - APP/View/Region/show.ctp, line 46
View::_evaluate() - CORE/Cake/View/View.php, line 948
View::_render() - CORE/Cake/View/View.php, line 910
View::render() - CORE/Cake/View/View.php, line 471
Controller::render() - CORE/Cake/Controller/Controller.php, line 954
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 198
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 165
[main] - APP/webroot/index.php, line 108
| Source ID |
Type |
Tax ID |
Position |
| ENSMUSG00000031816-ENSMUSG00000046714 |
CGP |
10090 |
8:121095012-121118895  |
| Gene | Transcript | Position | Biotype |
|---|
(MTHFSD)