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Coexpression cluster:C3846: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279478680178771!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017177688610053!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322258951135625!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915204347481439!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462373238662889!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154147415328454!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122788374821324!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000756738499678106!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128105719035506!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294548847515765!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.026965061350629!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017293397942188!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767621991097904!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276811404731117!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246552994890619!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140217290466343
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279478680178771!CTCFL#140690;3:19.7464743589744:0.000129837200555116:0.0017177688610053!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322258951135625!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00915204347481439!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462373238662889!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154147415328454!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122788374821324!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000756738499678106!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128105719035506!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294548847515765!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.026965061350629!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.017293397942188!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767621991097904!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276811404731117!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246552994890619!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140217290466343
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}}
}}

Revision as of 16:23, 26 November 2012


Full id: C3846_astrocytoma_alveolar_mesothelioma_small_mucinous_Pericytes_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:110198761..110198791,+p4@GSTM4
Hg19::chr1:110198920..110198942,+p3@GSTM4
Hg19::chr1:110198944..110198996,+p2@GSTM4


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
organ system subdivision2.20e-22223
adult organism2.50e-22114
central nervous system1.02e-1881
multi-tissue structure5.16e-18342
brain5.20e-1768
future brain5.20e-1768
neural tube1.08e-1656
neural rod1.08e-1656
future spinal cord1.08e-1656
neural keel1.08e-1656
regional part of nervous system9.83e-1653
regional part of brain9.83e-1653
nervous system1.29e-1589
anatomical cluster2.86e-15373
neurectoderm7.74e-1486
neural plate1.74e-1382
presumptive neural plate1.74e-1382
organ3.48e-13503
multi-cellular organism1.58e-12656
structure with developmental contribution from neural crest2.89e-11132
ectoderm-derived structure3.87e-11171
ectoderm3.87e-11171
presumptive ectoderm3.87e-11171
regional part of forebrain4.64e-1141
forebrain4.64e-1141
anterior neural tube4.64e-1141
future forebrain4.64e-1141
telencephalon2.81e-1034
brain grey matter1.04e-0934
gray matter1.04e-0934
pre-chordal neural plate1.98e-0961
ecto-epithelium2.14e-09104
anatomical group2.14e-09625
cerebral hemisphere2.17e-0932
regional part of telencephalon2.31e-0932
anatomical system2.58e-09624
embryo5.97e-09592
germ layer2.37e-08560
germ layer / neural crest2.37e-08560
embryonic tissue2.37e-08560
presumptive structure2.37e-08560
germ layer / neural crest derived structure2.37e-08560
epiblast (generic)2.37e-08560
developing anatomical structure5.19e-08581
embryonic structure6.13e-08564
organ part7.63e-08218
posterior neural tube3.72e-0715
chordal neural plate3.72e-0715
cerebral cortex4.83e-0725
pallium4.83e-0725


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0279478680178771
CTCFL#140690319.74647435897440.0001298372005551160.0017177688610053
E2F6#187635.017155731697390.00791769806886330.0322258951135625
EBF1#187938.9064668465690.00141523283560980.00915204347481439
ELF1#199734.258097958807540.01295179875054610.0462373238662889
GABPB1#255337.067683836182170.002832212825417420.0154147415328454
HNF4A#3172323.13229036295378.07584663437677e-050.00122788374821324
HNF4G#3174328.75342252644684.20470658818262e-050.000756738499678106
IRF1#365937.63716375356390.002244692747297240.0128105719035506
MYC#460935.22228187160940.007020843755740150.0294548847515765
NFKB1#479035.488063424193840.006049381815655430.026965061350629
PAX5#507936.669565531177830.003370290999677260.017293397942188
REST#597839.650028716128020.001112636247114590.00767621991097904
SIN3A#2594235.408884726815140.006318961977991520.0276811404731117
SP1#666735.69838137814090.005403962701712170.0246552994890619
ZBTB7A#5134137.35190930787590.002516255860282270.0140217290466343



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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