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Coexpression cluster:C1713: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00138960583318047!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352459611363479!E2F4#1874;5:12.6680603152844:3.06319883889696e-06:0.000103399296553187!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.0032261901574704!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00330605856833571!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572791893398874!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109067422548918!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673927360511694!HMGN3#9324;4:6.54283817868047:0.0010080127776835:0.00721957526323462!IRF1#3659;5:7.6371637535639:3.84754333311872e-05:0.000723633312025187!IRF3#3661;2:18.7927808845958:0.00433962977712151:0.0205853020072123!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130620943984004!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.0329472885500962!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256754439699738!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222003384058615!NRF1#4899;3:7.32616766862654:0.00483968981711754:0.0226873901346532!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127776693441846!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00247871621392696!SMARCB1#6598;3:10.9516294686944:0.00151187284834318:0.00965149684646171!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204132476982204!SP2#6668;2:10.4614121975379:0.0135319118334714:0.04777591494459!SREBF1#6720;2:18.8023397761953:0.00433531272958737:0.0205779087472333!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.013525670031931!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918206600152897!TFAP2C#7022;4:8.64738288788818:0.000339051887817405:0.00344826566479325!USF1#7391;4:5.08919942176637:0.0026686777536004:0.0147156301957905!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00352595140785529
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}}
}}

Revision as of 15:03, 26 November 2012


Full id: C1713_Alveolar_Renal_Hodgkin_chronic_MCF7_Placental_Melanocyte



Phase1 CAGE Peaks

Hg19::chr14:104181771..104181827,-p1@XRCC3
Hg19::chr16:3030386..3030400,-p2@PKMYT1
Hg19::chr16:3030407..3030489,-p1@PKMYT1
Hg19::chr19:12917364..12917407,+p2@RNASEH2A
Hg19::chr19:14247387..14247409,-p1@ASF1B


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


GO IDGO nameFDR corrected p-value
GO:0006259DNA metabolic process0.0279660708108065



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>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell4.78e-23253
animal cell5.26e-16679
eukaryotic cell5.26e-16679
native cell2.12e-11722
embryonic cell1.63e-10250
migratory neural crest cell5.70e-0941
epithelial cell of nephron7.32e-0715
neurectodermal cell9.82e-0759
Uber Anatomy
Ontology termp-valuen
larynx2.89e-079
nephron epithelium7.32e-0715
renal tubule7.32e-0715
nephron tubule7.32e-0715
nephron7.32e-0715
uriniferous tubule7.32e-0715
nephrogenic mesenchyme7.32e-0715
Disease
Ontology termp-valuen
cancer6.75e-38235
disease of cellular proliferation5.77e-37239
cell type cancer9.89e-19143
organ system cancer8.91e-18137
hematologic cancer2.32e-1751
immune system cancer2.32e-1751
carcinoma1.96e-15106
leukemia4.45e-1439
myeloid leukemia1.40e-1031


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
CCNT2#90556.336201576962639.78880505817628e-050.00138960583318047
E2F1#186954.907389214879320.0003512818099256460.00352459611363479
E2F4#1874512.66806031528443.06319883889696e-060.000103399296553187
E2F6#187655.017155731697390.0003144978599297790.0032261901574704
EGR1#195854.988179094810140.0003237398000590710.00330605856833571
ELF1#199754.258097958807540.0007142416939776840.00572791893398874
GABPB1#255345.654147068945740.001776696502096670.0109067422548918
HEY1#2346254.040111043105710.0009288852205177990.00673927360511694
HMGN3#932446.542838178680470.00100801277768350.00721957526323462
IRF1#365957.63716375356393.84754333311872e-050.000723633312025187
IRF3#3661218.79278088459580.004339629777121510.0205853020072123
MAX#414956.452555509007128.93743970843928e-050.00130620943984004
MXI1#460135.976942977255580.008653004889366880.0329472885500962
MYC#460944.177825497287520.005691969036823440.0256754439699738
NFKB1#479044.390450739355070.004707732692524960.0222003384058615
NRF1#489937.326167668626540.004839689817117540.0226873901346532
PAX5#507945.335652424942260.002223389586187790.0127776693441846
SIN3A#2594255.408884726815140.0002159522671657270.00247871621392696
SMARCB1#6598310.95162946869440.001511872848343180.00965149684646171
SP1#666755.69838137814090.000166391843712550.00204132476982204
SP2#6668210.46141219753790.01353191183347140.04777591494459
SREBF1#6720218.80233977619530.004335312729587370.0205779087472333
TAF1#687253.343046285745290.002394600090870310.013525670031931
TBP#690853.706770687096390.001428755106721120.00918206600152897
TFAP2C#702248.647382887888180.0003390518878174050.00344826566479325
USF1#739145.089199421766370.00266867775360040.0147156301957905
YY1#752854.911170749853860.00034993140821360.00352595140785529



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.