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Coexpression cluster:C2362: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487159541447114!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106415585685879!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240416719248227!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234646339348127!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.037850964041301!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0320032762483962!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466127106304414!NFYA#4800;3:13.8191855248729:0.000613241180673451:0.00508667267638429!NFYB#4801;3:12.5698449401523:0.00081145639769735:0.00618686631034557!SP2#6668;3:19.6151478703835:0.000217100426924534:0.00248561187103391!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0280991515946019!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158606569899491!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342335725785482!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613106603761005
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487159541447114!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106415585685879!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240416719248227!FOS#2353;3:6.7484664816708:0.00503245277631794:0.0234646339348127!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.037850964041301!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0320032762483962!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466127106304414!NFYA#4800;3:13.8191855248729:0.000613241180673451:0.00508667267638429!NFYB#4801;3:12.5698449401523:0.00081145639769735:0.00618686631034557!SP2#6668;3:19.6151478703835:0.000217100426924534:0.00248561187103391!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0280991515946019!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158606569899491!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342335725785482!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613106603761005
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}}
}}

Revision as of 15:27, 26 November 2012


Full id: C2362_Neutrophils_CD14_Whole_Eosinophils_Hepatocyte_Mesenchymal_blood



Phase1 CAGE Peaks

Hg19::chr16:1993170..1993226,-p1@SEPX1
Hg19::chr16:1993230..1993248,-p2@SEPX1
Hg19::chr16:1993260..1993271,-p3@SEPX1
Hg19::chr19:1155118..1155189,-p@chr19:1155118..1155189
-


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


Uber Anatomy
Ontology termp-valuen
mesoderm4.93e-18315
mesoderm-derived structure4.93e-18315
presumptive mesoderm4.93e-18315
lateral plate mesoderm3.45e-15203
musculoskeletal system2.00e-14167
trunk2.98e-12199
mesenchyme1.17e-11160
entire embryonic mesenchyme1.17e-11160
trunk mesenchyme1.80e-10122
organism subdivision2.52e-10264
epithelial vesicle2.65e-1078
hemolymphoid system6.66e-09108
subdivision of trunk7.75e-09112
hematopoietic system1.64e-0898
blood island1.64e-0898
somite2.16e-0871
presomitic mesoderm2.16e-0871
presumptive segmental plate2.16e-0871
dermomyotome2.16e-0871
trunk paraxial mesoderm2.16e-0871
circulatory system2.80e-08112
dense mesenchyme tissue2.99e-0873
muscle tissue3.93e-0864
musculature3.93e-0864
musculature of body3.93e-0864
paraxial mesoderm5.31e-0872
presumptive paraxial mesoderm5.31e-0872
cardiovascular system6.23e-08109
multilaminar epithelium6.61e-0883
skeletal muscle tissue7.61e-0862
striated muscle tissue7.61e-0862
myotome7.61e-0862
epithelial tube8.81e-08117
multi-cellular organism1.51e-07656
unilaminar epithelium5.77e-07148
bone marrow5.84e-0776
anatomical group8.70e-07625
anatomical system9.79e-07624


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#90534.752151182721970.01386206996689490.0487159541447114
E2F1#186944.907389214879320.001724022357361790.0106415585685879
EBF1#187936.679850134926750.005184294118278910.0240416719248227
FOS#235336.74846648167080.005032452776317940.0234646339348127
GABPB1#255335.300762877136630.01012678824234270.037850964041301
IRF1#365935.727872815172930.008097114790333330.0320032762483962
MAX#414934.839416631755340.01315737137836840.0466127106304414
NFYA#4800313.81918552487290.0006132411806734510.00508667267638429
NFYB#4801312.56984494015230.000811456397697350.00618686631034557
SP2#6668319.61514787038350.0002171004269245340.00248561187103391
SPI1#668836.153242631392040.006580387113059030.0280991515946019
TCF7L2#693438.077632422353010.002978381685834620.0158606569899491
ZBTB7A#5134135.513931980906920.009038352821081090.0342335725785482
ZEB1#6935312.66632401315790.000793336075912850.00613106603761005



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.