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Coexpression cluster:C1841: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;5:24.3578017923036:1.16482472299935e-07:6.73605366806918e-06!CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000628702121763892!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322936210728603!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00573452400656022!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000389337439622114!GABPB1#2553;5:7.06768383618217:5.6685482528729e-05:0.00094874601118877!GTF2F1#2962;5:12.7396608767577:2.97806917252935e-06:0.000101113968241155!IRF4#3662;5:21.9145126867441:1.97628413609567e-07:1.07110087643848e-05!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109163580231312!JUNB#3726;5:30.6106326598211:3.71486060097063e-08:2.46490677449029e-06!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000984796876252953!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130712402423987!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.000266643544996242!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276592474605524!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00239145404362733!PAX5#5079;5:6.66956553117783:7.57493746384605e-05:0.00117046736763814!POU2F2#5452;5:9.10612405774252:1.59639992500654e-05:0.000369845633912508!SETDB1#9869;5:40.3200261780105:9.36422298056125e-09:7.149050320664e-07!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00248226269321168!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.00057469469225418!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.00022050243713115!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.013544716144411!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00919281386094426!TCF12#6938;5:10.6344649021864:7.34844389925727e-06:0.000211189909849898!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00136889109579165!USF2#7392;5:12.9921973850696:2.69963551658264e-06:9.42967336844062e-05
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}}
}}

Revision as of 15:08, 26 November 2012


Full id: C1841_melanoma_Mast_schwannoma_CD14_extraskeletal_Macrophage_giant



Phase1 CAGE Peaks

Hg19::chr1:158985457..158985468,+p12@IFI16
Hg19::chr1:158985469..158985489,+p7@IFI16
Hg19::chr1:158985493..158985535,+p4@IFI16
Hg19::chr1:158985536..158985545,+p18@IFI16
Hg19::chr1:158985553..158985574,+p14@IFI16


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>

Cell Type
Ontology termp-valuen
myeloid lineage restricted progenitor cell1.52e-2266
granulocyte monocyte progenitor cell7.08e-2267
myeloid leukocyte4.05e-2172
monopoietic cell5.60e-2059
monocyte5.60e-2059
monoblast5.60e-2059
promonocyte5.60e-2059
myeloid cell5.80e-19108
common myeloid progenitor5.80e-19108
macrophage dendritic cell progenitor1.10e-1861
defensive cell2.14e-1648
phagocyte2.14e-1648
classical monocyte6.29e-1442
CD14-positive, CD16-negative classical monocyte6.29e-1442
stuff accumulating cell3.59e-1187
hematopoietic oligopotent progenitor cell1.15e-10161
hematopoietic multipotent progenitor cell1.15e-10161
hematopoietic lineage restricted progenitor cell1.44e-09120
hematopoietic stem cell3.36e-09168
angioblastic mesenchymal cell3.36e-09168
hematopoietic cell6.87e-09177
motile cell5.19e-08386
nongranular leukocyte8.96e-08115
leukocyte1.43e-07136
mesenchymal cell2.67e-07354
Uber Anatomy
Ontology termp-valuen
immune system2.12e-2193
bone marrow2.91e-2176
bone element3.29e-1982
hemolymphoid system3.80e-18108
hematopoietic system6.24e-1898
blood island6.24e-1898
skeletal element5.02e-1790
skeletal system9.78e-14100
lateral plate mesoderm1.93e-08203


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
BATF#10538524.35780179230361.16482472299935e-076.73605366806918e-06
CEBPB#105157.971147625824823.10621793420244e-050.000628702121763892
E2F6#187655.017155731697390.0003144978599297790.00322936210728603
ELF1#199754.258097958807540.0007142416939776840.00573452400656022
FOS#235358.99795530889441.69470025615156e-050.000389337439622114
GABPB1#255357.067683836182175.6685482528729e-050.00094874601118877
GTF2F1#2962512.73966087675772.97806917252935e-060.000101113968241155
IRF4#3662521.91451268674411.97628413609567e-071.07110087643848e-05
JUN#3725512.51282919233633.25800591331781e-060.000109163580231312
JUNB#3726530.61063265982113.71486060097063e-082.46490677449029e-06
JUND#372756.994663941871035.97069468343598e-050.000984796876252953
MAX#414956.452555509007128.93743970843928e-050.00130712402423987
MXI1#460159.96157162875931.01894348670516e-050.000266643544996242
MYC#460955.22228187160940.0002573944848850610.00276592474605524
NFKB1#479055.488063424193840.0002008162847462320.00239145404362733
PAX5#507956.669565531177837.57493746384605e-050.00117046736763814
POU2F2#545259.106124057742521.59639992500654e-050.000369845633912508
SETDB1#9869540.32002617801059.36422298056125e-097.149050320664e-07
SIN3A#2594255.408884726815140.0002159522671657270.00248226269321168
SPI1#668858.204323508522732.68916109982495e-050.00057469469225418
STAT3#6774510.51946499715427.759040745861e-060.00022050243713115
TAF1#687253.343046285745290.002394600090870310.013544716144411
TBP#690853.706770687096390.001428755106721120.00919281386094426
TCF12#6938510.63446490218647.34844389925727e-060.000211189909849898
USF1#739156.361499277207969.59569864925045e-050.00136889109579165
USF2#7392512.99219738506962.69963551658264e-069.42967336844062e-05



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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