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Coexpression cluster:C1662: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148900194999617!CHD2#1106;4:8.27521826729349:0.000402837356710173:0.0038768826665549!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298674450479702!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287591051242279!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.0057261601502522!ELK4#2005;3:9.74140899508082:0.0021255865657434:0.0122865915065129!ETS1#2113;4:7.78300873776187:0.000512103594768887:0.00443957726687705!FOS#2353;3:5.39877318533664:0.0115389531727874:0.0421871011136578!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109048193454674!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.0329436853908059!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0221953274952426!NFYA#4800;3:11.0553484198983:0.00147089290764443:0.00941059693589048!NFYB#4801;3:10.0558759521219:0.00193816560672546:0.0113866275412499!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127741547470495!PBX3#5090;3:13.1487076120465:0.000886046932280843:0.00660230133850449!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232395235482192!SP2#6668;4:20.9228243950757:1.03516506540382e-05:0.000269269250973125!SREBF1#6720;2:18.8023397761953:0.00433531272958737:0.0205769735577793!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135190896205419!TCF12#6938;4:8.50757192174914:0.000361421557849226:0.00361106917442029!THAP1#55145;2:12.5476578411405:0.00952843466738653:0.0358867720240599!USF2#7392;4:10.3937579080557:0.000164617972868753:0.00202622704401175!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00352493116728589!ZBTB33#10009;2:12.6658900119925:0.00935701605965159:0.0353380125932578
|tf_chipseq_enrich=CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148900194999617!CHD2#1106;4:8.27521826729349:0.000402837356710173:0.0038768826665549!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298674450479702!EGR1#1958;4:3.99054327584811:0.006780098300144:0.0287591051242279!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.0057261601502522!ELK4#2005;3:9.74140899508082:0.0021255865657434:0.0122865915065129!ETS1#2113;4:7.78300873776187:0.000512103594768887:0.00443957726687705!FOS#2353;3:5.39877318533664:0.0115389531727874:0.0421871011136578!GABPB1#2553;4:5.65414706894574:0.00177669650209667:0.0109048193454674!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.0329436853908059!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0221953274952426!NFYA#4800;3:11.0553484198983:0.00147089290764443:0.00941059693589048!NFYB#4801;3:10.0558759521219:0.00193816560672546:0.0113866275412499!PAX5#5079;4:5.33565242494226:0.00222338958618779:0.0127741547470495!PBX3#5090;3:13.1487076120465:0.000886046932280843:0.00660230133850449!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232395235482192!SP2#6668;4:20.9228243950757:1.03516506540382e-05:0.000269269250973125!SREBF1#6720;2:18.8023397761953:0.00433531272958737:0.0205769735577793!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135190896205419!TCF12#6938;4:8.50757192174914:0.000361421557849226:0.00361106917442029!THAP1#55145;2:12.5476578411405:0.00952843466738653:0.0358867720240599!USF2#7392;4:10.3937579080557:0.000164617972868753:0.00202622704401175!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00352493116728589!ZBTB33#10009;2:12.6658900119925:0.00935701605965159:0.0353380125932578
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1662_Eosinophils_Dendritic_Neutrophils_Whole_renal_splenic_giant



Phase1 CAGE Peaks

Hg19::chr12:129308446..129308453,-p7@SLC15A4
Hg19::chr12:129308487..129308588,-p1@SLC15A4
Hg19::chr3:13057835..13057855,-p@chr3:13057835..13057855
-
Hg19::chr3:44552063..44552064,-p4@ZNF852
Hg19::chr6:42897306..42897321,+p5@CNPY3


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:0006857oligopeptide transport0.00350288472860002
GO:0015833peptide transport0.00401801483574708



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
leukocyte4.89e-56136
nongranular leukocyte2.35e-49115
hematopoietic stem cell9.68e-42168
angioblastic mesenchymal cell9.68e-42168
hematopoietic lineage restricted progenitor cell1.40e-39120
myeloid leukocyte1.61e-3872
hematopoietic cell2.49e-38177
classical monocyte4.22e-3842
CD14-positive, CD16-negative classical monocyte4.22e-3842
defensive cell5.71e-3648
phagocyte5.71e-3648
hematopoietic oligopotent progenitor cell7.71e-36161
hematopoietic multipotent progenitor cell7.71e-36161
monopoietic cell1.26e-3159
monocyte1.26e-3159
monoblast1.26e-3159
promonocyte1.26e-3159
macrophage dendritic cell progenitor3.65e-3061
myeloid lineage restricted progenitor cell6.66e-2766
granulocyte monocyte progenitor cell2.61e-2667
stuff accumulating cell7.85e-2187
myeloid cell1.63e-20108
common myeloid progenitor1.63e-20108
lymphocyte of B lineage7.49e-1624
pro-B cell7.49e-1624
lymphocyte2.60e-1453
common lymphoid progenitor2.60e-1453
granulocyte5.64e-148
intermediate monocyte8.25e-149
CD14-positive, CD16-positive monocyte8.25e-149
lymphoid lineage restricted progenitor cell1.72e-1352
nucleate cell1.72e-1355
mesenchymal cell7.76e-12354
motile cell1.09e-11386
connective tissue cell3.69e-11361
blood cell1.38e-0911
stem cell9.34e-09441
multi fate stem cell1.23e-07427
somatic stem cell1.30e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.37e-3298
blood island1.37e-3298
hemolymphoid system3.86e-29108
immune system2.61e-2593
bone marrow2.97e-2476
bone element1.62e-2182
skeletal element1.30e-1990
skeletal system2.09e-17100
lateral plate mesoderm1.58e-11203
connective tissue3.18e-11371
musculoskeletal system3.58e-07167


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#90545.068961261570110.002709998091280770.0148900194999617
CHD2#110648.275218267293490.0004028373567101730.0038768826665549
E2F1#186943.925911371903460.007214984547106360.0298674450479702
EGR1#195843.990543275848110.0067800983001440.0287591051242279
ELF1#199754.258097958807540.0007142416939776840.0057261601502522
ELK4#200539.741408995080820.00212558656574340.0122865915065129
ETS1#211347.783008737761870.0005121035947688870.00443957726687705
FOS#235335.398773185336640.01153895317278740.0421871011136578
GABPB1#255345.654147068945740.001776696502096670.0109048193454674
MXI1#460135.976942977255580.008653004889366880.0329436853908059
NFKB1#479044.390450739355070.004707732692524960.0221953274952426
NFYA#4800311.05534841989830.001470892907644430.00941059693589048
NFYB#4801310.05587595212190.001938165606725460.0113866275412499
PAX5#507945.335652424942260.002223389586187790.0127741547470495
PBX3#5090313.14870761204650.0008860469322808430.00660230133850449
SIN3A#2594244.327107781452110.004977052855762880.0232395235482192
SP2#6668420.92282439507571.03516506540382e-050.000269269250973125
SREBF1#6720218.80233977619530.004335312729587370.0205769735577793
TAF1#687253.343046285745290.002394600090870310.0135190896205419
TCF12#693848.507571921749140.0003614215578492260.00361106917442029
THAP1#55145212.54765784114050.009528434667386530.0358867720240599
USF2#7392410.39375790805570.0001646179728687530.00202622704401175
YY1#752854.911170749853860.00034993140821360.00352493116728589
ZBTB33#10009212.66589001199250.009357016059651590.0353380125932578



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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