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Coexpression cluster:C1366: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:11.2315872630044:0.00159345997118423:0.0100397783500549!BATF#10538;4:16.2385345282024:3.98325915717398e-05:0.000742075638808586!BCL11A#53335;3:14.1847275518035:0.000808083184942481:0.00616880343192806!BHLHE40#8553;3:22.4359067734887:0.000210319610478028:0.00244659944293993!CCNT2#905;5:5.28016798080219:0.000510094397483253:0.00446702572352453!CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159795244826778!CHD2#1106;4:6.89601522274457:0.00111539132013599:0.00766081507850076!E2F1#1869;5:4.08949101239944:0.00174981759776199:0.0107575465088689!E2F6#1876;5:4.18096310974782:0.00157359875958697:0.0099742113766161!EBF1#1879;4:5.93764456437934:0.00197515363642171:0.0114895327299904!EGR1#1958;6:4.98817909481014:6.48943962979974e-05:0.00105486472450841!ELF1#1997;6:4.25809795880754:0.000167722477628883:0.00205186457081913!ELK4#2005;4:10.823787772312:0.000195059997301046:0.00234915487293865!FOSL2#2355;3:8.46510030228085:0.00359831563461509:0.0182217070676671!GABPB1#2553;4:4.71178922412145:0.00473005431155596:0.0222864811984387!HDAC2#3066;5:11.1796835305219:1.29408913564529e-05:0.00031681522559226!HEY1#23462;6:4.04011104310571:0.000229896855580751:0.0025300524446784!IRF1#3659;5:6.36430312796992:0.00020566751420509:0.00243949000750317!JUN#3725;3:6.25641459616817:0.00848634685095487:0.0324096090527983!JUND#3727;4:4.66310929458068:0.00491764340826023:0.0229867860142009!MYC#4609;6:5.2222818716094:4.92821127172503e-05:0.000853561288569968!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438250254073027!NFYB#4801;3:8.37989662676823:0.00370399687862904:0.0186834933594368!NRF1#4899;5:10.1752328730924:2.0585884796849e-05:0.000455405469667043!PAX5#5079;5:5.55797127598152:0.000397717619661286:0.00388561557341488!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380065467095966!SP1#6667;4:3.7989209187606:0.0105224661679851:0.0389424466377814!SPI1#6688;4:5.46954900568182:0.0026973005361414:0.0148421164749247!SREBF1#6720;2:15.6686164801628:0.00641128316580946:0.0278890417157722!TAF7#6879;3:5.71653470246196:0.0109272937988966:0.0402084218392334!TBP#6908;6:3.70677068709639:0.00038541647290796:0.00377638718585556!TCF12#6938;4:7.08964326812428:0.00100299157265771:0.00718755570583218!USF1#7391;5:5.3012493976733:0.000500332754985889:0.00441113055866717
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}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1366_Eosinophils_CD14_immature_Natural_CD34_CD8_Mast



Phase1 CAGE Peaks

Hg19::chr12:57914742..57914754,+p14@MBD6
Hg19::chr17:62971568..62971582,-p4@AMZ2P1
Hg19::chr17:62972242..62972279,+p@chr17:62972242..62972279
+
Hg19::chr20:23342363..23342382,-p@chr20:23342363..23342382
-
Hg19::chr3:5020582..5020599,+p10@BHLHE40
Hg19::chr6:31620000..31620025,+p6@APOM


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
leukocyte7.64e-44136
hematopoietic stem cell2.64e-38168
angioblastic mesenchymal cell2.64e-38168
hematopoietic cell2.22e-36177
hematopoietic oligopotent progenitor cell1.09e-33161
hematopoietic multipotent progenitor cell1.09e-33161
classical monocyte1.64e-3342
CD14-positive, CD16-negative classical monocyte1.64e-3342
nongranular leukocyte5.39e-33115
hematopoietic lineage restricted progenitor cell7.42e-33120
defensive cell1.32e-2648
phagocyte1.32e-2648
myeloid leukocyte2.60e-2672
granulocyte monocyte progenitor cell2.20e-2267
myeloid cell2.99e-21108
common myeloid progenitor2.99e-21108
macrophage dendritic cell progenitor4.86e-2161
myeloid lineage restricted progenitor cell2.07e-2066
monopoietic cell1.03e-1959
monocyte1.03e-1959
monoblast1.03e-1959
promonocyte1.03e-1959
lymphocyte1.76e-1153
common lymphoid progenitor1.76e-1153
lymphoid lineage restricted progenitor cell3.42e-1152
nucleate cell1.46e-1055
stuff accumulating cell1.69e-0987
intermediate monocyte2.09e-089
CD14-positive, CD16-positive monocyte2.09e-089
mesenchymal cell6.86e-08354
lymphocyte of B lineage1.98e-0724
pro-B cell1.98e-0724
connective tissue cell4.84e-07361
motile cell7.07e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.50e-2198
blood island1.50e-2198
bone marrow5.11e-2076
bone element1.60e-1882
immune system2.19e-1793
hemolymphoid system4.48e-17108
skeletal element2.21e-1590
skeletal system1.33e-13100


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
ATF3#467311.23158726300440.001593459971184230.0100397783500549
BATF#10538416.23853452820243.98325915717398e-050.000742075638808586
BCL11A#53335314.18472755180350.0008080831849424810.00616880343192806
BHLHE40#8553322.43590677348870.0002103196104780280.00244659944293993
CCNT2#90555.280167980802190.0005100943974832530.00446702572352453
CEBPB#105145.314098417216540.003008047293917460.0159795244826778
CHD2#110646.896015222744570.001115391320135990.00766081507850076
E2F1#186954.089491012399440.001749817597761990.0107575465088689
E2F6#187654.180963109747820.001573598759586970.0099742113766161
EBF1#187945.937644564379340.001975153636421710.0114895327299904
EGR1#195864.988179094810146.48943962979974e-050.00105486472450841
ELF1#199764.258097958807540.0001677224776288830.00205186457081913
ELK4#2005410.8237877723120.0001950599973010460.00234915487293865
FOSL2#235538.465100302280850.003598315634615090.0182217070676671
GABPB1#255344.711789224121450.004730054311555960.0222864811984387
HDAC2#3066511.17968353052191.29408913564529e-050.00031681522559226
HEY1#2346264.040111043105710.0002298968555807510.0025300524446784
IRF1#365956.364303127969920.000205667514205090.00243949000750317
JUN#372536.256414596168170.008486346850954870.0324096090527983
JUND#372744.663109294580680.004917643408260230.0229867860142009
MYC#460965.22228187160944.92821127172503e-050.000853561288569968
NFKB1#479043.658708949462560.01207927289015230.0438250254073027
NFYB#480138.379896626768230.003703996878629040.0186834933594368
NRF1#4899510.17523287309242.0585884796849e-050.000455405469667043
PAX5#507955.557971275981520.0003977176196612860.00388561557341488
POLR2A#543062.147453176558070.01019570676818780.0380065467095966
SP1#666743.79892091876060.01052246616798510.0389424466377814
SPI1#668845.469549005681820.00269730053614140.0148421164749247
SREBF1#6720215.66861648016280.006411283165809460.0278890417157722
TAF7#687935.716534702461960.01092729379889660.0402084218392334
TBP#690863.706770687096390.000385416472907960.00377638718585556
TCF12#693847.089643268124280.001002991572657710.00718755570583218
USF1#739155.30124939767330.0005003327549858890.00441113055866717



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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