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Coexpression cluster:C723: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;8:5.79719827332714:7.09770251647579e-06:0.000204716087577524!E2F1#1869;11:4.90738921487932:2.51269297258347e-08:1.75299359628354e-06!E2F4#1874;8:9.21313477475232:1.99706038053359e-07:1.08011905273199e-05!E2F6#1876;9:4.1049455986615:1.83835844928222e-05:0.000418110448790474!EGR1#1958;7:3.17429578760645:0.00199357209099962:0.0115940904116221!ELF1#1997;11:4.25809795880754:1.19731042846735e-07:6.90479866585873e-06!ELK4#2005;4:5.90388423944292:0.00334112168340882:0.0172573396386515!ETS1#2113;5:4.42216405554652:0.00310836378716529:0.016342028973962!FOS#2353;6:4.90797562303331:0.000528682880176561:0.00457078736115562!GABPB1#2553;9:5.78265041142178:9.50989655291635e-07:4.06550997171523e-05!GTF2F1#2962;5:5.79075494398075:0.000918925041780732:0.00668232923259559!HEY1#23462;11:4.04011104310571:2.1344242734918e-07:1.13675235440699e-05!MAX#4149;7:4.10617168754999:0.000396333145794484:0.00387426407840042!MXI1#4601;5:4.5279871039815:0.00279761876947351:0.0153198671699373!MYC#4609;9:4.27277607677133:1.30375226575527e-05:0.000318658045596103!NFKB1#4790;7:3.49240399721426:0.00110207548522866:0.00769639997337322!NFYB#4801;5:7.61808784251657:0.000257397641240345:0.00276169634821249!PAX5#5079;6:3.63794483518791:0.00264989689588002:0.0146360242164479!POLR2A#5430;11:2.14745317655807:0.000223198342238743:0.00248461006875635!POU2F2#5452;6:4.96697675876865:0.00049515413177051:0.00437841015730931!RFX5#5993;6:6.5715877239246:0.000104500564341874:0.00145732867396194!SIN3A#25942;8:3.93373434677464:0.000131554682498111:0.00172975443603427!SMARCB1#6598;4:6.63735119314815:0.00217555538509292:0.0125511146695973!SPI1#6688;5:3.72923795841942:0.00657139769228244:0.028083730402827!STAT1#6772;3:5.64725113559978:0.0138689600283293:0.048717217691332!STAT3#6774;6:5.73788999844777:0.000223133323888784:0.00248574092945287!TAF1#6872;11:3.34304628574529:1.71447392661505e-06:6.47587495196198e-05!TAF7#6879;7:7.27558962131522:9.39481399808184e-06:0.000250047140455063!TBP#6908;11:3.70677068709639:5.5042384307836e-07:2.54812569801688e-05!TCF7L2#6934;6:5.87464176171128:0.000195714842587612:0.00235405533168347!TFAP2C#7022;5:4.91328573175465:0.00193982427985066:0.0113950901604884!THAP1#55145;3:8.55522125532309:0.004407746242643:0.0208818602783122!USF1#7391;9:5.20486304498833:2.37429471822852e-06:8.40857802906302e-05!USF2#7392;6:7.08665311912887:6.8302134157013e-05:0.00109023484475383!YY1#7528;10:4.46470068168532:1.09711041274109e-06:4.55228901057873e-05!ZNF143#7702;4:4.9094096553556:0.00649801564418536:0.0278304800435954!ZNF263#10127;5:3.73720074409576:0.00651090818209497:0.0278765522744155
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}}
}}

Revision as of 14:25, 26 November 2012


Full id: C723_CD14_CD4_Eosinophils_CD8_Natural_Neutrophils_CD19



Phase1 CAGE Peaks

Hg19::chr10:43633914..43633935,+p2@CSGALNACT2
Hg19::chr11:82868158..82868179,+p2@PCF11
Hg19::chr16:21513575..21513614,-p1@LOC100271836
Hg19::chr16:30346739..30346761,-p1@LOC595101
Hg19::chr17:18218587..18218624,+p1@SMCR8
Hg19::chr18:76829385..76829438,+p1@ATP9B
Hg19::chr2:201729366..201729392,-p1@CLK1
Hg19::chr5:65440032..65440099,+p2@SREK1
Hg19::chr7:120590822..120590857,+p1@ING3
Hg19::chrX:73834345..73834364,-p4@RLIM
Hg19::chrX:73834386..73834435,-p2@RLIM


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:0005849mRNA cleavage factor complex0.0280344945489482
GO:0015917aminophospholipid transport0.0280344945489482
GO:0006379mRNA cleavage0.04982443207512



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
hematopoietic stem cell1.36e-50168
angioblastic mesenchymal cell1.36e-50168
leukocyte3.67e-50136
hematopoietic oligopotent progenitor cell1.35e-46161
hematopoietic multipotent progenitor cell1.35e-46161
hematopoietic cell3.30e-45177
hematopoietic lineage restricted progenitor cell1.09e-41120
nongranular leukocyte8.92e-39115
myeloid cell1.42e-31108
common myeloid progenitor1.42e-31108
myeloid leukocyte1.63e-3172
granulocyte monocyte progenitor cell3.86e-2867
myeloid lineage restricted progenitor cell4.68e-2766
classical monocyte4.76e-2642
CD14-positive, CD16-negative classical monocyte4.76e-2642
macrophage dendritic cell progenitor3.88e-2561
defensive cell4.01e-2448
phagocyte4.01e-2448
monopoietic cell5.36e-2459
monocyte5.36e-2459
monoblast5.36e-2459
promonocyte5.36e-2459
nucleate cell8.17e-1455
lymphoid lineage restricted progenitor cell2.95e-1352
lymphocyte3.55e-1353
common lymphoid progenitor3.55e-1353
mature alpha-beta T cell1.67e-0918
alpha-beta T cell1.67e-0918
immature T cell1.67e-0918
mature T cell1.67e-0918
immature alpha-beta T cell1.67e-0918
T cell2.19e-0825
pro-T cell2.19e-0825
mesenchymal cell2.90e-07354
stuff accumulating cell6.27e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.27e-3098
blood island5.27e-3098
hemolymphoid system3.50e-28108
immune system7.75e-2393
bone marrow1.67e-2276
bone element6.38e-2182
adult organism3.42e-19114
skeletal element8.02e-1790
skeletal system4.87e-14100
neural tube4.66e-0856
neural rod4.66e-0856
future spinal cord4.66e-0856
neural keel4.66e-0856
regional part of nervous system2.67e-0753
regional part of brain2.67e-0753
regional part of forebrain6.43e-0741
forebrain6.43e-0741
anterior neural tube6.43e-0741
future forebrain6.43e-0741


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
CEBPB#105185.797198273327147.09770251647579e-060.000204716087577524
E2F1#1869114.907389214879322.51269297258347e-081.75299359628354e-06
E2F4#187489.213134774752321.99706038053359e-071.08011905273199e-05
E2F6#187694.10494559866151.83835844928222e-050.000418110448790474
EGR1#195873.174295787606450.001993572090999620.0115940904116221
ELF1#1997114.258097958807541.19731042846735e-076.90479866585873e-06
ELK4#200545.903884239442920.003341121683408820.0172573396386515
ETS1#211354.422164055546520.003108363787165290.016342028973962
FOS#235364.907975623033310.0005286828801765610.00457078736115562
GABPB1#255395.782650411421789.50989655291635e-074.06550997171523e-05
GTF2F1#296255.790754943980750.0009189250417807320.00668232923259559
HEY1#23462114.040111043105712.1344242734918e-071.13675235440699e-05
MAX#414974.106171687549990.0003963331457944840.00387426407840042
MXI1#460154.52798710398150.002797618769473510.0153198671699373
MYC#460994.272776076771331.30375226575527e-050.000318658045596103
NFKB1#479073.492403997214260.001102075485228660.00769639997337322
NFYB#480157.618087842516570.0002573976412403450.00276169634821249
PAX5#507963.637944835187910.002649896895880020.0146360242164479
POLR2A#5430112.147453176558070.0002231983422387430.00248461006875635
POU2F2#545264.966976758768650.000495154131770510.00437841015730931
RFX5#599366.57158772392460.0001045005643418740.00145732867396194
SIN3A#2594283.933734346774640.0001315546824981110.00172975443603427
SMARCB1#659846.637351193148150.002175555385092920.0125511146695973
SPI1#668853.729237958419420.006571397692282440.028083730402827
STAT1#677235.647251135599780.01386896002832930.048717217691332
STAT3#677465.737889998447770.0002231333238887840.00248574092945287
TAF1#6872113.343046285745291.71447392661505e-066.47587495196198e-05
TAF7#687977.275589621315229.39481399808184e-060.000250047140455063
TBP#6908113.706770687096395.5042384307836e-072.54812569801688e-05
TCF7L2#693465.874641761711280.0001957148425876120.00235405533168347
TFAP2C#702254.913285731754650.001939824279850660.0113950901604884
THAP1#5514538.555221255323090.0044077462426430.0208818602783122
USF1#739195.204863044988332.37429471822852e-068.40857802906302e-05
USF2#739267.086653119128876.8302134157013e-050.00109023484475383
YY1#7528104.464700681685321.09711041274109e-064.55228901057873e-05
ZNF143#770244.90940965535560.006498015644185360.0278304800435954
ZNF263#1012753.737200744095760.006510908182094970.0278765522744155



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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