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Coexpression cluster:C1055: Difference between revisions

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|id=C1055
|id=C1055
|kegg_enrichment=hsa04115;p53_signaling_pathway;3.91E-07
|kegg_enrichment=hsa04115;p53_signaling_pathway;3.91E-07
|ontology_enrichment_celltype=CL:0000738!1.31e-35!140;CL:0000037!8.30e-35!172;CL:0000566!8.30e-35!172;CL:0002032!1.23e-31!165;CL:0000837!1.23e-31!165;CL:0000988!3.46e-31!182;CL:0002031!8.47e-28!124;CL:0002087!4.37e-27!119;CL:0000542!1.56e-21!53;CL:0000051!1.56e-21!53;CL:0000838!2.60e-21!52;CL:0000763!2.62e-12!112;CL:0000049!2.62e-12!112;CL:0000791!8.85e-12!18;CL:0000789!8.85e-12!18;CL:0002420!8.85e-12!18;CL:0002419!8.85e-12!18;CL:0000790!8.85e-12!18;CL:0000766!3.36e-11!76;CL:0000084!4.47e-11!25;CL:0000827!4.47e-11!25;CL:0002057!5.79e-10!42;CL:0000945!1.17e-09!24;CL:0000826!1.17e-09!24;CL:0000860!4.75e-09!45;CL:0000557!8.31e-09!71;CL:0000236!1.22e-08!14;CL:0000839!1.48e-08!70;CL:0000625!4.05e-08!11;CL:0002009!2.14e-07!65;CL:0002194!5.58e-07!63;CL:0000576!5.58e-07!63;CL:0000040!5.58e-07!63;CL:0000559!5.58e-07!63
|ontology_enrichment_celltype=CL:0000738!6.80e-40!136;CL:0000037!8.80e-39!168;CL:0000566!8.80e-39!168;CL:0002032!2.03e-35!161;CL:0000837!2.03e-35!161;CL:0000988!1.02e-34!177;CL:0002031!5.15e-32!120;CL:0002087!8.18e-31!115;CL:0002242!3.35e-22!55;CL:0000542!1.34e-21!53;CL:0000051!1.34e-21!53;CL:0000838!1.87e-21!52;CL:0000763!6.16e-15!108;CL:0000049!6.16e-15!108;CL:0000766!4.64e-14!72;CL:0000791!6.85e-12!18;CL:0000789!6.85e-12!18;CL:0002420!6.85e-12!18;CL:0002419!6.85e-12!18;CL:0000790!6.85e-12!18;CL:0000860!1.70e-11!42;CL:0002057!1.70e-11!42;CL:0000557!2.14e-11!67;CL:0000839!3.44e-11!66;CL:0000084!5.90e-11!25;CL:0000827!5.90e-11!25;CL:0000945!6.67e-10!24;CL:0000826!6.67e-10!24;CL:0002009!6.94e-10!61;CL:0000473!1.45e-09!48;CL:0000234!1.45e-09!48;CL:0002194!2.82e-09!59;CL:0000576!2.82e-09!59;CL:0000040!2.82e-09!59;CL:0000559!2.82e-09!59;CL:0000236!2.61e-08!14;CL:0000625!3.16e-08!11
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.40e-34!115;UBERON:0001049!8.72e-17!57;UBERON:0005068!8.72e-17!57;UBERON:0006241!8.72e-17!57;UBERON:0007135!8.72e-17!57;UBERON:0003080!2.86e-14!42;UBERON:0002780!4.86e-14!41;UBERON:0001890!4.86e-14!41;UBERON:0006240!4.86e-14!41;UBERON:0001017!6.42e-14!82;UBERON:0002390!3.27e-13!102;UBERON:0003061!3.27e-13!102;UBERON:0005743!3.89e-13!86;UBERON:0000073!6.24e-13!94;UBERON:0001016!6.24e-13!94;UBERON:0002616!1.13e-12!59;UBERON:0002193!2.54e-12!112;UBERON:0000955!1.13e-11!69;UBERON:0006238!1.13e-11!69;UBERON:0002020!1.55e-11!34;UBERON:0003528!1.55e-11!34;UBERON:0001893!1.92e-11!34;UBERON:0002791!3.47e-11!33;UBERON:0001869!1.30e-10!32;UBERON:0002346!5.00e-09!90;UBERON:0002619!1.17e-08!22;UBERON:0003075!1.89e-08!86;UBERON:0007284!1.89e-08!86;UBERON:0000956!3.58e-08!25;UBERON:0000203!3.58e-08!25;UBERON:0001950!4.25e-08!20;UBERON:0000178!6.90e-08!15;UBERON:0000179!6.90e-08!15;UBERON:0000463!6.90e-08!15
|ontology_enrichment_uberon=UBERON:0007023!2.14e-30!114;UBERON:0002390!1.29e-15!98;UBERON:0003061!1.29e-15!98;UBERON:0001049!1.69e-14!56;UBERON:0005068!1.69e-14!56;UBERON:0006241!1.69e-14!56;UBERON:0007135!1.69e-14!56;UBERON:0002193!1.72e-14!108;UBERON:0000073!1.54e-13!53;UBERON:0002616!1.54e-13!53;UBERON:0002780!1.99e-12!41;UBERON:0001890!1.99e-12!41;UBERON:0003080!1.99e-12!41;UBERON:0006240!1.99e-12!41;UBERON:0001016!8.53e-12!89;UBERON:0001017!1.03e-11!81;UBERON:0001893!3.04e-10!34;UBERON:0003528!4.03e-10!34;UBERON:0002020!4.03e-10!34;UBERON:0000955!5.02e-10!68;UBERON:0006238!5.02e-10!68;UBERON:0002791!1.47e-09!32;UBERON:0001869!1.94e-09!32;UBERON:0002405!2.29e-09!93;UBERON:0002371!4.49e-08!76;UBERON:0000178!5.53e-08!15;UBERON:0000179!5.53e-08!15;UBERON:0000463!5.53e-08!15;UBERON:0002346!8.78e-08!86;UBERON:0001474!9.36e-08!82;UBERON:0002619!9.65e-08!22;UBERON:0001950!2.20e-07!20;UBERON:0000956!2.68e-07!25;UBERON:0000203!2.68e-07!25;UBERON:0003075!2.68e-07!82;UBERON:0007284!2.68e-07!82
|tf_chipseq_enrich=CCNT2#905;6:4.75215118272197:0.000323589541710397:0.0033109991326239!E2F1#1869;7:4.29396556301941:9.58670853279727e-05:0.00137060404169311!E2F6#1876;5:3.13572233231087:0.0102488050142096:0.0381513739263985!EGR1#1958;5:3.11761193425634:0.0105139099038836:0.0389218147047958!HEY1#23462;8:4.04011104310571:1.4081650274634e-05:0.000339099255944779!HMGN3#9324;5:5.11159232709412:0.00110951597588993:0.0077086707694231!IRF1#3659;4:3.81858187678195:0.0132613631682617:0.0469047516909403!NFKB1#4790;7:4.80205549616961:4.48248622098168e-05:0.00079387210180279!PAX5#5079;5:4.16847845698614:0.00284750870610728:0.0154376537456986!PBX3#5090;4:10.9572563433721:0.000261492197563197:0.00280159864806142!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127209912217321!POU2F2#5452;4:4.55306202887126:0.00706247384683113:0.0294603069892238!TAF1#6872;8:3.34304628574529:6.40776711117462e-05:0.0010435377971682!TAF7#6879;4:5.71653470246196:0.00306854155518016:0.0161766398203756!TBP#6908;6:2.78007801532229:0.00639018112126301:0.0278041963972665!YY1#7528;7:4.29727440612212:9.53674534900876e-05:0.00136458165160313!ZNF263#10127;4:4.11092081850534:0.0101999278231626:0.0379924484440702
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}}
}}

Revision as of 10:45, 19 October 2012


Full id: C1055_CD19_thymus_CD4_CD8_Neutrophils_Natural_cerebellum



Phase1 CAGE Peaks

Hg19::chr17:8151353..8151381,-p1@CTC1
Hg19::chr1:204485503..204485555,+p1@MDM4
Hg19::chr2:206950781..206950947,-p1@INO80D
Hg19::chr4:76439596..76439643,-p2@RCHY1
Hg19::chr4:78741389..78741433,-p@chr4:78741389..78741433
-
Hg19::chr5:56469653..56469722,+p2@GPBP1
Hg19::chr7:21467642..21467671,+p2@SP4
Hg19::chr7:21467674..21467727,+p1@SP4


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:0045023G0 to G1 transition0.0105964942920282
GO:0000320re-entry into mitotic cell cycle0.0105964942920282
GO:0042177negative regulation of protein catabolic process0.0190677949582778
GO:0006357regulation of transcription from RNA polymerase II promoter0.0190677949582778
GO:0009895negative regulation of catabolic process0.0190677949582778
GO:0050821protein stabilization0.0233248915267865
GO:0042176regulation of protein catabolic process0.0233248915267865
GO:0006366transcription from RNA polymerase II promoter0.0233248915267865
GO:0031647regulation of protein stability0.0247044173842433
GO:0009894regulation of catabolic process0.026464343452305



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
leukocyte6.80e-40136
hematopoietic stem cell8.80e-39168
angioblastic mesenchymal cell8.80e-39168
hematopoietic oligopotent progenitor cell2.03e-35161
hematopoietic multipotent progenitor cell2.03e-35161
hematopoietic cell1.02e-34177
hematopoietic lineage restricted progenitor cell5.15e-32120
nongranular leukocyte8.18e-31115
nucleate cell3.35e-2255
lymphocyte1.34e-2153
common lymphoid progenitor1.34e-2153
lymphoid lineage restricted progenitor cell1.87e-2152
myeloid cell6.16e-15108
common myeloid progenitor6.16e-15108
myeloid leukocyte4.64e-1472
mature alpha-beta T cell6.85e-1218
alpha-beta T cell6.85e-1218
immature T cell6.85e-1218
mature T cell6.85e-1218
immature alpha-beta T cell6.85e-1218
classical monocyte1.70e-1142
CD14-positive, CD16-negative classical monocyte1.70e-1142
granulocyte monocyte progenitor cell2.14e-1167
myeloid lineage restricted progenitor cell3.44e-1166
T cell5.90e-1125
pro-T cell5.90e-1125
lymphocyte of B lineage6.67e-1024
pro-B cell6.67e-1024
macrophage dendritic cell progenitor6.94e-1061
defensive cell1.45e-0948
phagocyte1.45e-0948
monopoietic cell2.82e-0959
monocyte2.82e-0959
monoblast2.82e-0959
promonocyte2.82e-0959
B cell2.61e-0814
CD8-positive, alpha-beta T cell3.16e-0811
Uber Anatomy
Ontology termp-valuen
adult organism2.14e-30114
hematopoietic system1.29e-1598
blood island1.29e-1598
neural tube1.69e-1456
neural rod1.69e-1456
future spinal cord1.69e-1456
neural keel1.69e-1456
hemolymphoid system1.72e-14108
regional part of nervous system1.54e-1353
regional part of brain1.54e-1353
regional part of forebrain1.99e-1241
forebrain1.99e-1241
anterior neural tube1.99e-1241
future forebrain1.99e-1241
nervous system8.53e-1289
central nervous system1.03e-1181
telencephalon3.04e-1034
brain grey matter4.03e-1034
gray matter4.03e-1034
brain5.02e-1068
future brain5.02e-1068
regional part of telencephalon1.47e-0932
cerebral hemisphere1.94e-0932
immune system2.29e-0993
bone marrow4.49e-0876
blood5.53e-0815
haemolymphatic fluid5.53e-0815
organism substance5.53e-0815
neurectoderm8.78e-0886
bone element9.36e-0882
regional part of cerebral cortex9.65e-0822
neocortex2.20e-0720
cerebral cortex2.68e-0725
pallium2.68e-0725
neural plate2.68e-0782
presumptive neural plate2.68e-0782


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#90564.752151182721970.0003235895417103970.0033109991326239
E2F1#186974.293965563019419.58670853279727e-050.00137060404169311
E2F6#187653.135722332310870.01024880501420960.0381513739263985
EGR1#195853.117611934256340.01051390990388360.0389218147047958
HEY1#2346284.040111043105711.4081650274634e-050.000339099255944779
HMGN3#932455.111592327094120.001109515975889930.0077086707694231
IRF1#365943.818581876781950.01326136316826170.0469047516909403
NFKB1#479074.802055496169614.48248622098168e-050.00079387210180279
PAX5#507954.168478456986140.002847508706107280.0154376537456986
PBX3#5090410.95725634337210.0002614921975631970.00280159864806142
POLR2A#543082.147453176558070.002210725788971910.0127209912217321
POU2F2#545244.553062028871260.007062473846831130.0294603069892238
TAF1#687283.343046285745296.40776711117462e-050.0010435377971682
TAF7#687945.716534702461960.003068541555180160.0161766398203756
TBP#690862.780078015322290.006390181121263010.0278041963972665
YY1#752874.297274406122129.53674534900876e-050.00136458165160313
ZNF263#1012744.110920818505340.01019992782316260.0379924484440702



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.