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Coexpression cluster:C1725: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0017033!DNA topoisomerase I binding!0.0054750971388202!10210$GO:0051457!maintenance of protein localization in nucleus!0.0136861311971243!10210$GO:0032507!maintenance of cellular protein localization!0.0284495579902943!10210$GO:0051651!maintenance of cellular localization!0.0284495579902943!10210$GO:0045185!maintenance of protein localization!0.0284495579902943!10210$GO:0051235!maintenance of localization!0.0373691275791586!10210
|gostat_on_coexpression_clusters=GO:0017033!DNA topoisomerase I binding!0.0054750971388202!10210$GO:0051457!maintenance of protein localization in nucleus!0.0136861311971243!10210$GO:0032507!maintenance of cellular protein localization!0.0284495579902943!10210$GO:0051651!maintenance of cellular localization!0.0284495579902943!10210$GO:0045185!maintenance of protein localization!0.0284495579902943!10210$GO:0051235!maintenance of localization!0.0373691275791586!10210
|id=C1725
|id=C1725
|ontology_enrichment_celltype=CL:0000738!1.92e-30!140;CL:0000037!3.00e-24!172;CL:0000566!3.00e-24!172;CL:0002031!2.36e-22!124;CL:0000988!5.24e-22!182;CL:0002032!3.08e-21!165;CL:0000837!3.08e-21!165;CL:0002087!1.20e-20!119;CL:0000838!4.22e-15!52;CL:0000542!6.57e-15!53;CL:0000051!6.57e-15!53;CL:0002057!9.02e-13!42;CL:0000766!2.13e-11!76;CL:0000860!3.11e-11!45;CL:0000791!4.08e-11!18;CL:0000789!4.08e-11!18;CL:0002420!4.08e-11!18;CL:0002419!4.08e-11!18;CL:0000790!4.08e-11!18;CL:0000084!9.38e-10!25;CL:0000827!9.38e-10!25;CL:0000763!1.84e-08!112;CL:0000049!1.84e-08!112;CL:0000557!2.87e-08!71;CL:0000839!3.02e-08!70;CL:0000625!6.85e-08!11;CL:0000236!8.89e-07!14
|ontology_enrichment_celltype=CL:0000738!2.95e-33!136;CL:0000037!5.29e-28!168;CL:0000566!5.29e-28!168;CL:0000988!6.34e-26!177;CL:0002031!2.39e-25!120;CL:0002032!7.85e-25!161;CL:0000837!7.85e-25!161;CL:0002087!1.67e-23!115;CL:0002242!8.45e-15!55;CL:0000838!2.15e-14!52;CL:0000766!2.31e-14!72;CL:0000542!2.85e-14!53;CL:0000051!2.85e-14!53;CL:0000860!3.53e-14!42;CL:0002057!3.53e-14!42;CL:0000763!1.97e-11!108;CL:0000049!1.97e-11!108;CL:0000473!5.21e-11!48;CL:0000234!5.21e-11!48;CL:0000839!6.38e-11!66;CL:0000791!6.59e-11!18;CL:0000789!6.59e-11!18;CL:0002420!6.59e-11!18;CL:0002419!6.59e-11!18;CL:0000790!6.59e-11!18;CL:0000557!7.78e-11!67;CL:0000084!1.55e-09!25;CL:0000827!1.55e-09!25;CL:0002009!3.09e-09!61;CL:0002194!1.06e-08!59;CL:0000576!1.06e-08!59;CL:0000040!1.06e-08!59;CL:0000559!1.06e-08!59;CL:0000625!7.62e-08!11;CL:0000236!9.99e-07!14
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.32e-22!115;UBERON:0001017!1.35e-16!82;UBERON:0001049!1.02e-15!57;UBERON:0005068!1.02e-15!57;UBERON:0006241!1.02e-15!57;UBERON:0007135!1.02e-15!57;UBERON:0005743!1.64e-15!86;UBERON:0000073!5.78e-15!94;UBERON:0001016!5.78e-15!94;UBERON:0002780!8.04e-15!41;UBERON:0001890!8.04e-15!41;UBERON:0006240!8.04e-15!41;UBERON:0003080!1.48e-14!42;UBERON:0002390!2.85e-13!102;UBERON:0003061!2.85e-13!102;UBERON:0002616!3.58e-13!59;UBERON:0000955!5.98e-13!69;UBERON:0006238!5.98e-13!69;UBERON:0001893!1.69e-12!34;UBERON:0002020!2.11e-12!34;UBERON:0003528!2.11e-12!34;UBERON:0002791!3.85e-12!33;UBERON:0001869!6.28e-12!32;UBERON:0002193!2.45e-11!112;UBERON:0002619!1.06e-09!22;UBERON:0000956!2.13e-09!25;UBERON:0000203!2.13e-09!25;UBERON:0001950!5.52e-09!20;UBERON:0000178!1.09e-08!15;UBERON:0000179!1.09e-08!15;UBERON:0000463!1.09e-08!15;UBERON:0002346!1.36e-08!90;UBERON:0003075!3.32e-08!86;UBERON:0007284!3.32e-08!86;UBERON:0003056!1.49e-07!61;UBERON:0002371!8.96e-07!80;UBERON:0001474!9.93e-07!86
|ontology_enrichment_uberon=UBERON:0007023!3.45e-21!114;UBERON:0001017!9.72e-17!81;UBERON:0001049!1.40e-16!56;UBERON:0005068!1.40e-16!56;UBERON:0006241!1.40e-16!56;UBERON:0007135!1.40e-16!56;UBERON:0001016!6.74e-16!89;UBERON:0002390!8.88e-16!98;UBERON:0003061!8.88e-16!98;UBERON:0000073!9.67e-16!53;UBERON:0002616!9.67e-16!53;UBERON:0002780!1.58e-14!41;UBERON:0001890!1.58e-14!41;UBERON:0003080!1.58e-14!41;UBERON:0006240!1.58e-14!41;UBERON:0000955!1.40e-13!68;UBERON:0006238!1.40e-13!68;UBERON:0002193!2.43e-13!108;UBERON:0001893!2.80e-12!34;UBERON:0003528!4.55e-12!34;UBERON:0002020!4.55e-12!34;UBERON:0001869!1.17e-11!32;UBERON:0002791!1.48e-11!32;UBERON:0002619!1.65e-09!22;UBERON:0000956!3.67e-09!25;UBERON:0000203!3.67e-09!25;UBERON:0002371!4.64e-09!76;UBERON:0001950!7.83e-09!20;UBERON:0001474!1.52e-08!82;UBERON:0002405!1.81e-08!93;UBERON:0002346!2.04e-08!86;UBERON:0003075!5.72e-08!82;UBERON:0007284!5.72e-08!82;UBERON:0000178!7.27e-08!15;UBERON:0000179!7.27e-08!15;UBERON:0000463!7.27e-08!15;UBERON:0004765!1.97e-07!90
|tf_chipseq_enrich=CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319520793577088!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352561223782669!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674021007056614!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413747950130536!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402174535634321!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222023434036854!NR2C2#7182;3:19.5687665431445:0.000275017170096661:0.00293057016913837!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232405626040874!SP2#6668;2:10.4614121975379:0.0135319118334714:0.0477775300870831!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135278649261862!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918376136083501!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298379745577413
|tf_chipseq_enrich=CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319520793577088!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352561223782669!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674021007056614!HNF4G#3174;2:11.5013690105787:0.0112743830492105:0.0413747950130536!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402174535634321!NFKB1#4790;4:4.39045073935507:0.00470773269252496:0.0222023434036854!NR2C2#7182;3:19.5687665431445:0.000275017170096661:0.00293057016913837!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232405626040874!SP2#6668;2:10.4614121975379:0.0135319118334714:0.0477775300870831!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135278649261862!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00918376136083501!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298379745577413
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}}
}}

Revision as of 11:37, 19 October 2012


Full id: C1725_Neutrophils_Eosinophils_Mast_CD8_Natural_CD4_cord



Phase1 CAGE Peaks

Hg19::chr14:45431091..45431175,-p1@KLHL28
Hg19::chr3:39093481..39093520,+p1@WDR48
Hg19::chr4:4291944..4292011,+p1@ZBTB49
Hg19::chr6:42750549..42750592,-p@chr6:42750549..42750592
-
Hg19::chr9:32550839..32550962,-p3@TOPORS


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:0017033DNA topoisomerase I binding0.0054750971388202
GO:0051457maintenance of protein localization in nucleus0.0136861311971243
GO:0032507maintenance of cellular protein localization0.0284495579902943
GO:0051651maintenance of cellular localization0.0284495579902943
GO:0045185maintenance of protein localization0.0284495579902943
GO:0051235maintenance of localization0.0373691275791586



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
leukocyte2.95e-33136
hematopoietic stem cell5.29e-28168
angioblastic mesenchymal cell5.29e-28168
hematopoietic cell6.34e-26177
hematopoietic lineage restricted progenitor cell2.39e-25120
hematopoietic oligopotent progenitor cell7.85e-25161
hematopoietic multipotent progenitor cell7.85e-25161
nongranular leukocyte1.67e-23115
nucleate cell8.45e-1555
lymphoid lineage restricted progenitor cell2.15e-1452
myeloid leukocyte2.31e-1472
lymphocyte2.85e-1453
common lymphoid progenitor2.85e-1453
classical monocyte3.53e-1442
CD14-positive, CD16-negative classical monocyte3.53e-1442
myeloid cell1.97e-11108
common myeloid progenitor1.97e-11108
defensive cell5.21e-1148
phagocyte5.21e-1148
myeloid lineage restricted progenitor cell6.38e-1166
mature alpha-beta T cell6.59e-1118
alpha-beta T cell6.59e-1118
immature T cell6.59e-1118
mature T cell6.59e-1118
immature alpha-beta T cell6.59e-1118
granulocyte monocyte progenitor cell7.78e-1167
T cell1.55e-0925
pro-T cell1.55e-0925
macrophage dendritic cell progenitor3.09e-0961
monopoietic cell1.06e-0859
monocyte1.06e-0859
monoblast1.06e-0859
promonocyte1.06e-0859
CD8-positive, alpha-beta T cell7.62e-0811
B cell9.99e-0714
Uber Anatomy
Ontology termp-valuen
adult organism3.45e-21114
central nervous system9.72e-1781
neural tube1.40e-1656
neural rod1.40e-1656
future spinal cord1.40e-1656
neural keel1.40e-1656
nervous system6.74e-1689
hematopoietic system8.88e-1698
blood island8.88e-1698
regional part of nervous system9.67e-1653
regional part of brain9.67e-1653
regional part of forebrain1.58e-1441
forebrain1.58e-1441
anterior neural tube1.58e-1441
future forebrain1.58e-1441
brain1.40e-1368
future brain1.40e-1368
hemolymphoid system2.43e-13108
telencephalon2.80e-1234
brain grey matter4.55e-1234
gray matter4.55e-1234
cerebral hemisphere1.17e-1132
regional part of telencephalon1.48e-1132
regional part of cerebral cortex1.65e-0922
cerebral cortex3.67e-0925
pallium3.67e-0925
bone marrow4.64e-0976
neocortex7.83e-0920
bone element1.52e-0882
immune system1.81e-0893
neurectoderm2.04e-0886
neural plate5.72e-0882
presumptive neural plate5.72e-0882
blood7.27e-0815
haemolymphatic fluid7.27e-0815
organism substance7.27e-0815
skeletal element1.97e-0790


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
CHD2#110636.206413700470110.007774550126275590.0319520793577088
E2F1#186954.907389214879320.0003512818099256460.00352561223782669
HEY1#2346254.040111043105710.0009288852205177990.00674021007056614
HNF4G#3174211.50136901057870.01127438304921050.0413747950130536
NANOG#79923211.69791139240510.01091164951956080.0402174535634321
NFKB1#479044.390450739355070.004707732692524960.0222023434036854
NR2C2#7182319.56876654314450.0002750171700966610.00293057016913837
SIN3A#2594244.327107781452110.004977052855762880.0232405626040874
SP2#6668210.46141219753790.01353191183347140.0477775300870831
TAF1#687253.343046285745290.002394600090870310.0135278649261862
TBP#690853.706770687096390.001428755106721120.00918376136083501
YY1#752843.928936599883080.007193866269917620.0298379745577413



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.