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Coexpression cluster:C4802: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4802_Mast_Neutrophils_Eosinophils_Natural_CD14_Basophils_CD8
|full_id=C4802_Mast_Neutrophils_Eosinophils_Natural_CD14_Basophils_CD8
|id=C4802
|id=C4802

Revision as of 17:56, 12 September 2012


Full id: C4802_Mast_Neutrophils_Eosinophils_Natural_CD14_Basophils_CD8



Phase1 CAGE Peaks

Hg19::chr9:132222772..132222790,+p@chr9:132222772..132222790
+
Hg19::chr9:132222825..132222843,+p@chr9:132222825..132222843
+
Hg19::chr9:132222848..132222877,+p@chr9:132222848..132222877
+


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>

Uber Anatomy
Ontology termp-valuen
hematopoietic system1.94e-19102
blood island1.94e-19102
hemolymphoid system5.38e-16112
bone marrow1.18e-1580
bone element2.37e-1586
lateral plate mesoderm2.64e-14216
skeletal element2.26e-10101
skeletal system2.26e-10101
immune system1.70e-08115


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#90536.336201576962630.003930750035764890.0191386295098018
CEBPB#105137.971147625824820.001974187055288560.0115878222822054
CTCF#1066435.360256373075030.0064925092527670.0281672900697767
CTCFL#140690319.74647435897440.0001298372005551160.00172454119150144
E2F1#186934.907389214879320.008460985347239390.0328143209432335
E2F4#1874312.66806031528440.0004917987006298980.00439375230924602
E2F6#187635.017155731697390.00791769806886330.0324739423740973
EGR1#195834.988179094810140.008056488137383440.0322837572259598
ELF1#199734.258097958807540.01295179875054610.0465331765698264
EP300#203336.77394172622320.003216880500103790.0168616202032793
ESR1#2099330.76860329615453.43136389821584e-050.000679886575916835
ETS1#211339.728760922202340.001085840092584840.00765933090837956
FOS#235338.99795530889440.001372499272417130.00902489778454779
FOSL1#8061339.7135797163731.59554825631833e-050.000372957619385923
FOSL2#2355316.93020060456170.0002060162053171620.00244140774618394
FOXA1#3169311.08141974938550.000734755275698670.00584797334542702
FOXA2#3170324.63046375266526.68983856509345e-050.00107771101326515
GABPB1#255337.067683836182170.002832212825417420.015493058625276
HDAC2#3066313.41562023662630.0004140761399857210.00393966456991607
HMGN3#932438.178547723350590.001827766942164210.0109342508690966
HNF4A#3172323.13229036295378.07584663437677e-050.00123543774226992
HNF4G#3174328.75342252644684.20470658818262e-050.0007611983902985
JUND#372736.994663941871030.002921845042734990.0157792323500801
MXI1#460139.96157162875930.001011470541259020.00723937581267482
MYC#460935.22228187160940.007020843755740150.0296418280715425
NANOG#79923329.24477848101273.99627955670032e-050.000741986561106178
PAX5#507936.669565531177830.003370290999677260.0173779225729595
RAD21#5885310.35503389545630.0009004912073565420.00669274133255834
REST#597839.650028716128020.001112636247114590.00772007819641248
RXRA#6256320.07461713913330.0001235730348432220.00166119760406633
SIN3A#2594235.408884726815140.006318961977991520.0278575799923789
SMC3#9126315.04493284493280.0002935825420371870.00311031315762038
SP1#666735.69838137814090.005403962701712170.0248113799887509
SPI1#668838.204323508522730.001810593189410520.0109475216875381
SREBF1#6720347.00584944048839.62099323994382e-060.000255481035592803
TAF7#6879311.43306940492390.0006690181981945830.00546213192630113
TCF12#6938310.63446490218640.0008313523990202070.0063247095863397
TCF7L2#6934310.77017656313730.0008003181298398380.00617953756929934
USF1#739136.361499277207960.00388404057290560.0191351154957162
YY1#752834.911170749853860.008441455341808260.0331522263168169
ZBTB7A#5134137.35190930787590.002516255860282270.0141082968697063
ZNF263#1012738.221841637010680.001799043925565870.0110231943996582



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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