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Coexpression cluster:C2138: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101266922464243!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319839096667028!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428111393365014!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186199270898034!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172615962177139!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079428877412123!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0280888155352423!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404783795159636!STAT2#6773;3:48.9478283898305:1.42094046481278e-05:0.000340136606015544!STAT3#6774;3:7.88959874786568:0.00319076048168013:0.016738991056168!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482715884091698!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342236433282897!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.0097600713442927!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248125831543171
|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101266922464243!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319839096667028!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428111393365014!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186199270898034!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172615962177139!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079428877412123!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0280888155352423!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404783795159636!STAT2#6773;3:48.9478283898305:1.42094046481278e-05:0.000340136606015544!STAT3#6774;3:7.88959874786568:0.00319076048168013:0.016738991056168!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0482715884091698!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342236433282897!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.0097600713442927!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248125831543171
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}}
}}

Revision as of 15:19, 26 November 2012


Full id: C2138_Smooth_CD14_mesothelioma_Hair_meningioma_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:57335090..57335155,-p1@UBE2L6
Hg19::chr15:74287118..74287142,+p2@PML
Hg19::chr17:41158760..41158822,+p1@IFI35
Hg19::chr17:41158825..41158847,+p2@IFI35


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


p.valueFDRnGenesnPathwayName
7.03959989046011e-050.02228033365330632139Ubiquitin mediated proteolysis (KEGG):04120
5.70320151504265e-060.003610126559021993511Signaling in Immune system (Reactome):REACT_6900



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:0031571G1 DNA damage checkpoint0.0286350242431562
GO:0006977DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest0.0286350242431562
GO:0042771DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis0.0286350242431562
GO:0031575G1/S transition checkpoint0.0286350242431562
GO:0016605PML body0.0286350242431562
GO:0030330DNA damage response, signal transduction by p53 class mediator0.0286350242431562
GO:0016525negative regulation of angiogenesis0.0286350242431562
GO:0008630DNA damage response, signal transduction resulting in induction of apoptosis0.0286350242431562
GO:0005626insoluble fraction0.0286350242431562
GO:0000077DNA damage checkpoint0.0300596940472044
GO:0007093mitotic cell cycle checkpoint0.0300596940472044
GO:0031570DNA integrity checkpoint0.0300596940472044
GO:0008629induction of apoptosis by intracellular signals0.0349571040718196
GO:0045765regulation of angiogenesis0.0349571040718196
GO:0042770DNA damage response, signal transduction0.0369141724117895
GO:0001666response to hypoxia0.0379388436354144
GO:0030308negative regulation of cell growth0.0379388436354144
GO:0045792negative regulation of cell size0.0379388436354144
GO:0000075cell cycle checkpoint0.0379388436354144
GO:0045926negative regulation of growth0.0392541470303728
GO:0007088regulation of mitosis0.0410548490495792



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
nongranular leukocyte3.52e-18115
leukocyte4.20e-18136
myeloid leukocyte3.54e-1772
monopoietic cell3.51e-1659
monocyte3.51e-1659
monoblast3.51e-1659
promonocyte3.51e-1659
defensive cell4.82e-1648
phagocyte4.82e-1648
hematopoietic lineage restricted progenitor cell8.84e-16120
classical monocyte7.66e-1542
CD14-positive, CD16-negative classical monocyte7.66e-1542
macrophage dendritic cell progenitor1.24e-1461
myeloid lineage restricted progenitor cell1.64e-1466
connective tissue cell2.38e-13361
granulocyte monocyte progenitor cell4.44e-1367
hematopoietic stem cell1.40e-12168
angioblastic mesenchymal cell1.40e-12168
hematopoietic cell2.42e-12177
mesenchymal cell4.26e-12354
hematopoietic oligopotent progenitor cell5.05e-12161
hematopoietic multipotent progenitor cell5.05e-12161
multi fate stem cell5.56e-12427
somatic stem cell1.06e-10433
stem cell3.99e-10441
motile cell1.94e-09386
myeloid cell1.37e-08108
common myeloid progenitor1.37e-08108
Uber Anatomy
Ontology termp-valuen
hemolymphoid system2.07e-19108
immune system1.37e-1793
hematopoietic system5.18e-1798
blood island5.18e-1798
bone marrow3.04e-1376
connective tissue4.98e-13371
skeletal element5.26e-1190
bone element1.04e-1082
skeletal system5.94e-10100
musculoskeletal system5.05e-09167
lateral plate mesoderm2.37e-08203
mesoderm9.34e-07315
mesoderm-derived structure9.34e-07315
presumptive mesoderm9.34e-07315


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
EGR1#195844.988179094810140.001615011500076050.0101266922464243
IRF1#365935.727872815172930.008097114790333330.0319839096667028
IRF4#3662210.95725634337210.01174530180688030.0428111393365014
MXI1#460137.471178721569470.003741314738550960.0186199270898034
RAD21#588537.766275421592250.0033411193858720.0172615962177139
SIN3A#2594245.408884726815140.001168172384885160.0079428877412123
SPI1#668836.153242631392040.006580387113059030.0280888155352423
STAT1#6772315.52994062289940.000434088655175550.00404783795159636
STAT2#6773348.94782838983051.42094046481278e-050.000340136606015544
STAT3#677437.889598747865680.003190760481680130.016738991056168
USF1#739134.771124457905970.01370465887188020.0482715884091698
ZBTB7A#5134135.513931980906920.009038352821081090.0342236433282897
ZNF143#7702310.12565741417090.001534861610688180.0097600713442927
ZNF263#1012748.221841637010680.0002187871180958320.00248125831543171



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.