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Coexpression cluster:C2930: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2930_Eosinophils_Neutrophils_CD14_Whole_aorta_bladder_colon
|id=C2930
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2930_Eosinophils_Neutrophils_CD14_Whole_aorta_bladder_colon



Phase1 CAGE Peaks

Hg19::chr8:9008131..9008144,-p3@PPP1R3B
Hg19::chr8:9008147..9008153,-p6@PPP1R3B
Hg19::chr8:9008160..9008180,-p1@PPP1R3B
Hg19::chr8:9008184..9008198,-p2@PPP1R3B


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>

Cell Type
Ontology termp-valuen
endothelial cell of vascular tree3.62e-0924
endothelial cell3.15e-0736
Uber Anatomy
Ontology termp-valuen
circulatory system2.00e-14112
lateral plate mesoderm1.79e-13203
cardiovascular system3.02e-13109
mesoderm3.25e-13315
mesoderm-derived structure3.25e-13315
presumptive mesoderm3.25e-13315
multi-cellular organism5.59e-12656
vessel1.72e-1068
splanchnic layer of lateral plate mesoderm2.29e-1083
epithelial tube4.59e-10117
vasculature4.60e-1078
vascular system4.60e-1078
epithelial tube open at both ends1.17e-0959
blood vessel1.17e-0959
blood vasculature1.17e-0959
vascular cord1.17e-0959
embryo3.15e-07592
developing anatomical structure6.94e-07581


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.11.34758
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.14.42006
MA0106.10.869173
MA0107.10.453492
MA0108.23.84935
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.11.43218
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.11.63368
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.14.94783
MA0146.13.58384
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.21.79838
MA0047.20.856092
MA0112.21.05083
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.35343
MA0102.21.75932
MA0258.11.88931
MA0259.10.471671
MA0442.10



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#90546.336201576962630.0006203100587215640.00513877704630931
CTCF#1066445.360256373075030.001211145381643620.00820463206288372
E2F6#187645.017155731697390.00157802193473060.00999739356028686
ELF1#199744.258097958807540.003041525565781240.0161327520855575
GATA1#2623413.56030814380042.95627390049268e-050.000615530880968012
GATA2#2624412.7449317335543.78864877853583e-050.000725091973211479
GATA3#2625427.2365163572061.81561517799785e-066.79888969433191e-05
HEY1#2346244.040111043105710.00375304636917980.0186703062661127
HMGN3#932448.178547723350590.0002234570284440470.00248669457577708
IRF1#365947.63716375356390.0002938853996185490.00308163627015679
MEF2A#4205418.74323090964418.0978922767748e-060.000224869920631237
NANOG#79923429.24477848101271.36586687657858e-065.35070407813168e-05
NFKB1#479045.488063424193840.001102199566301980.0076952082696044
PAX5#507946.669565531177830.0005052774169483260.0044505918991875
RAD21#5885410.35503389545638.6948481184721e-050.00130134887166109
SMC3#9126415.04493284493281.95092670935632e-050.000439880903709984
STAT1#6772420.70658749719925.43610708103893e-060.000165715583022949
STAT3#6774410.51946499715428.16377768286615e-050.00123603475996065
TAF1#687243.343046285745290.008005664898701650.0323481888170968
TAF7#6879411.43306940492395.85061525419808e-050.000972362200084649
TBP#690843.706770687096390.005296377814784350.0245157294064735
TFAP2C#7022410.80922860986027.32289634782688e-050.00114955053610505
YY1#752844.911170749853860.00171871838055440.010712014617576
ZNF143#7702413.50087655222793.00867915035614e-050.000622471160427981
ZNF263#1012748.221841637010680.0002187871180958320.00250163212467819



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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