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Coexpression cluster:C2671: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2671_skeletal_smooth_heart_CD14_left_bladder_mature
|id=C2671
}}

Latest revision as of 12:10, 17 September 2013


Full id: C2671_skeletal_smooth_heart_CD14_left_bladder_mature



Phase1 CAGE Peaks

Hg19::chr2:173940557..173940625,+p1@ZAK
Hg19::chr2:173940628..173940639,+p4@ZAK
Hg19::chr2:173940642..173940663,+p2@ZAK
Hg19::chr2:173940668..173940682,+p3@ZAK


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
fibroblast6.08e-1076
skin fibroblast3.14e-0923
classical monocyte1.04e-0742
CD14-positive, CD16-negative classical monocyte1.04e-0742
Uber Anatomy
Ontology termp-valuen
surface structure3.27e-1399
musculoskeletal system2.94e-09167
multi-cellular organism1.60e-08656
anatomical system1.37e-07624
skin of body1.61e-0741
organ1.84e-07503
anatomical group2.03e-07625
integument5.01e-0746
integumental system5.01e-0746


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)
MA0003.16.84463
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.16.90671
MA0017.10.577281
MA0019.10.873355
MA0024.15.72457
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.11.8712
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.13.36035
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.11.29536
MA0105.13.51257
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.11.57689
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.17.46487
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.27.80125
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.13.05999
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.110.6881
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.28.14977
MA0102.21.75932
MA0258.11.88931
MA0259.11.1888
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#90546.336201576962630.0006203100587215640.00512779501526211
CTCF#1066445.360256373075030.001211145381643620.00818392938104803
CTCFL#140690419.74647435897446.5732084880439e-060.000193216808692039
E2F1#186944.907389214879320.001724022357361790.0106610913008768
E2F4#1874412.66806031528443.88145892637771e-050.000727784001457741
E2F6#187645.017155731697390.00157802193473060.00997862877460214
EGR1#195844.988179094810140.001615011500076050.0101541259440397
ELF1#199744.258097958807540.003041525565781240.0161090262470017
HDAC2#3066413.41562023662633.0859005065161e-050.000627264233164724
HEY1#2346244.040111043105710.00375304636917980.0186356872415143
MYC#460945.22228187160940.001344309395272740.00888540781804249
PAX5#507946.669565531177830.0005052774169483260.00444384573883505
RAD21#5885410.35503389545638.6948481184721e-050.00129633296594591
SIN3A#2594245.408884726815140.001168172384885160.00797195215009284
SMC3#9126415.04493284493281.95092670935632e-050.000438649805378826
TAF1#687243.343046285745290.008005664898701650.0322720254884785
TBP#690843.706770687096390.005296377814784350.0244604405500249
YY1#752844.911170749853860.00171871838055440.0106960570222096
ZBTB7A#5134147.35190930787590.000342223540015990.00346971015393942



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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