Personal tools

Coexpression cluster:C3073: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C3073_Eosinophils_Neutrophils_granulocyte_cerebellum_CD14_parietal_vagina
|

Latest revision as of 12:18, 17 September 2013


Full id: C3073_Eosinophils_Neutrophils_granulocyte_cerebellum_CD14_parietal_vagina



Phase1 CAGE Peaks

Hg19::chr11:10315741..10315773,-p1@SBF2
Hg19::chr12:116715460..116715476,-p4@MED13L
Hg19::chr12:116715483..116715524,-p1@MED13L


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:0051262protein tetramerization0.0255556082703558
GO:0046839phospholipid dephosphorylation0.0255556082703558
GO:0019902phosphatase binding0.0255556082703558
GO:0000119mediator complex0.0255556082703558
GO:0042552myelination0.0255556082703558
GO:0007272ensheathment of neurons0.0255556082703558
GO:0008366axon ensheathment0.0255556082703558
GO:0001508regulation of action potential0.0275084560595357
GO:0030258lipid modification0.0275084560595357
GO:0004437inositol or phosphatidylinositol phosphatase activity0.0275084560595357
GO:0051259protein oligomerization0.0275084560595357
GO:0005774vacuolar membrane0.0275084560595357
GO:0044437vacuolar part0.0275084560595357
GO:0019208phosphatase regulator activity0.0327190157182835
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0428065030946804



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
adult organism7.83e-29114
hematopoietic system4.27e-1498
blood island4.27e-1498
bone marrow3.67e-1276
hemolymphoid system3.82e-12108
neural tube5.73e-1256
neural rod5.73e-1256
future spinal cord5.73e-1256
neural keel5.73e-1256
bone element8.43e-1282
regional part of nervous system1.73e-1153
regional part of brain1.73e-1153
skeletal system3.24e-11100
regional part of forebrain1.31e-1041
forebrain1.31e-1041
anterior neural tube1.31e-1041
future forebrain1.31e-1041
skeletal element1.32e-1090
brain2.07e-1068
future brain2.07e-1068
immune system3.66e-1093
nervous system4.89e-1089
central nervous system8.34e-1081
organ5.09e-09503
telencephalon5.91e-0934
brain grey matter1.64e-0834
gray matter1.64e-0834
regional part of telencephalon1.86e-0832
cerebral hemisphere1.94e-0832
neural plate1.94e-0782
presumptive neural plate1.94e-0782
neurectoderm2.72e-0786
ectoderm-derived structure4.47e-07171
ectoderm4.47e-07171
presumptive ectoderm4.47e-07171
regional part of cerebral cortex5.66e-0722
cerebral cortex6.95e-0725
pallium6.95e-0725


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)
MA0003.11.0927
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
MA0058.12.8588
MA0059.10.714521
MA0060.11.23283
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.19.66582
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.11.76247
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.15.21222
MA0163.13.96434
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.210.17
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
E2F6#187635.017155731697390.00791769806886330.0320386078502136
EGR1#195834.988179094810140.008056488137383440.0319054893288408
NFYB#4801211.17319550235760.01025467135054530.0381107259689559
SMC3#9126210.02995522995520.0126656379767470.045707897880217
YY1#752834.911170749853860.008441455341808260.0327897182446206
ZBTB7A#5134137.35190930787590.002516255860282270.0139591652922564



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3073&oldid=3070190"