Personal tools

Coexpression cluster:C530: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:25, 17 September 2013


Full id: C530_papillary_salivary_skin_Smooth_leiomyoma_lung_Keratinocyte



Phase1 CAGE Peaks

Hg19::chr11:36376725..36376731,+p@chr11:36376725..36376731
+
Hg19::chr14:85880761..85880773,+p@chr14:85880761..85880773
+
Hg19::chr1:152670795..152670806,+p2@LCE2A
Hg19::chr1:152670815..152670829,+p1@LCE2A
Hg19::chr1:152730499..152730507,+p1@KPRP
Hg19::chr20:9013530..9013537,-p@chr20:9013530..9013537
-
Hg19::chr2:69180083..69180096,-p4@GKN2
Hg19::chr2:69180112..69180125,-p3@GKN2
Hg19::chr3:1113044..1113048,+p@chr3:1113044..1113048
+
Hg19::chr3:677239..677244,+p@chr3:677239..677244
+
Hg19::chr3:677267..677274,+p@chr3:677267..677274
+
Hg19::chr4:14094655..14094663,+p@chr4:14094655..14094663
+
Hg19::chr4:55527639..55527644,-p@chr4:55527639..55527644
-
Hg19::chr5:83381628..83381664,-p@chr5:83381628..83381664
-
Hg19::chr6:38754506..38754523,+p@chr6:38754506..38754523
+
Hg19::chrX:55684394..55684406,-p@chrX:55684394..55684406
-
Hg19::chrX:55684426..55684441,-p@chrX:55684426..55684441
-


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:0031424keratinization0.0317244887273977
GO:0009913epidermal cell differentiation0.0317244887273977
GO:0048730epidermis morphogenesis0.0317244887273977
GO:0048729tissue morphogenesis0.0317244887273977
GO:0008544epidermis development0.0427933892514428
GO:0007398ectoderm development0.0427933892514428



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
thyroid gland1.48e-405
pharyngeal pouch1.48e-405
thyroid diverticulum1.48e-405
pharyngeal pouch 21.48e-405
thyroid primordium1.48e-405
entire pharyngeal arch endoderm2.25e-1911
early pharyngeal endoderm2.25e-1911
pharyngeal arch system1.85e-1218
endocrine gland4.03e-0735
Disease
Ontology termp-valuen
papillary adenocarcinoma5.42e-1951
adenocarcinoma2.15e-0925


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)
MA0003.10.000498485
MA0004.10.631966
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.00118158
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.302644
MA0040.10.548121
MA0041.10.664972
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.0777637
MA0056.10
MA0057.10.551171
MA0058.10.467197
MA0059.12.08941
MA0060.10.0509127
MA0061.10.640118
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.000460837
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.11.52135
MA0084.11.10674
MA0087.10.591148
MA0088.10.0797435
MA0089.10
MA0090.11.58262
MA0091.11.19125
MA0092.11.08245
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.372085
MA0103.10.34743
MA0105.10.14145
MA0106.10.33677
MA0107.10.259598
MA0108.20.471286
MA0109.10
MA0111.10.184188
MA0113.10.350573
MA0114.10.072201
MA0115.10.850405
MA0116.10.0765991
MA0117.10.656858
MA0119.10.142224
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.830767
MA0139.10.0351037
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.0651126
MA0145.10.0322091
MA0146.10.000760962
MA0147.10.569428
MA0148.10.240905
MA0149.10.261654
MA0062.20.148712
MA0035.20.740647
MA0039.20.0350337
MA0138.20.38342
MA0002.20.393994
MA0137.20.398112
MA0104.20.188874
MA0047.20.87164
MA0112.20.0286692
MA0065.20.376744
MA0150.11.55881
MA0151.10
MA0152.10.753898
MA0153.10.714423
MA0154.10.137179
MA0155.10.025611
MA0156.10.800227
MA0157.10.421609
MA0158.10
MA0159.10.571105
MA0160.10.252705
MA0161.10
MA0162.10.00317087
MA0163.10.0944046
MA0164.10.361105
MA0080.20.740384
MA0018.20.337929
MA0099.20.754549
MA0079.22.92288e-06
MA0102.21.14323
MA0258.10.0605489
MA0259.10.591641
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

No analysis results for this cluster

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:C530&oldid=3067647"