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Coexpression cluster:C34

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Full id: C34_placenta_chorionic_choriocarcinoma_mesothelioma_Wilms_Smooth_bile



Phase1 CAGE Peaks


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
0.000115651661790730.0366037509567662457Steroid hormone biosynthesis (KEGG):00140
6.40868917991401e-050.03660375095676626155Myometrial Relaxation and Contraction Pathways (Wikipathways):WP289



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:0007565female pregnancy4.52546383755931e-20
GO:0022414reproductive process3.42221756911212e-14
GO:0051704multi-organism process1.99898290084869e-12
GO:0005615extracellular space0.000141411534361725
GO:0044421extracellular region part0.000141411534361725
GO:0048856anatomical structure development0.000382184068535946
GO:0005179hormone activity0.000626187379131387
GO:0048513organ development0.00119064252033395
GO:0032502developmental process0.00147711722873278
GO:0000267cell fraction0.00192807537599954
GO:0048731system development0.00253408582451526
GO:0007275multicellular organismal development0.00362898409182289
GO:0005509calcium ion binding0.0102040531114813
GO:0006694steroid biosynthetic process0.0102040531114813
GO:0032501multicellular organismal process0.016636182008562
GO:0042446hormone biosynthetic process0.0168072988696188
GO:0008202steroid metabolic process0.0302048214899774
GO:0017156calcium ion-dependent exocytosis0.0302048214899774
GO:0030246carbohydrate binding0.0302048214899774
GO:0005625soluble fraction0.0324457152566783
GO:0005516calmodulin binding0.037111778004254
GO:0005515protein binding0.0419747494165031
GO:0005102receptor binding0.0490815773895158



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><br>


Uber Anatomy
Ontology termp-valuen
placenta7.35e-184
allantois7.35e-184
chorion8.16e-117


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
MA0004.10.0388998
MA0006.12.54466e-05
MA0007.10.0223389
MA0009.10.207469
MA0014.10
MA0017.10.0977899
MA0019.10.0429676
MA0024.10.00048742
MA0025.10.235869
MA0027.10.750423
MA0028.11.84027e-08
MA0029.12.52354
MA0030.10.189928
MA0031.11.9196
MA0038.10.23797
MA0040.11.18963
MA0041.10.33298
MA0042.10.52148
MA0043.10.126167
MA0046.10.288411
MA0048.10.00443716
MA0050.10.23966
MA0051.10.222763
MA0052.10.0932932
MA0055.10.0224129
MA0056.10
MA0057.11.61945e-05
MA0058.10.0931415
MA0059.10.0171135
MA0060.11.66318e-10
MA0061.19.3226e-05
MA0063.10
MA0066.11.68187
MA0067.10.437953
MA0068.10.000793715
MA0069.10.18066
MA0070.10.682158
MA0071.11.17238
MA0072.10.495433
MA0073.15.0483e-12
MA0074.10.084036
MA0076.13.31645e-10
MA0077.10.142728
MA0078.10.0694063
MA0081.10.554578
MA0083.12.23329
MA0084.10.141152
MA0087.10.348697
MA0088.10.00206988
MA0089.10
MA0090.11.29619
MA0091.11.30232
MA0092.10.710854
MA0093.10.0367929
MA0095.10
MA0098.10
MA0100.10.00307482
MA0101.18.54139e-05
MA0103.10.71029
MA0105.11.06417e-10
MA0106.10.420177
MA0107.10.000644758
MA0108.21.39749
MA0109.10
MA0111.10.74586
MA0113.10.627981
MA0114.10.515819
MA0115.11.62057
MA0116.10.243094
MA0117.10.18025
MA0119.10.728634
MA0122.10.349115
MA0124.10.367165
MA0125.11.19634
MA0130.10
MA0131.14.10935e-05
MA0132.10
MA0133.10
MA0135.10.269884
MA0136.10.201014
MA0139.11.24014e-08
MA0140.12.95438
MA0141.12.7642
MA0142.10.0530603
MA0143.10.406708
MA0144.13.54503
MA0145.11.47934
MA0146.13.19675e-14
MA0147.14.24119e-07
MA0148.11.8198
MA0149.11.35917e-07
MA0062.23.73957e-12
MA0035.23.99991
MA0039.25.20206e-13
MA0138.20.0252022
MA0002.20.536681
MA0137.21.48146
MA0104.21.12339e-09
MA0047.21.29074
MA0112.20.72474
MA0065.20.0468961
MA0150.10.106247
MA0151.10
MA0152.10.667624
MA0153.10.0974786
MA0154.10.193951
MA0155.10.0170688
MA0156.10.000568331
MA0157.11.10351
MA0158.10
MA0159.12.31034
MA0160.11.19154
MA0161.10
MA0162.10
MA0163.12.70012e-15
MA0164.11.57733
MA0080.20.0369202
MA0018.20.138935
MA0099.20.670527
MA0079.20
MA0102.20.682227
MA0258.12.33047
MA0259.14.50032e-07
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
GATA3#2625452.303840669312542.89708442636e-071.46593314149521e-05



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