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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:09, 17 September 2013


Full id: C264_giant_keratoacanthoma_colon_fibrosarcoma_HES3GFP_Hep2_acute



Phase1 CAGE Peaks

Hg19::chr12:86197155..86197167,-p@chr12:86197155..86197167
-
Hg19::chr12:86197182..86197191,-p@chr12:86197182..86197191
-
Hg19::chr13:113719164..113719184,+p@chr13:113719164..113719184
+
Hg19::chr13:44875147..44875164,-p@chr13:44875147..44875164
-
Hg19::chr13:44875179..44875188,-p@chr13:44875179..44875188
-
Hg19::chr1:18081804..18081883,+p1@ACTL8
Hg19::chr1:18085798..18085805,+p@chr1:18085798..18085805
+
Hg19::chr1:18085810..18085839,+p@chr1:18085810..18085839
+
Hg19::chr1:18085848..18085860,+p@chr1:18085848..18085860
+
Hg19::chr3:156837518..156837521,-p@chr3:156837518..156837521
-
Hg19::chr3:195076891..195076916,-p@chr3:195076891..195076916
-
Hg19::chr3:195076933..195076946,-p10@ACAP2
Hg19::chr3:2582028..2582039,+p@chr3:2582028..2582039
+
Hg19::chr4:21449426..21449445,-p@chr4:21449426..21449445
-
Hg19::chr5:114881383..114881387,+p@chr5:114881383..114881387
+
Hg19::chr5:142254387..142254415,+p7@ARHGAP26
Hg19::chr5:142254452..142254462,+p29@ARHGAP26
Hg19::chr5:142359457..142359470,+p@chr5:142359457..142359470
+
Hg19::chr8:120427971..120427981,+p@chr8:120427971..120427981
+
Hg19::chr8:120438506..120438508,+p@chr8:120438506..120438508
+
Hg19::chr8:127698108..127698113,+p@chr8:127698108..127698113
+
Hg19::chr8:127704087..127704091,+p@chr8:127704087..127704091
+
Hg19::chr8:127737509..127737521,+p@chr8:127737509..127737521
+
Hg19::chr8:127745909..127745927,+p@chr8:127745909..127745927
+
Hg19::chr8:127747780..127747797,+p@chr8:127747780..127747797
+
Hg19::chr8:127751345..127751347,+p@chr8:127751345..127751347
+
Hg19::chr8:127769091..127769093,+p@chr8:127769091..127769093
+
Hg19::chr8:127769885..127769888,+p@chr8:127769885..127769888
+
Hg19::chr8:128258299..128258301,-p@chr8:128258299..128258301
-
Hg19::chr8:128269679..128269686,-p@chr8:128269679..128269686
-
Hg19::chr8:128269736..128269748,-p@chr8:128269736..128269748
-
Hg19::chr8:128269825..128269838,-p@chr8:128269825..128269838
-
Hg19::chr8:128270083..128270098,-p@chr8:128270083..128270098
-
Hg19::chr8:128270240..128270252,-p@chr8:128270240..128270252
-
Hg19::chr8:128270278..128270291,-p@chr8:128270278..128270291
-
Hg19::chr8:128270444..128270453,-p@chr8:128270444..128270453
-
Hg19::chr8:128270554..128270566,-p@chr8:128270554..128270566
-
Hg19::chr8:128270603..128270612,-p@chr8:128270603..128270612
-
Hg19::chr8:128270813..128270822,-p@chr8:128270813..128270822
-
Hg19::chr8:128270842..128270851,-p@chr8:128270842..128270851
-
Hg19::chr8:128270857..128270869,-p@chr8:128270857..128270869
-
Hg19::chr8:128270900..128270912,-p@chr8:128270900..128270912
-
Hg19::chr8:128270948..128270958,-p@chr8:128270948..128270958
-
Hg19::chr8:128270983..128270993,-p@chr8:128270983..128270993
-
Hg19::chr8:128280926..128280930,-p@chr8:128280926..128280930
-
Hg19::chr9:117647322..117647330,+p@chr9:117647322..117647330
+
Hg19::chr9:117647355..117647366,+p@chr9:117647355..117647366
+
Hg19::chr9:117647523..117647530,+p@chr9:117647523..117647530
+
Hg19::chr9:125145910..125145939,+p@chr9:125145910..125145939
+
Hg19::chr9:22217093..22217104,+p@chr9:22217093..22217104
+


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:0005100Rho GTPase activator activity0.040961049527346



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
larynx2.45e-129


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)
MA0003.11.12054e-11
MA0004.12.18455
MA0006.10.00567344
MA0007.10.110204
MA0009.10.258013
MA0014.14.60776e-10
MA0017.10.467829
MA0019.11.44199
MA0024.10.188822
MA0025.10.356605
MA0027.11.73957
MA0028.10.0374073
MA0029.10.582164
MA0030.11.69097
MA0031.10.155068
MA0038.10.480379
MA0040.11.75176
MA0041.10.594159
MA0042.10.275526
MA0043.10.258233
MA0046.10.698499
MA0048.10.0564256
MA0050.10.513982
MA0051.10.0597778
MA0052.10.207152
MA0055.10.187017
MA0056.10
MA0057.10.000151315
MA0058.11.9621
MA0059.12.92115
MA0060.10.0523458
MA0061.10.0331301
MA0063.10
MA0066.10.0614483
MA0067.10.506892
MA0068.10.037411
MA0069.10.69234
MA0070.12.72264
MA0071.11.55969
MA0072.10.667425
MA0073.15.65941e-05
MA0074.10.215555
MA0076.10.181093
MA0077.10.231873
MA0078.10.100741
MA0081.10.540458
MA0083.10.263276
MA0084.10.671627
MA0087.11.23512
MA0088.10.0377312
MA0089.10
MA0090.12.20023
MA0091.10.0310353
MA0092.10.242464
MA0093.11.49748
MA0095.10
MA0098.10
MA0100.10.235688
MA0101.10.210941
MA0103.10.533443
MA0105.10.000520404
MA0106.10.0771872
MA0107.10.0425218
MA0108.20.153324
MA0109.10
MA0111.10.0868786
MA0113.10.285402
MA0114.10.0396474
MA0115.10.442812
MA0116.10.0131948
MA0117.10.284729
MA0119.10.751112
MA0122.13.14044
MA0124.10.40896
MA0125.10.342802
MA0130.10
MA0131.10.109406
MA0132.10
MA0133.10
MA0135.10.279516
MA0136.10.850843
MA0139.10.0609175
MA0140.10.402184
MA0141.10.0587281
MA0142.10.426077
MA0143.10.597738
MA0144.10.877098
MA0145.10.000592025
MA0146.11.33043e-08
MA0147.11.35799
MA0148.11.36867
MA0149.15.94865
MA0062.20.132115
MA0035.20.178284
MA0039.21.70387e-09
MA0138.22.92092
MA0002.20.4368
MA0137.20.239842
MA0104.20.913411
MA0047.20.538333
MA0112.21.28179e-05
MA0065.20.00067466
MA0150.10.192284
MA0151.10
MA0152.10.185335
MA0153.11.58074
MA0154.10.358946
MA0155.10.000315107
MA0156.10.426253
MA0157.10.122941
MA0158.10
MA0159.10.0470488
MA0160.10.159221
MA0161.10
MA0162.11.0635e-08
MA0163.14.46751e-07
MA0164.11.54604
MA0080.20.366667
MA0018.20.0777542
MA0099.20.185685
MA0079.20
MA0102.20.705393
MA0258.10.00108048
MA0259.10.82616
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
SETDB1#986954.032002617801050.00786318448419670.0322883983779594



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

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