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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.347910860252101,

Latest revision as of 11:28, 17 September 2013


Full id: C660_Monocytederived_liposarcoma_Smooth_Synoviocyte_pituitary_Chondrocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:113826524..113826537,+p@chr12:113826524..113826537
+
Hg19::chr12:113827227..113827411,+p@chr12:113827227..113827411
+
Hg19::chr12:113827798..113827869,+p@chr12:113827798..113827869
+
Hg19::chr12:113827870..113828002,+p@chr12:113827870..113828002
+
Hg19::chr12:113828019..113828031,+p@chr12:113828019..113828031
+
Hg19::chr12:113828038..113828067,+p@chr12:113828038..113828067
+
Hg19::chr12:113828070..113828082,+p@chr12:113828070..113828082
+
Hg19::chr12:113828083..113828138,+p@chr12:113828083..113828138
+
Hg19::chr12:113828163..113828232,+p@chr12:113828163..113828232
+
Hg19::chr12:113828235..113828264,+p@chr12:113828235..113828264
+
Hg19::chr12:113828268..113828337,+p@chr12:113828268..113828337
+
Hg19::chr12:113828339..113828367,+p@chr12:113828339..113828367
+
Hg19::chr12:113828372..113828491,+p@chr12:113828372..113828491
+


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
fibroblast3.32e-0876
mesothelial cell6.08e-0719
Uber Anatomy
Ontology termp-valuen
organ3.19e-12503
multi-cellular organism2.04e-09656
neural tube8.87e-0956
neural rod8.87e-0956
future spinal cord8.87e-0956
neural keel8.87e-0956
regional part of nervous system4.05e-0853
regional part of brain4.05e-0853
anatomical system7.80e-08624
anatomical group8.66e-08625
neural plate1.13e-0782
presumptive neural plate1.13e-0782
regional part of forebrain5.08e-0741
forebrain5.08e-0741
anterior neural tube5.08e-0741
future forebrain5.08e-0741


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)
MA0003.10.000247383
MA0004.10.297884
MA0006.10.169524
MA0007.10.282081
MA0009.10.724811
MA0014.10.000874969
MA0017.10.199401
MA0019.10.428118
MA0024.10.6245
MA0025.10.854131
MA0027.12.32165
MA0028.10.181601
MA0029.10.642879
MA0030.10.63197
MA0031.10.570886
MA0038.12.67375
MA0040.10.648455
MA0041.10.313738
MA0042.10.286538
MA0043.10.725115
MA0046.10.714324
MA0048.10.0323146
MA0050.10.287284
MA0051.10.383704
MA0052.10.652145
MA0055.10.00493639
MA0056.10
MA0057.11.68462
MA0058.10.219229
MA0059.10.218203
MA0060.10.2996
MA0061.10.0732084
MA0063.10
MA0066.11.00709
MA0067.11.03434
MA0068.10.0529803
MA0069.10.710614
MA0070.121.9931
MA0071.10.35315
MA0072.10.695528
MA0073.16.36752
MA0074.10.383033
MA0076.10.231962
MA0077.10.688123
MA0078.10.473657
MA0081.10.218332
MA0083.10.732051
MA0084.11.21913
MA0087.10.693179
MA0088.11.19474
MA0089.10
MA0090.10.243681
MA0091.10.30011
MA0092.10.268302
MA0093.10.511707
MA0095.10
MA0098.10
MA0100.10.399896
MA0101.10.17426
MA0103.10.489275
MA0105.10.0255214
MA0106.10.424592
MA0107.10.121572
MA0108.20.568002
MA0109.10
MA0111.11.30787
MA0113.10.439505
MA0114.10.118142
MA0115.10.959312
MA0116.10.123927
MA0117.10.76111
MA0119.10.205526
MA0122.11.8483
MA0124.10.918678
MA0125.10.83671
MA0130.10
MA0131.10.490408
MA0132.10
MA0133.10
MA0135.10.754112
MA0136.10.393782
MA0139.10.0663461
MA0140.11.65424
MA0141.10.216821
MA0142.10.541045
MA0143.10.439666
MA0144.10.108694
MA0145.10.0164225
MA0146.10.104779
MA0147.10.793354
MA0148.10.319209
MA0149.13.38351
MA0062.20.0702147
MA0035.21.65207
MA0039.20.0426227
MA0138.20.474787
MA0002.20.99121
MA0137.20.186529
MA0104.20.088751
MA0047.20.413608
MA0112.20.0689988
MA0065.20.0171659
MA0150.10.238884
MA0151.10
MA0152.15.5792
MA0153.10.820317
MA0154.10.0246626
MA0155.10.0132945
MA0156.10.18827
MA0157.10.515488
MA0158.10
MA0159.10.398903
MA0160.10.332385
MA0161.10
MA0162.12.87855
MA0163.10.02611
MA0164.10.450848
MA0080.20.171855
MA0018.20.425847
MA0099.21.67556
MA0079.22.14432e-07
MA0102.21.25596
MA0258.10.335505
MA0259.10.132107
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
EGR1#1958103.837060842161641.64056155090743e-050.000378900061510882



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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