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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:30, 17 September 2013


Full id: C96_non_acute_tonsil_spleen_Burkitt_lymphoma_appendix



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

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:0007516hemocyte development0.00197934237787974
GO:0042386hemocyte differentiation0.00197934237787974
GO:0032501multicellular organismal process0.00520319331889394
GO:0007275multicellular organismal development0.00520319331889394
GO:0032502developmental process0.00888402511410301
GO:0030097hemopoiesis0.00888402511410301
GO:0048534hemopoietic or lymphoid organ development0.00941251521246637
GO:0002520immune system development0.0095615194149862
GO:0050793regulation of developmental process0.0176344319756542
GO:0048075positive regulation of eye pigmentation0.0176344319756542
GO:0048073regulation of eye pigmentation0.0176344319756542
GO:0048087positive regulation of pigmentation0.0176344319756542
GO:0048712negative regulation of astrocyte differentiation0.0176344319756542
GO:0008283cell proliferation0.0286470947735556
GO:0017163negative regulator of basal transcription activity0.0286470947735556
GO:0048070regulation of pigmentation during development0.0286470947735556
GO:0002376immune system process0.0327294183578825
GO:0014014negative regulation of gliogenesis0.0327294183578825
GO:0045686negative regulation of glial cell differentiation0.0327294183578825
GO:0042827platelet dense granule0.0327294183578825
GO:0048710regulation of astrocyte differentiation0.0327294183578825
GO:0006906vesicle fusion0.0416427502949157
GO:0048731system development0.0450969045074524
GO:0005068transmembrane receptor protein tyrosine kinase adaptor protein activity0.0450969045074524
GO:0048069eye pigmentation0.0450969045074524
GO:0042127regulation of cell proliferation0.0450969045074524



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><br><br>


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)
MA0003.10.000330743
MA0004.10.577883
MA0006.10.000286676
MA0007.10.107866
MA0009.12.28737
MA0014.11.45598e-10
MA0017.10.891322
MA0019.10.558539
MA0024.10.41113
MA0025.10.17865
MA0027.12.60643
MA0028.10.00154031
MA0029.10.127369
MA0030.10.245799
MA0031.10.293827
MA0038.10.047012
MA0040.10.132557
MA0041.10.0598655
MA0042.10.116095
MA0043.10.0853493
MA0046.10.646931
MA0048.11.59703
MA0050.11.51052
MA0051.10.540004
MA0052.11.79653
MA0055.12.01041
MA0056.10
MA0057.10.00994698
MA0058.11.332
MA0059.19.90875
MA0060.10.00230929
MA0061.10.000529631
MA0063.10
MA0066.10.0951875
MA0067.10.114553
MA0068.10.118703
MA0069.11.31266
MA0070.10.185865
MA0071.12.35327
MA0072.10.593858
MA0073.10.00012325
MA0074.10.536928
MA0076.10.00383909
MA0077.10.342275
MA0078.12.33465
MA0081.10.930524
MA0083.10.224208
MA0084.10.215415
MA0087.10.587354
MA0088.10.000128121
MA0089.10
MA0090.10.524172
MA0091.12.56292
MA0092.10.0479231
MA0093.10.477586
MA0095.10
MA0098.10
MA0100.15.24153
MA0101.10.00110271
MA0103.12.63793
MA0105.13.00584e-07
MA0106.10.00287423
MA0107.10.000143583
MA0108.20.155784
MA0109.10
MA0111.10.759218
MA0113.10.428095
MA0114.10.384606
MA0115.10.281231
MA0116.12.49292
MA0117.10.0253495
MA0119.11.34816
MA0122.10.124826
MA0124.10.513694
MA0125.10.163879
MA0130.10
MA0131.10.15513
MA0132.10
MA0133.10
MA0135.11.98739
MA0136.10.783448
MA0139.10.0436403
MA0140.10.105699
MA0141.11.75174
MA0142.10.124495
MA0143.10.282914
MA0144.10.29638
MA0145.11.54616
MA0146.10.0150436
MA0147.10.167511
MA0148.10.0142724
MA0149.10.0493329
MA0062.20.000381421
MA0035.20.104799
MA0039.20.000818354
MA0138.20.378416
MA0002.22.93937
MA0137.20.146128
MA0104.20.146597
MA0047.20.00233723
MA0112.21.57112
MA0065.20.0658561
MA0150.10.00478263
MA0151.10
MA0152.10.421972
MA0153.10.0382859
MA0154.17.11213
MA0155.10.250359
MA0156.10.767435
MA0157.10.980048
MA0158.10
MA0159.10.83316
MA0160.10.800915
MA0161.10
MA0162.18.25551e-08
MA0163.11.752e-05
MA0164.12.47467
MA0080.20.373959
MA0018.20.148447
MA0099.20.0112727
MA0079.22.52702e-13
MA0102.20.238831
MA0258.12.21678
MA0259.10.0159144
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
MEF2C#4208132.740038818388330.00107857570305480.00761426036577937



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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