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{{Coexpression_clusters
{
|full_id=C3798_vagina_Mast_liver_breast_CD14_thymus_heart
 

Latest revision as of 12:33, 17 September 2013


Full id: C3798_vagina_Mast_liver_breast_CD14_thymus_heart



Phase1 CAGE Peaks

Hg19::chr19:42721785..42721796,-p5@DEDD2
Hg19::chr1:161494328..161494332,+p1@HSPA6
Hg19::chr6:108581708..108581720,+p@chr6:108581708..108581720
+


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:0008633activation of pro-apoptotic gene products0.00576937228265875
GO:0016075rRNA catabolic process0.00576937228265875
GO:0008625induction of apoptosis via death domain receptors0.0211481377612689
GO:0030159receptor signaling complex scaffold activity0.0211481377612689
GO:0032947protein complex scaffold0.0211481377612689
GO:0030262apoptotic nuclear changes0.0211481377612689
GO:0008624induction of apoptosis by extracellular signals0.0273899974692192
GO:0006997nuclear organization and biogenesis0.0273899974692192
GO:0006401RNA catabolic process0.0294688058009177
GO:0006986response to unfolded protein0.0309188534090734
GO:0051789response to protein stimulus0.0309188534090734
GO:0016072rRNA metabolic process0.0355400924226299
GO:0008632apoptotic program0.0394474321398882



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
classical monocyte7.61e-3042
CD14-positive, CD16-negative classical monocyte7.61e-3042
myeloid lineage restricted progenitor cell1.76e-2566
defensive cell7.49e-2548
phagocyte7.49e-2548
myeloid leukocyte5.24e-2472
granulocyte monocyte progenitor cell6.54e-2267
monopoietic cell7.88e-2159
monocyte7.88e-2159
monoblast7.88e-2159
promonocyte7.88e-2159
macrophage dendritic cell progenitor7.92e-2061
myeloid cell7.70e-16108
common myeloid progenitor7.70e-16108
hematopoietic lineage restricted progenitor cell3.54e-12120
stuff accumulating cell2.21e-1087
leukocyte3.21e-10136
hematopoietic oligopotent progenitor cell3.09e-09161
hematopoietic multipotent progenitor cell3.09e-09161
nongranular leukocyte6.34e-09115
hematopoietic stem cell2.25e-08168
angioblastic mesenchymal cell2.25e-08168
hematopoietic cell2.19e-07177
Uber Anatomy
Ontology termp-valuen
bone marrow4.77e-1876
adult organism1.04e-17114
immune system2.97e-1693
bone element5.83e-1682
hematopoietic system8.25e-1498
blood island8.25e-1498
skeletal element1.24e-1390
hemolymphoid system1.82e-12108
skeletal system2.79e-11100
organ5.09e-07503


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.21.34467
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.181755
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
PPARGC1A#108911116.6837121212120.008545763211786680.032567449884174



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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