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Coexpression cluster:C3332: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3332_leiomyoma_Fibroblast_Mallassezderived_Smooth_CD14_Osteoblast_mesenchymal
|id=C3332
}}

Latest revision as of 12:24, 17 September 2013


Full id: C3332_leiomyoma_Fibroblast_Mallassezderived_Smooth_CD14_Osteoblast_mesenchymal



Phase1 CAGE Peaks

Hg19::chr12:75874525..75874549,+p1@GLIPR1
Hg19::chr12:75874561..75874574,+p3@GLIPR1
Hg19::chr12:75874580..75874611,+p2@GLIPR1


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
multi fate stem cell4.77e-38427
somatic stem cell1.65e-35433
stem cell7.10e-33441
somatic cell2.89e-30588
connective tissue cell3.60e-24361
mesenchymal cell1.58e-23354
macrophage dendritic cell progenitor1.14e-2261
monopoietic cell3.75e-2259
monocyte3.75e-2259
monoblast3.75e-2259
promonocyte3.75e-2259
defensive cell2.68e-2148
phagocyte2.68e-2148
myeloid leukocyte1.22e-2072
classical monocyte2.28e-1842
CD14-positive, CD16-negative classical monocyte2.28e-1842
granulocyte monocyte progenitor cell1.74e-1767
motile cell3.72e-17386
myeloid lineage restricted progenitor cell7.12e-1666
muscle precursor cell1.97e-1558
myoblast1.97e-1558
multi-potent skeletal muscle stem cell1.97e-1558
vascular associated smooth muscle cell2.61e-1432
muscle cell2.69e-1455
smooth muscle cell3.31e-1443
smooth muscle myoblast3.31e-1443
native cell7.06e-14722
leukocyte4.62e-13136
contractile cell5.15e-1359
nongranular leukocyte4.71e-12115
animal cell1.65e-11679
eukaryotic cell1.65e-11679
fibroblast5.26e-1176
electrically responsive cell7.84e-1161
electrically active cell7.84e-1161
hematopoietic lineage restricted progenitor cell2.18e-09120
stuff accumulating cell1.67e-0887
myeloid cell4.47e-08108
common myeloid progenitor4.47e-08108
mesodermal cell1.40e-07121
skin fibroblast2.43e-0723
Uber Anatomy
Ontology termp-valuen
musculoskeletal system4.99e-32167
mesoderm1.12e-26315
mesoderm-derived structure1.12e-26315
presumptive mesoderm1.12e-26315
lateral plate mesoderm9.34e-26203
connective tissue3.92e-24371
bone marrow4.13e-1976
hematopoietic system5.56e-1998
blood island5.56e-1998
skeletal element5.97e-1990
skeletal system2.14e-18100
bone element1.45e-1682
hemolymphoid system2.33e-16108
immune system5.48e-1593
somite7.88e-1471
presomitic mesoderm7.88e-1471
presumptive segmental plate7.88e-1471
dermomyotome7.88e-1471
trunk paraxial mesoderm7.88e-1471
artery1.12e-1342
arterial blood vessel1.12e-1342
arterial system1.12e-1342
dense mesenchyme tissue1.17e-1373
paraxial mesoderm1.79e-1372
presumptive paraxial mesoderm1.79e-1372
skeletal muscle tissue8.74e-1362
striated muscle tissue8.74e-1362
myotome8.74e-1362
multilaminar epithelium2.06e-1283
muscle tissue4.28e-1264
musculature4.28e-1264
musculature of body4.28e-1264
systemic artery1.04e-1133
systemic arterial system1.04e-1133
epithelial vesicle1.05e-1178
cardiovascular system1.25e-11109
circulatory system1.39e-10112
splanchnic layer of lateral plate mesoderm1.97e-0983
epithelial tube open at both ends3.06e-0959
blood vessel3.06e-0959
blood vasculature3.06e-0959
vascular cord3.06e-0959
vasculature5.45e-0978
vascular system5.45e-0978
tissue2.96e-07773
vessel6.44e-0768


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.18.72191
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
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
MA0108.22.59836
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
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.15.66197
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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
CEBPB#105137.971147625824820.001974187055288560.0115037729100754
ELF1#199734.258097958807540.01295179875054610.0460688273860188
EP300#203336.77394172622320.003216880500103790.0167089959989228
FOS#235338.99795530889440.001372499272417130.00895666405348491
JUN#3725312.51282919233630.0005103313992726250.00443452042671051
MEF2A#4205318.74323090964410.0001518243905622470.00194939605679007
NFKB1#479035.488063424193840.006049381815655430.0268938952598858
PAX5#507936.669565531177830.003370290999677260.0172501750411808
POU2F2#545239.106124057742520.001324165192682130.00880576176749627
SRF#6722313.79717826216780.0003806615025800190.00374243685097944
STAT3#6774310.51946499715420.0008589184530415310.0064170959523002
YY1#752834.911170749853860.008441455341808260.0328385724454543



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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