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Coexpression cluster:C482: Difference between revisions

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{{Coexpression_clusters
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|full_id=C482_CD14_Mast_Fibroblast_Smooth_Neutrophils_Basophils_Mesenchymal
|id=C482
}}

Latest revision as of 11:24, 17 September 2013


Full id: C482_CD14_Mast_Fibroblast_Smooth_Neutrophils_Basophils_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr19:54371114..54371180,+p1@MYADM
Hg19::chr19:54376789..54376808,+p1@CU680730
Hg19::chr19:54376870..54376881,+p3@CU680730
Hg19::chr19:54376882..54376900,+p13@MYADM
Hg19::chr19:54376940..54376951,+p21@MYADM
Hg19::chr19:54376953..54376990,+p9@MYADM
Hg19::chr19:54376994..54377008,+p19@MYADM
Hg19::chr19:54377035..54377067,+p4@MYADM
Hg19::chr19:54377068..54377094,+p6@MYADM
Hg19::chr19:54377109..54377143,+p11@MYADM
Hg19::chr19:54377161..54377188,-p@chr19:54377161..54377188
-
Hg19::chr19:54377174..54377207,+p10@MYADM
Hg19::chr19:54377395..54377415,+p15@MYADM
Hg19::chr19:54377455..54377484,+p5@MYADM
Hg19::chr19:54377502..54377530,+p@chr19:54377502..54377530
+
Hg19::chr19:54377553..54377565,+p@chr19:54377553..54377565
+
Hg19::chr19:54377568..54377592,+p@chr19:54377568..54377592
+
Hg19::chr19:54377605..54377620,+p@chr19:54377605..54377620
+
Hg19::chr19:54377633..54377725,+p@chr19:54377633..54377725
+
Hg19::chr19:54377736..54378002,+p@chr19:54377736..54378002
+


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
classical monocyte4.18e-1642
CD14-positive, CD16-negative classical monocyte4.18e-1642
defensive cell6.16e-1548
phagocyte6.16e-1548
multi fate stem cell9.27e-15427
somatic stem cell1.89e-13433
myeloid leukocyte7.67e-1372
stem cell1.21e-12441
granulocyte monocyte progenitor cell9.75e-1167
somatic cell7.67e-10588
myeloid lineage restricted progenitor cell2.18e-0966
macrophage dendritic cell progenitor3.27e-0961
mesenchymal cell3.64e-09354
connective tissue cell5.13e-09361
smooth muscle cell1.14e-0843
smooth muscle myoblast1.14e-0843
monopoietic cell1.23e-0859
monocyte1.23e-0859
monoblast1.23e-0859
promonocyte1.23e-0859
contractile cell1.33e-0859
fibroblast1.51e-0876
stuff accumulating cell1.70e-0887
mesodermal cell8.21e-08121
muscle cell8.24e-0855
vascular associated smooth muscle cell1.05e-0732
muscle precursor cell1.42e-0758
myoblast1.42e-0758
multi-potent skeletal muscle stem cell1.42e-0758
Uber Anatomy
Ontology termp-valuen
mesoderm3.41e-29315
mesoderm-derived structure3.41e-29315
presumptive mesoderm3.41e-29315
lateral plate mesoderm4.25e-21203
musculoskeletal system4.54e-14167
epithelial tube9.99e-11117
circulatory system4.36e-10112
cardiovascular system5.40e-10109
artery2.73e-0942
arterial blood vessel2.73e-0942
arterial system2.73e-0942
trunk mesenchyme3.76e-09122
bone marrow3.80e-0976
connective tissue9.13e-09371
epithelial vesicle1.13e-0878
splanchnic layer of lateral plate mesoderm1.47e-0883
epithelial tube open at both ends2.20e-0859
blood vessel2.20e-0859
blood vasculature2.20e-0859
vascular cord2.20e-0859
hematopoietic system2.60e-0898
blood island2.60e-0898
bone element7.26e-0882
hemolymphoid system8.27e-08108
mesenchyme9.20e-08160
entire embryonic mesenchyme9.20e-08160
multi-cellular organism1.03e-07656
systemic artery1.08e-0733
systemic arterial system1.08e-0733
muscle tissue1.31e-0764
musculature1.31e-0764
musculature of body1.31e-0764
skeletal muscle tissue1.94e-0762
striated muscle tissue1.94e-0762
myotome1.94e-0762
vessel2.22e-0768
dense mesenchyme tissue3.22e-0773
somite4.10e-0771
presomitic mesoderm4.10e-0771
presumptive segmental plate4.10e-0771
dermomyotome4.10e-0771
trunk paraxial mesoderm4.10e-0771
vasculature4.97e-0778
vascular system4.97e-0778
anatomical system5.83e-07624
paraxial mesoderm6.76e-0772
presumptive paraxial mesoderm6.76e-0772
skeletal system8.07e-07100
anatomical group9.29e-07625


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)
MA0003.10.127484
MA0004.10.180726
MA0006.13.34937
MA0007.10.168078
MA0009.10.561062
MA0014.10.13276
MA0017.11.69072
MA0019.13.05468
MA0024.10.467291
MA0025.10.684106
MA0027.12.13512
MA0028.10.0924235
MA0029.10.484339
MA0030.10.474212
MA0031.10.41796
MA0038.10.25521
MA0040.10.489524
MA0041.10.193578
MA0042.10.171628
MA0043.10.561349
MA0046.10.551181
MA0048.10.113667
MA0050.11.56879
MA0051.10.702073
MA0052.10.492957
MA0055.110.8081
MA0056.10
MA0057.10.395732
MA0058.10.119655
MA0059.10.118893
MA0060.10.0338613
MA0061.11.56479
MA0063.10
MA0066.10.710255
MA0067.10.858361
MA0068.10.0158377
MA0069.10.547689
MA0070.10.537571
MA0071.12.62683
MA0072.10.533514
MA0073.10.202089
MA0074.10.251422
MA0076.10.129195
MA0077.10.526569
MA0078.10.33032
MA0081.10.118989
MA0083.10.567893
MA0084.11.03923
MA0087.10.531309
MA0088.11.66996
MA0089.10
MA0090.10.138104
MA0091.11.62784
MA0092.10.157193
MA0093.10.0855877
MA0095.10
MA0098.10
MA0100.10.265855
MA0101.10.0872967
MA0103.10.27232
MA0105.16.01528
MA0106.10.28721
MA0107.11.15991
MA0108.20.415325
MA0109.10
MA0111.10.146643
MA0113.10.300221
MA0114.10.188951
MA0115.10.785493
MA0116.10.0541555
MA0117.10.595385
MA0119.10.109564
MA0122.11.50144
MA0124.10.746208
MA0125.10.667416
MA0130.10
MA0131.10.345226
MA0132.10
MA0133.10
MA0135.10.588754
MA0136.10.260607
MA0139.10.0220308
MA0140.10.224213
MA0141.10.755821
MA0142.10.39079
MA0143.10.300362
MA0144.10.0449457
MA0145.18.3011
MA0146.10.253174
MA0147.10.0556388
MA0148.10.198049
MA0149.10.21714
MA0062.20.0239298
MA0035.20.223695
MA0039.20.00467442
MA0138.20.331323
MA0002.21.24341
MA0137.20.0959012
MA0104.20.0336072
MA0047.20.277681
MA0112.20.0489386
MA0065.20.623555
MA0150.11.94158
MA0151.10
MA0152.10.229055
MA0153.10.65174
MA0154.10.786718
MA0155.10.752516
MA0156.10.0971366
MA0157.10.367703
MA0158.10
MA0159.10.785302
MA0160.13.3113
MA0161.10
MA0162.10.680828
MA0163.10.0840723
MA0164.10.310173
MA0080.20.289769
MA0018.23.0419
MA0099.20.229319
MA0079.20.00354552
MA0102.21.07547
MA0258.11.01888
MA0259.10.0592752
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
POLR2A#5430192.040080517730175.50039674165619e-060.000166653883174305



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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