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{{Coexpression_clusters
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|full_id=C4200_Mast_immature_CD4_Natural_CD8_Basophils_hairy
|id=C4200
}}

Latest revision as of 12:41, 17 September 2013


Full id: C4200_Mast_immature_CD4_Natural_CD8_Basophils_hairy



Phase1 CAGE Peaks

Hg19::chr2:235403097..235403137,+p@chr2:235403097..235403137
+
Hg19::chr6:159071015..159071096,+p1@SYTL3
Hg19::chr6:159071097..159071104,+p9@SYTL3


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
leukocyte2.02e-50136
hematopoietic cell1.33e-38177
hematopoietic stem cell6.27e-38168
angioblastic mesenchymal cell6.27e-38168
hematopoietic lineage restricted progenitor cell3.20e-36120
hematopoietic oligopotent progenitor cell4.88e-35161
hematopoietic multipotent progenitor cell4.88e-35161
nongranular leukocyte2.29e-33115
myeloid leukocyte8.92e-3272
classical monocyte8.22e-2942
CD14-positive, CD16-negative classical monocyte8.22e-2942
granulocyte monocyte progenitor cell3.39e-2567
defensive cell1.33e-2448
phagocyte1.33e-2448
myeloid lineage restricted progenitor cell6.07e-2366
myeloid cell1.04e-22108
common myeloid progenitor1.04e-22108
macrophage dendritic cell progenitor1.51e-2161
monopoietic cell5.86e-2059
monocyte5.86e-2059
monoblast5.86e-2059
promonocyte5.86e-2059
T cell8.97e-2025
pro-T cell8.97e-2025
mature alpha-beta T cell5.81e-1918
alpha-beta T cell5.81e-1918
immature T cell5.81e-1918
mature T cell5.81e-1918
immature alpha-beta T cell5.81e-1918
CD8-positive, alpha-beta T cell4.45e-1211
lymphoid lineage restricted progenitor cell1.08e-1152
lymphocyte2.80e-1153
common lymphoid progenitor2.80e-1153
nucleate cell1.67e-1055
granulocyte3.90e-108
mesenchymal cell1.36e-08354
blood cell1.72e-0811
CD4-positive, alpha-beta T cell6.71e-086
connective tissue cell6.94e-08361
stuff accumulating cell9.37e-0887
circulating cell2.84e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.62e-3398
blood island4.62e-3398
hemolymphoid system4.92e-30108
immune system6.37e-2493
bone marrow3.31e-2376
bone element5.82e-2282
skeletal element2.18e-1890
skeletal system8.29e-15100
lateral plate mesoderm1.50e-09203
adult organism1.69e-08114
connective tissue2.90e-07371
blood4.26e-0715
haemolymphatic fluid4.26e-0715
organism substance4.26e-0715


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
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.11.55947
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.11.3784
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
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.11.98824
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
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
BCL11A#53335218.91297006907140.003639406248379680.0183914428400119
BCL3#602223.03140186915890.002464674760842910.0138577748235624
MEF2A#4205212.4954872730960.008235029478029740.0324930387871075
MEF2C#4208227.54090299508270.001729119938369690.010649735050032



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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