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Coexpression cluster:C3131: Difference between revisions

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{{Coexpression_clusters
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MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;0.387745,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3131_CD8_Natural_Peripheral_CD4_Eosinophils_CD14_Basophils
|id=C3131
}}

Latest revision as of 12:19, 17 September 2013


Full id: C3131_CD8_Natural_Peripheral_CD4_Eosinophils_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr11:207734..207745,+p7@RIC8A
Hg19::chr11:208610..208627,-p@chr11:208610..208627
-
Hg19::chr11:236025..236096,+p3@PSMD13


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:0001965G-protein alpha-subunit binding0.00188387666372531
GO:0005838proteasome regulatory particle (sensu Eukaryota)0.00565079814737156
GO:0000502proteasome complex (sensu Eukaryota)0.0232098562760032



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
leukocyte1.36e-25136
myeloid leukocyte2.81e-1972
hematopoietic cell1.39e-18177
hematopoietic stem cell2.14e-18168
angioblastic mesenchymal cell2.14e-18168
hematopoietic lineage restricted progenitor cell1.93e-17120
nongranular leukocyte4.37e-17115
granulocyte monocyte progenitor cell1.40e-1567
classical monocyte2.52e-1542
CD14-positive, CD16-negative classical monocyte2.52e-1542
hematopoietic oligopotent progenitor cell7.05e-15161
hematopoietic multipotent progenitor cell7.05e-15161
macrophage dendritic cell progenitor8.28e-1461
myeloid lineage restricted progenitor cell8.86e-1466
defensive cell1.04e-1348
phagocyte1.04e-1348
mesenchymal cell1.86e-13354
multi fate stem cell4.53e-13427
stem cell1.14e-12441
somatic stem cell1.18e-12433
monopoietic cell1.81e-1259
monocyte1.81e-1259
monoblast1.81e-1259
promonocyte1.81e-1259
connective tissue cell1.92e-12361
myeloid cell4.88e-11108
common myeloid progenitor4.88e-11108
motile cell6.23e-11386
intermediate monocyte7.77e-109
CD14-positive, CD16-positive monocyte7.77e-109
blood cell1.11e-0811
somatic cell3.28e-08588
CD4-positive, alpha-beta T cell1.53e-076
granulocyte6.56e-078
native cell8.00e-07722
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.69e-1498
blood island1.69e-1498
bone element1.83e-1482
bone marrow3.13e-1476
skeletal element3.06e-1390
hemolymphoid system6.98e-13108
connective tissue3.18e-12371
immune system3.71e-1293
skeletal system1.74e-11100
lateral plate mesoderm4.31e-11203
musculoskeletal system2.06e-08167
mesoderm1.21e-07315
mesoderm-derived structure1.21e-07315
presumptive mesoderm1.21e-07315


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.03569
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
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
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
MA0162.10.8915
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
CCNT2#90536.336201576962630.003930750035764890.0189190102302064
EGR1#195834.988179094810140.008056488137383440.0319115395979895
HMGN3#932438.178547723350590.001827766942164210.0108318760524705
PAX5#507936.669565531177830.003370290999677260.017232440111392
SIN3A#2594235.408884726815140.006318961977991520.027548258057249
YY1#752834.911170749853860.008441455341808260.032800697761854



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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