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{{Coexpression_clusters
{
|full_id=C1020_Mast_CD4_acute_chronic_CD8_thymus_Peripheral
 

Latest revision as of 11:35, 17 September 2013


Full id: C1020_Mast_CD4_acute_chronic_CD8_thymus_Peripheral



Phase1 CAGE Peaks

Hg19::chr12:55378459..55378469,-p4@KIAA0748
Hg19::chr12:55378470..55378554,-p1@KIAA0748
Hg19::chr16:30671223..30671261,+p4@FBRS
Hg19::chr2:196521610..196521660,+p5@SLC39A10
Hg19::chrX:135861719..135861749,-p@chrX:135861719..135861749
-
Hg19::chrX:135863036..135863078,-p1@ARHGEF6
Hg19::chrX:135863084..135863115,-p2@ARHGEF6
Hg19::chrX:135863137..135863146,-p11@ARHGEF6


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell3.62e-70168
angioblastic mesenchymal cell3.62e-70168
hematopoietic cell2.73e-66177
hematopoietic oligopotent progenitor cell2.99e-65161
hematopoietic multipotent progenitor cell2.99e-65161
leukocyte3.01e-57136
hematopoietic lineage restricted progenitor cell1.00e-46120
nongranular leukocyte4.93e-44115
myeloid cell5.46e-36108
common myeloid progenitor5.46e-36108
nucleate cell1.98e-2655
lymphocyte5.75e-2653
common lymphoid progenitor5.75e-2653
lymphoid lineage restricted progenitor cell2.03e-2552
myeloid leukocyte7.62e-2472
granulocyte monocyte progenitor cell1.16e-2067
myeloid lineage restricted progenitor cell6.29e-2066
mesenchymal cell3.71e-18354
connective tissue cell2.32e-17361
macrophage dendritic cell progenitor5.74e-1761
monopoietic cell3.16e-1659
monocyte3.16e-1659
monoblast3.16e-1659
promonocyte3.16e-1659
T cell3.70e-1625
pro-T cell3.70e-1625
classical monocyte1.50e-1442
CD14-positive, CD16-negative classical monocyte1.50e-1442
defensive cell2.77e-1348
phagocyte2.77e-1348
mature alpha-beta T cell8.44e-1318
alpha-beta T cell8.44e-1318
immature T cell8.44e-1318
mature T cell8.44e-1318
immature alpha-beta T cell8.44e-1318
motile cell1.91e-12386
multi fate stem cell3.70e-12427
stem cell2.60e-11441
somatic stem cell5.19e-11433
lymphocyte of B lineage3.32e-0924
pro-B cell3.32e-0924
CD8-positive, alpha-beta T cell3.30e-0811
B cell6.96e-0814
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.16e-2898
blood island3.16e-2898
hemolymphoid system4.25e-27108
immune system1.70e-2093
bone marrow4.02e-1876
connective tissue1.92e-16371
bone element1.39e-1582
skeletal element6.18e-1390
adult organism1.17e-11114
skeletal system1.09e-10100
blood5.42e-0815
haemolymphatic fluid5.42e-0815
organism substance5.42e-0815
lateral plate mesoderm4.35e-07203
Disease
Ontology termp-valuen
hematologic cancer4.58e-1551
immune system cancer4.58e-1551
leukemia1.46e-1439
myeloid leukemia1.47e-1031


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)
MA0003.10.248189
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.134069
MA0017.10.337901
MA0019.14.8903
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.12.12623
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.131075
MA0074.11.36092
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.11.69066
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.199853
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.13.58758
MA0136.10.564434
MA0139.10.155155
MA0140.11.28413
MA0141.10.359385
MA0142.10.724856
MA0143.11.49284
MA0144.10.218541
MA0145.10.830366
MA0146.10.418694
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.22.21238
MA0039.20.00133745
MA0138.20.653421
MA0002.21.61227
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0752715
MA0163.10.0517199
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.032423
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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#543082.147453176558070.002210725788971910.0127153866435971



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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