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Coexpression cluster:C2446: Difference between revisions

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{{Coexpression_clusters
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of circadian clock!0.0235747706921152!5187$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.0235747706921152!7128$GO:0000155!two-component sensor activity!0.0350534801834528!5187$GO:0000160!two-component signal transduction system (phosphorelay)!0.0350534801834528!5187$GO:0004673!protein histidine kinase activity!0.0350534801834528!5187$GO:0007623!circadian rhythm!0.0350534801834528!5187$GO:0016775!phosphotransferase activity, nitrogenous group as acceptor!0.0350534801834528!5187$GO:0048523!negative regulation of cellular process!0.0350534801834528!7128;5187$GO:0048519!negative regulation of biological process!0.0350534801834528!7128;5187$GO:0050794!regulation of cellular process!0.0421090180801356!7128;1831;5187$GO:0050789!regulation of biological 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70662,MA0099.2;0.7872,MA0079.2;1.38179,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2446_Mast_CD4_CD8_CD19_Natural_Neutrophils_Peripheral
|id=C2446
}}

Latest revision as of 12:06, 17 September 2013


Full id: C2446_Mast_CD4_CD8_CD19_Natural_Neutrophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr17:8059638..8059683,-p1@PER1
Hg19::chr6:138188358..138188371,+p2@TNFAIP3
Hg19::chrX:106957890..106957911,-p@chrX:106957890..106957911
-
Hg19::chrX:106960285..106960299,-p1@TSC22D3


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:0009649entrainment of circadian clock0.0235747706921152
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0235747706921152
GO:0000155two-component sensor activity0.0350534801834528
GO:0000160two-component signal transduction system (phosphorelay)0.0350534801834528
GO:0004673protein histidine kinase activity0.0350534801834528
GO:0007623circadian rhythm0.0350534801834528
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0350534801834528
GO:0048523negative regulation of cellular process0.0350534801834528
GO:0048519negative regulation of biological process0.0350534801834528
GO:0050794regulation of cellular process0.0421090180801356
GO:0050789regulation of biological process0.0477491028920505



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-22136
classical monocyte2.57e-1642
CD14-positive, CD16-negative classical monocyte2.57e-1642
hematopoietic lineage restricted progenitor cell3.23e-16120
nongranular leukocyte3.61e-16115
myeloid leukocyte2.19e-1372
defensive cell2.21e-1348
phagocyte2.21e-1348
hematopoietic stem cell1.31e-11168
angioblastic mesenchymal cell1.31e-11168
hematopoietic cell3.13e-11177
granulocyte monocyte progenitor cell9.87e-1167
hematopoietic oligopotent progenitor cell6.66e-10161
hematopoietic multipotent progenitor cell6.66e-10161
mature alpha-beta T cell1.05e-0918
alpha-beta T cell1.05e-0918
immature T cell1.05e-0918
mature T cell1.05e-0918
immature alpha-beta T cell1.05e-0918
macrophage dendritic cell progenitor1.28e-0961
monopoietic cell7.01e-0959
monocyte7.01e-0959
monoblast7.01e-0959
promonocyte7.01e-0959
myeloid lineage restricted progenitor cell8.23e-0966
stuff accumulating cell2.04e-0887
lymphoid lineage restricted progenitor cell2.16e-0752
lymphocyte9.30e-0753
common lymphoid progenitor9.30e-0753
Uber Anatomy
Ontology termp-valuen
adult organism3.18e-26114
hematopoietic system4.84e-1598
blood island4.84e-1598
hemolymphoid system5.60e-13108
bone marrow3.46e-1076
immune system8.06e-1093
bone element1.57e-0882
skeletal element7.83e-0890


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)
MA0003.10.720743
MA0004.11.69588
MA0006.11.31813
MA0007.11.65296
MA0009.11.20602
MA0014.13.08565
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.10.248209
MA0058.11.47358
MA0059.10.604454
MA0060.12.70115
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.12.27878
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.11.22348
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.23.07509
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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
BHLHE40#8553222.43590677348870.002891464496853120.0156394251689286
MAX#414934.839416631755340.01315737137836840.0466206177908537
MEF2C#4208220.6556772463120.003402570579445040.0173566996554977
PBX3#5090210.95725634337210.01174530180688030.0428380504769958
POU2F2#545236.829593043306890.004860473775203740.0227613227786074
USF1#739134.771124457905970.01370465887188020.048304170224437
USF2#739239.74414803880220.001718341848410070.0107199034888059



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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