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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.136654746181948

Latest revision as of 12:02, 17 September 2013


Full id: C2290_Neutrophils_CD8_Eosinophils_CD14_CD4_hepatocellular_Natural



Phase1 CAGE Peaks

Hg19::chr14:24899263..24899272,+p3@KHNYN
Hg19::chr2:42396472..42396563,+p1@EML4
Hg19::chr2:42396574..42396604,+p2@EML4
Hg19::chr7:130626272..130626369,-p@chr7:130626272..130626369
-


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:0003993acid phosphatase activity0.0442717532085247
GO:0007067mitosis0.0474160538625392
GO:0000087M phase of mitotic cell cycle0.0474160538625392
GO:0005874microtubule0.0474160538625392
GO:0000279M phase0.0474160538625392
GO:0007017microtubule-based process0.0474160538625392
GO:0000278mitotic cell cycle0.0474160538625392
GO:0004252serine-type endopeptidase activity0.0474160538625392
GO:0022403cell cycle phase0.0474160538625392
GO:0008236serine-type peptidase activity0.0474160538625392
GO:0017171serine hydrolase activity0.0474160538625392



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
leukocyte8.09e-42136
nongranular leukocyte2.07e-34115
hematopoietic lineage restricted progenitor cell2.64e-32120
hematopoietic stem cell9.05e-28168
angioblastic mesenchymal cell9.05e-28168
hematopoietic oligopotent progenitor cell1.58e-25161
hematopoietic multipotent progenitor cell1.58e-25161
hematopoietic cell1.67e-24177
myeloid leukocyte6.68e-2472
classical monocyte1.48e-2342
CD14-positive, CD16-negative classical monocyte1.48e-2342
defensive cell2.30e-2248
phagocyte2.30e-2248
granulocyte monocyte progenitor cell2.31e-2067
macrophage dendritic cell progenitor8.09e-2061
monopoietic cell9.70e-1959
monocyte9.70e-1959
monoblast9.70e-1959
promonocyte9.70e-1959
myeloid lineage restricted progenitor cell1.69e-1766
lymphocyte8.64e-1453
common lymphoid progenitor8.64e-1453
lymphoid lineage restricted progenitor cell1.72e-1352
myeloid cell2.71e-12108
common myeloid progenitor2.71e-12108
nucleate cell2.75e-1255
mesenchymal cell3.21e-11354
mature alpha-beta T cell1.10e-1018
alpha-beta T cell1.10e-1018
immature T cell1.10e-1018
mature T cell1.10e-1018
immature alpha-beta T cell1.10e-1018
connective tissue cell1.49e-10361
motile cell5.49e-09386
CD8-positive, alpha-beta T cell4.76e-0711
T cell6.03e-0725
pro-T cell6.03e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.31e-2398
blood island2.31e-2398
hemolymphoid system6.52e-19108
bone element1.23e-1882
bone marrow2.65e-1776
skeletal element2.21e-1590
immune system1.00e-1493
skeletal system1.22e-14100
connective tissue8.70e-12371


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)
MA0003.11.45381
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.13.66086
MA0059.11.47051
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.14.51906
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
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
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.12.92476
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.24.29465
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.15.86746
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.22.02192
MA0099.20.7872
MA0079.23.5408
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
ATF3#467211.23158726300440.01119559039922220.0411246576288817
E2F6#187645.017155731697390.00157802193473060.00995752720931237
HEY1#2346244.040111043105710.00375304636917980.0185712313915839
MAX#414946.452555509007120.0005767613195645490.0048483882367999
REST#597837.237521537096020.004104697304192610.0195749078425832
TAF1#687243.343046285745290.008005664898701650.0321590690547906
THAP1#55145215.68457230142570.005840469678357920.0262432910010766
USF1#739134.771124457905970.01370465887188020.0482895029662717



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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