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Coexpression cluster:C2743: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213,

Latest revision as of 12:12, 17 September 2013


Full id: C2743_immature_migratory_cord_CD19_CD14_Dendritic_Natural



Phase1 CAGE Peaks

Hg19::chr3:5229456..5229471,+p7@EDEM1
Hg19::chr3:5229484..5229499,+p4@EDEM1
Hg19::chr3:71114592..71114612,-p@chr3:71114592..71114612
-
Hg19::chr9:5438330..5438382,-p3@C9orf46


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:0030433ER-associated protein catabolic process0.018538133087335
GO:0006515misfolded or incompletely synthesized protein catabolic process0.018538133087335
GO:0004571mannosyl-oligosaccharide 1,2-alpha-mannosidase activity0.018538133087335
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.018538133087335
GO:0015924mannosyl-oligosaccharide mannosidase activity0.018538133087335
GO:0015923mannosidase activity0.0216246375331606
GO:0030176integral to endoplasmic reticulum membrane0.0226045344575232
GO:0051789response to protein stimulus0.0226045344575232
GO:0006986response to unfolded protein0.0226045344575232
GO:0031227intrinsic to endoplasmic reticulum membrane0.0226045344575232
GO:0031301integral to organelle membrane0.0467722791504351
GO:0031300intrinsic to organelle membrane0.0468754537772942



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
leukocyte1.29e-50136
hematopoietic stem cell3.18e-42168
angioblastic mesenchymal cell3.18e-42168
hematopoietic cell1.77e-41177
hematopoietic oligopotent progenitor cell3.17e-38161
hematopoietic multipotent progenitor cell3.17e-38161
hematopoietic lineage restricted progenitor cell1.54e-37120
nongranular leukocyte2.55e-37115
myeloid leukocyte7.26e-2972
granulocyte monocyte progenitor cell2.64e-2667
classical monocyte1.43e-2342
CD14-positive, CD16-negative classical monocyte1.43e-2342
macrophage dendritic cell progenitor2.16e-2361
myeloid cell2.71e-23108
common myeloid progenitor2.71e-23108
myeloid lineage restricted progenitor cell1.18e-2266
mesenchymal cell3.52e-22354
monopoietic cell5.49e-2259
monocyte5.49e-2259
monoblast5.49e-2259
promonocyte5.49e-2259
defensive cell5.21e-2148
phagocyte5.21e-2148
connective tissue cell8.41e-21361
motile cell2.45e-18386
multi fate stem cell8.60e-15427
somatic stem cell1.30e-14433
stem cell1.20e-13441
lymphocyte1.32e-1353
common lymphoid progenitor1.32e-1353
lymphoid lineage restricted progenitor cell3.52e-1352
nucleate cell2.43e-1255
somatic cell3.40e-12588
stuff accumulating cell1.06e-0987
lymphocyte of B lineage2.15e-0924
pro-B cell2.15e-0924
dendritic cell4.44e-0910
native cell2.68e-08722
animal cell5.80e-08679
eukaryotic cell5.80e-08679
conventional dendritic cell8.21e-088
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.72e-2598
blood island4.72e-2598
immune system8.17e-2493
hemolymphoid system1.26e-23108
bone marrow2.21e-2376
bone element9.51e-2282
connective tissue3.98e-20371
skeletal element5.73e-2090
skeletal system1.04e-17100
lateral plate mesoderm5.11e-08203


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)
MA0003.11.8989
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.12.45009
MA0017.10.577281
MA0019.12.02743
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
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.13.49299
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
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
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.12.29123
MA0103.10.521546
MA0105.13.51257
MA0106.10.869173
MA0107.12.00595
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
MA0131.12.17614
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
MA0145.10.195821
MA0146.16.62067
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.20.199162
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
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.11.57817
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.327251
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
BCL3#602217.27355140186920.004834494208076070.0226772845541099
PAX5#507935.002174148383370.01196533174786410.0435144258797679
SPI1#668836.153242631392040.006580387113059030.0281106450302999



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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