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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:32, 17 September 2013


Full id: C844_Mast_CD14_immature_Eosinophils_carcinoid_Natural_CD34



Phase1 CAGE Peaks

Hg19::chr17:7747614..7747633,+p@chr17:7747614..7747633
+
Hg19::chr17:7749921..7749951,+p@chr17:7749921..7749951
+
Hg19::chr1:155947466..155947477,-p@chr1:155947466..155947477
-
Hg19::chr1:155947503..155947518,-p@chr1:155947503..155947518
-
Hg19::chr1:224022601..224022610,-p@chr1:224022601..224022610
-
Hg19::chr2:201997565..201997576,+p42@CFLAR
Hg19::chr4:164087974..164088088,-p1@NAF1
Hg19::chr7:106810484..106810494,+p4@HBP1
Hg19::chr9:102590331..102590358,+p1@AB384783
Hg19::chrX:45613380..45613402,-p@chrX:45613380..45613402
-


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:0048523negative regulation of cellular process0.0489883656349895
GO:0048519negative regulation of biological process0.0489883656349895



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
leukocyte4.18e-45136
classical monocyte2.50e-4142
CD14-positive, CD16-negative classical monocyte2.50e-4142
myeloid leukocyte2.46e-3672
hematopoietic lineage restricted progenitor cell3.37e-36120
defensive cell1.52e-3448
phagocyte1.52e-3448
granulocyte monocyte progenitor cell2.04e-3467
hematopoietic cell7.96e-34177
nongranular leukocyte1.63e-33115
hematopoietic stem cell4.39e-33168
angioblastic mesenchymal cell4.39e-33168
hematopoietic oligopotent progenitor cell1.11e-31161
hematopoietic multipotent progenitor cell1.11e-31161
myeloid lineage restricted progenitor cell3.57e-3166
macrophage dendritic cell progenitor8.14e-3161
monopoietic cell2.63e-2859
monocyte2.63e-2859
monoblast2.63e-2859
promonocyte2.63e-2859
myeloid cell4.04e-26108
common myeloid progenitor4.04e-26108
stuff accumulating cell7.65e-1887
mesenchymal cell5.71e-10354
connective tissue cell2.33e-09361
circulating cell2.79e-096
Langerhans cell1.65e-075
motile cell2.84e-07386
conventional dendritic cell3.95e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.81e-3298
blood island4.81e-3298
hemolymphoid system1.09e-28108
bone marrow1.28e-2876
bone element2.99e-2882
immune system7.40e-2793
skeletal element2.02e-2490
skeletal system1.59e-20100
lateral plate mesoderm4.58e-10203
connective tissue5.33e-09371
musculoskeletal system1.38e-08167


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)
MA0003.10.00190472
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.0216849
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.10.802927
MA0058.10.796055
MA0059.11.44436
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.631708
MA0069.10.814052
MA0070.10.803003
MA0071.11.12112
MA0072.10.798564
MA0073.111.9975
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.228129
MA0105.11.60143
MA0106.10.516528
MA0107.11.01551
MA0108.20.666881
MA0109.10
MA0111.10.885497
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.536665
MA0117.10.865782
MA0119.10.760742
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.11.21476
MA0139.10.716757
MA0140.11.11568
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.602634
MA0146.10.0169564
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.21.11424
MA0039.20.233545
MA0138.20.569505
MA0002.20.129981
MA0137.20.255808
MA0104.20.845907
MA0047.21.25985
MA0112.20.133417
MA0065.22.94255
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.545933
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.403951
MA0163.11.30834
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.20.603497
MA0102.21.36707
MA0258.10.155735
MA0259.10.191914
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
BCL11A#5333538.510836531082120.004359854807656360.0206718516482872
IRF4#366236.574353806023240.008949141806857310.0339375243706017
NFKB1#479063.29283805451630.00391275252059270.0190705600381828



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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