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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0195372020314829

Latest revision as of 12:09, 17 September 2013


Full id: C2600_Dendritic_xeroderma_Smooth_gall_B_CD14_plasma



Phase1 CAGE Peaks

Hg19::chr1:79086118..79086182,+p1@IFI44L
Hg19::chr1:79101668..79101671,+p@chr1:79101668..79101671
+
Hg19::chr21:42798095..42798112,+p3@MX1
Hg19::chr21:42798124..42798146,+p2@MX1


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:0009615response to virus0.0467885317320146
GO:0051707response to other organism0.0467885317320146
GO:0006917induction of apoptosis0.0467885317320146
GO:0012502induction of programmed cell death0.0467885317320146
GO:0043065positive regulation of apoptosis0.0467885317320146
GO:0043068positive regulation of programmed cell death0.0467885317320146
GO:0003924GTPase activity0.0467885317320146
GO:0009607response to biotic stimulus0.0467885317320146
GO:0051704multi-organism process0.0479218179677381



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
leukocyte3.98e-29136
nongranular leukocyte4.45e-26115
hematopoietic lineage restricted progenitor cell1.27e-22120
defensive cell6.04e-2048
phagocyte6.04e-2048
classical monocyte6.22e-2042
CD14-positive, CD16-negative classical monocyte6.22e-2042
myeloid leukocyte5.09e-1972
monopoietic cell4.71e-1759
monocyte4.71e-1759
monoblast4.71e-1759
promonocyte4.71e-1759
macrophage dendritic cell progenitor1.08e-1661
granulocyte monocyte progenitor cell6.54e-1667
hematopoietic stem cell1.53e-15168
angioblastic mesenchymal cell1.53e-15168
myeloid lineage restricted progenitor cell1.50e-1466
hematopoietic oligopotent progenitor cell4.84e-14161
hematopoietic multipotent progenitor cell4.84e-14161
hematopoietic cell2.22e-13177
lymphoid lineage restricted progenitor cell9.36e-0952
lymphocyte1.12e-0853
common lymphoid progenitor1.12e-0853
stuff accumulating cell2.37e-0887
nucleate cell1.02e-0755
lymphocyte of B lineage8.35e-0724
pro-B cell8.35e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.23e-1898
blood island6.23e-1898
hemolymphoid system1.45e-17108
immune system4.44e-1693
bone marrow8.68e-1576
adult organism1.72e-13114
bone element1.69e-1182
skeletal element7.19e-1190
skeletal system1.89e-09100


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0050.12.80362
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
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
MA0091.11.70187
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
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
MA0119.13.57466
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
MA0145.10.195821
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.12.23474
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.11.07498
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
STAT1#6772315.52994062289940.000434088655175550.00405036943249167
STAT2#6773348.94782838983051.42094046481278e-050.00034029259620404
SUZ12#23512225.05789045553150.002325256716520610.0131860501828037
ZBTB33#10009215.83236251499060.005734248930324640.0258404911992654



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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