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{{Coexpression_clusters
{
|full_id=C1854_epididymis_CD4_CD19_CD14_CD14CD16_CD8_Macrophage
 

Latest revision as of 11:53, 17 September 2013


Full id: C1854_epididymis_CD4_CD19_CD14_CD14CD16_CD8_Macrophage



Phase1 CAGE Peaks

Hg19::chr1:26644414..26644426,+p2@CD52
Hg19::chr1:26644441..26644455,+p1@CD52
Hg19::chr1:26646672..26646699,+p@chr1:26646672..26646699
+
Hg19::chr1:26646748..26646770,+p@chr1:26646748..26646770
+
Hg19::chr1:26646869..26646893,+p@chr1:26646869..26646893
+


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

No GOStat results

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
leukocyte2.92e-66136
nongranular leukocyte9.53e-65115
hematopoietic lineage restricted progenitor cell3.08e-64120
hematopoietic stem cell6.74e-63168
angioblastic mesenchymal cell6.74e-63168
hematopoietic oligopotent progenitor cell1.72e-60161
hematopoietic multipotent progenitor cell1.72e-60161
hematopoietic cell5.26e-58177
lymphocyte1.15e-3753
common lymphoid progenitor1.15e-3753
lymphoid lineage restricted progenitor cell1.09e-3652
nucleate cell1.00e-3555
granulocyte monocyte progenitor cell4.23e-2767
defensive cell2.01e-2648
phagocyte2.01e-2648
myeloid leukocyte3.25e-2572
macrophage dendritic cell progenitor7.84e-2561
myeloid lineage restricted progenitor cell8.61e-2566
myeloid cell5.17e-24108
common myeloid progenitor5.17e-24108
classical monocyte6.14e-2442
CD14-positive, CD16-negative classical monocyte6.14e-2442
monopoietic cell3.92e-2359
monocyte3.92e-2359
monoblast3.92e-2359
promonocyte3.92e-2359
T cell1.02e-1725
pro-T cell1.02e-1725
lymphocyte of B lineage2.78e-1724
pro-B cell2.78e-1724
mature alpha-beta T cell3.19e-1618
alpha-beta T cell3.19e-1618
immature T cell3.19e-1618
mature T cell3.19e-1618
immature alpha-beta T cell3.19e-1618
B cell6.95e-1614
mesenchymal cell1.70e-13354
connective tissue cell1.06e-12361
CD8-positive, alpha-beta T cell7.45e-1111
motile cell5.86e-10386
stuff accumulating cell1.49e-0987
intermediate monocyte1.89e-089
CD14-positive, CD16-positive monocyte1.89e-089
multi fate stem cell8.47e-07427
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.51e-3298
blood island4.51e-3298
hemolymphoid system8.50e-30108
immune system1.02e-2393
bone marrow3.52e-2276
bone element1.59e-1982
skeletal element1.44e-1690
skeletal system1.38e-13100
connective tissue4.59e-12371
lateral plate mesoderm1.04e-07203
blood4.50e-0715
haemolymphatic fluid4.50e-0715
organism substance4.50e-0715


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)
MA0003.10.0497246
MA0004.11.51734
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.12.33564
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.11.48918
MA0051.10.731787
MA0052.12.35606
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.11.29682
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.12.7757
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.11.2972
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.818263
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.946108
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.3196
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
EBF1#187935.34388010794140.01187615563868110.0432382980808834



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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