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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.224505340200385

Latest revision as of 12:21, 17 September 2013


Full id: C3217_Mast_Macrophage_acute_Reticulocytes_CD14_granulocyte_Monocytederived



Phase1 CAGE Peaks

Hg19::chr12:102224578..102224667,-p1@GNPTAB
Hg19::chr4:79697495..79697538,+p1@BMP2K
Hg19::chr4:79697539..79697550,+p2@BMP2K


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:0003976UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity0.00659356832303857
GO:0016780phosphotransferase activity, for other substituted phosphate groups0.0346065531136793



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>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell8.17e-33108
common myeloid progenitor8.17e-33108
hematopoietic stem cell5.37e-27168
angioblastic mesenchymal cell5.37e-27168
hematopoietic oligopotent progenitor cell1.10e-26161
hematopoietic multipotent progenitor cell1.10e-26161
granulocyte monocyte progenitor cell1.08e-2367
myeloid lineage restricted progenitor cell1.85e-2366
hematopoietic cell1.83e-22177
myeloid leukocyte1.95e-2072
macrophage dendritic cell progenitor7.44e-2061
monopoietic cell5.29e-1959
monocyte5.29e-1959
monoblast5.29e-1959
promonocyte5.29e-1959
leukocyte6.98e-18136
hematopoietic lineage restricted progenitor cell1.06e-17120
defensive cell6.29e-1748
phagocyte6.29e-1748
nongranular leukocyte8.70e-14115
classical monocyte2.39e-1342
CD14-positive, CD16-negative classical monocyte2.39e-1342
mesenchymal cell1.38e-12354
connective tissue cell1.40e-10361
multi fate stem cell3.06e-08427
motile cell3.24e-08386
stem cell8.55e-08441
somatic stem cell1.69e-07433
lymphocyte of B lineage2.44e-0724
pro-B cell2.44e-0724
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.06e-24108
hematopoietic system5.74e-2398
blood island5.74e-2398
immune system1.39e-2193
bone marrow2.64e-1976
bone element3.67e-1782
adult organism1.18e-15114
skeletal element1.54e-1390
skeletal system2.25e-13100
connective tissue1.22e-09371
lateral plate mesoderm6.94e-09203
Disease
Ontology termp-valuen
myeloid leukemia7.37e-0931
leukemia6.33e-0739


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)
MA0003.13.22681
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
MA0009.11.3275
MA0014.12.44638
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.15.87909
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.11.77664
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.13.97071
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.213.0679
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
CCNT2#90536.336201576962630.003930750035764890.0189312244862923
CTCFL#140690319.74647435897440.0001298372005551160.00171277850054008
E2F1#186934.907389214879320.008460985347239390.0323885514305734
EGR1#195834.988179094810140.008056488137383440.031929704181094
HMGN3#932438.178547723350590.001827766942164210.0108392568095332
NANOG#79923219.49651898734180.003427255648501020.0174425784646849
NRF1#4899312.21027944771090.0005492172401020010.0046973793578751
SIN3A#2594235.408884726815140.006318961977991520.0275620644010799
TFAP2A#7020316.5186343730450.0002218033880766340.00247488504779226
TFAP2C#7022310.80922860986020.0007916746575753130.00613320299402923
YY1#752834.911170749853860.008441455341808260.0328153485611223



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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