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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=-0.

Latest revision as of 11:33, 17 September 2013


Full id: C922_Mast_Eosinophils_mature_Basophils_CD19_CD4_Natural



Phase1 CAGE Peaks

Hg19::chr19:18390783..18390870,-p@chr19:18390783..18390870
-
Hg19::chr19:18390896..18390921,-p@chr19:18390896..18390921
-
Hg19::chr19:18390965..18391043,-p@chr19:18390965..18391043
-
Hg19::chr19:18391292..18391321,-p2@BC169275
Hg19::chr19:18391593..18391611,-p6@JUND
Hg19::chr19:18391652..18391669,-p8@JUND
Hg19::chr19:18391708..18391737,-p7@JUND
Hg19::chr19:18391819..18391858,+p@chr19:18391819..18391858
+
Hg19::chr19:18392422..18392440,-p1@JUND


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
leukocyte5.87e-17136
classical monocyte2.37e-1642
CD14-positive, CD16-negative classical monocyte2.37e-1642
myeloid leukocyte8.38e-1572
hematopoietic cell2.20e-14177
defensive cell1.37e-1348
phagocyte1.37e-1348
hematopoietic stem cell8.40e-13168
angioblastic mesenchymal cell8.40e-13168
granulocyte monocyte progenitor cell6.02e-1267
hematopoietic lineage restricted progenitor cell8.89e-12120
hematopoietic oligopotent progenitor cell4.22e-11161
hematopoietic multipotent progenitor cell4.22e-11161
myeloid lineage restricted progenitor cell1.11e-1066
nongranular leukocyte1.14e-10115
macrophage dendritic cell progenitor1.00e-0961
myeloid cell1.17e-09108
common myeloid progenitor1.17e-09108
monopoietic cell6.64e-0959
monocyte6.64e-0959
monoblast6.64e-0959
promonocyte6.64e-0959
stuff accumulating cell9.10e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.78e-1398
blood island2.78e-1398
hemolymphoid system1.94e-11108
bone marrow7.87e-1176
bone element3.96e-1082
skeletal element1.28e-0890
immune system1.76e-0893
skeletal system2.36e-07100


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)
MA0003.116.6669
MA0004.10.415381
MA0006.10.265592
MA0007.11.81613
MA0009.10.870971
MA0014.13.79854
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.948258
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.12.85007
MA0056.10
MA0057.10.919325
MA0058.10.325084
MA0059.12.3679
MA0060.10.162248
MA0061.14.21471
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.719601
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0176541
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.650888
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.11.36936
MA0103.10.257174
MA0105.110.3095
MA0106.10.554855
MA0107.13.28039
MA0108.20.707575
MA0109.10
MA0111.10.959847
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.17.09566
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.15.77823
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.39929
MA0146.11.03863
MA0147.11.14329
MA0148.10.439278
MA0149.10.464973
MA0062.20.421263
MA0035.20.473658
MA0039.20.909157
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.943754
MA0047.20.542971
MA0112.21.97827
MA0065.20.182082
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.13.61595
MA0155.10.645215
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.18.531
MA0163.19.79626
MA0164.10.583138
MA0080.20.268439
MA0018.21.36887
MA0099.20.481058
MA0079.211.3195
MA0102.21.41188
MA0258.10.532421
MA0259.11.17199
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
BCLAF1#977449.623398937831930.0004748877913943970.00433311253236409
CCNT2#90596.336201576962636.0685885071852e-083.76587828343384e-06
EBF1#187943.958429709586220.012557390254080.0454192651340559
ETS1#211355.40486717900130.00101160998680460.00717887717686254
HEY1#2346273.142308589082220.001258763462843770.00845917233742619
NFKB1#479053.048924124552130.01316873026498510.0466039449745783
NRF1#489956.783488582061620.0003500419849025880.0035243454026069
PAX5#507964.446377020785220.0006322700088175870.00519173264021542
POLR2A#543092.147453176558070.001029412892608020.00728738921514874
SIN3A#2594253.004935959341740.01401618817346520.0491996328655442
SMARCB1#6598714.1965567186784.82541719506423e-083.13019718282803e-06
TAF7#687967.622046269949282.97588074999805e-050.000616540388115546
TCF12#693844.726428845416190.006680355302603970.0284191294276438
ZBTB7A#5134197.35190930787591.59170049418346e-081.16493067913123e-06



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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