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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:41, 17 September 2013


Full id: C1261_Dendritic_CD19_CD4_CD8_CD14_Natural_Peripheral



Phase1 CAGE Peaks

Hg19::chr21:45563531..45563542,+p@chr21:45563531..45563542
+
Hg19::chr21:45564916..45564931,-p@chr21:45564916..45564931
-
Hg19::chr3:107843890..107843896,+p@chr3:107843890..107843896
+
Hg19::chr3:88198926..88198939,+p8@C3orf38
Hg19::chr4:140005443..140005527,-p2@ELF2
Hg19::chr4:89205350..89205385,-p4@PPM1K
Hg19::chr4:89205847..89205873,-p2@PPM1K


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell4.21e-57168
angioblastic mesenchymal cell4.21e-57168
hematopoietic cell1.20e-55177
leukocyte6.71e-51136
hematopoietic oligopotent progenitor cell2.19e-50161
hematopoietic multipotent progenitor cell2.19e-50161
lymphocyte2.68e-4953
common lymphoid progenitor2.68e-4953
lymphoid lineage restricted progenitor cell1.60e-4852
nucleate cell1.06e-4655
nongranular leukocyte3.84e-41115
hematopoietic lineage restricted progenitor cell2.63e-39120
lymphocyte of B lineage1.92e-2324
pro-B cell1.92e-2324
T cell2.75e-2225
pro-T cell2.75e-2225
mature alpha-beta T cell1.13e-1918
alpha-beta T cell1.13e-1918
immature T cell1.13e-1918
mature T cell1.13e-1918
immature alpha-beta T cell1.13e-1918
B cell9.62e-1614
CD8-positive, alpha-beta T cell1.03e-1211
myeloid cell2.73e-12108
common myeloid progenitor2.73e-12108
mesenchymal cell7.73e-10354
connective tissue cell4.46e-09361
CD4-positive, alpha-beta T cell5.94e-086
myeloid leukocyte6.13e-0772
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.71e-1698
blood island6.71e-1698
hemolymphoid system1.48e-14108
blood2.51e-1315
haemolymphatic fluid2.51e-1315
organism substance2.51e-1315
connective tissue2.27e-08371
immune system1.89e-0793
hemopoietic organ3.00e-077
immune organ3.00e-077
Disease
Ontology termp-valuen
hematologic cancer1.27e-1251
immune system cancer1.27e-1251
leukemia7.73e-0939
lymphoma5.68e-0710


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)
MA0003.11.35295
MA0004.10.502801
MA0006.10.904424
MA0007.10.483857
MA0009.10.973289
MA0014.10.187674
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.12.46653
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.362619
MA0056.10
MA0057.10.115382
MA0058.10.406232
MA0059.10.404929
MA0060.10.638423
MA0061.12.43031
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.0022316
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.10.405093
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.538456
MA0089.10
MA0090.10.436918
MA0091.11.26109
MA0092.10.467172
MA0093.10.9112
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.88373
MA0105.10.695228
MA0106.10.648997
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.10.269076
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.11.00897
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.10.547495
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.254954
MA0145.10.581146
MA0146.10.828373
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.193221
MA0035.20.564239
MA0039.20.243958
MA0138.20.704862
MA0002.20.611548
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.0758925
MA0065.20.282161
MA0150.10.430951
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.685508
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.770207
MA0160.10.543522
MA0161.10
MA0162.10.780982
MA0163.10.382702
MA0164.10.678332
MA0080.20.911393
MA0018.20.650405
MA0099.20.572
MA0079.21.35081
MA0102.21.51913
MA0258.10.245543
MA0259.10.787775
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
CHD2#110657.38858773865490.0001498689600820670.00193260455883578
ELF1#199753.041498542005380.009719562269370750.0365696867155707
IRF3#3661213.42341491756850.00885816023056540.0336181327926167
MEF2C#4208211.80324414074970.01134538181234960.0416017249877109
NFKB1#479064.704054363594720.000216115061401970.00247813360757141
PAX5#507965.716770455295286.92762487228137e-050.00109939859297401
PBX3#5090412.52257867813950.0001356731131035550.00177697068716105
POLR2A#543072.147453176558070.004747636447610280.0223531874020363
TAF1#687262.865468244924540.003728330207471460.0185871916816131
TBP#690863.177232017511190.002074112051852660.0120216542862223
TCF12#693846.076837086963670.002165496819676230.01249653676374
YY1#752853.507979107038470.005072570672808980.0236158431104844



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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