Personal tools

Coexpression cluster:C1010: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
Line 1: Line 1:
{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0044073383089091,-0

Latest revision as of 11:35, 17 September 2013


Full id: C1010_CD19_Neutrophils_Eosinophils_CD14_Mast_CD8_CD4



Phase1 CAGE Peaks

Hg19::chr12:122238579..122238612,+p@chr12:122238579..122238612
+
Hg19::chr15:45879471..45879525,-p@chr15:45879471..45879525
-
Hg19::chr17:26926142..26926159,+p2@SPAG5-AS1
Hg19::chr18:3261789..3261859,-p@chr18:3261789..3261859
-
Hg19::chr2:65455489..65455504,-p4@LOC729324
Hg19::chr4:6911398..6911444,-p1@BC032036
Hg19::chr6:30585009..30585028,-p1@PPP1R10
Hg19::chr7:127291879..127291901,-p1@ENST00000490314


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:0004864protein phosphatase inhibitor activity0.0216354645001766
GO:0019212phosphatase inhibitor activity0.0216354645001766
GO:0019888protein phosphatase regulator activity0.0216354645001766
GO:0019208phosphatase regulator activity0.0216354645001766
GO:0006606protein import into nucleus0.0216354645001766
GO:0051170nuclear import0.0216354645001766
GO:0017038protein import0.0229600847756976
GO:0006913nucleocytoplasmic transport0.0229600847756976
GO:0051169nuclear transport0.0229600847756976
GO:0006605protein targeting0.0288767220063582
GO:0004857enzyme inhibitor activity0.0482884300439934



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
leukocyte1.02e-47136
hematopoietic cell4.14e-43177
hematopoietic stem cell5.69e-42168
angioblastic mesenchymal cell5.69e-42168
hematopoietic lineage restricted progenitor cell1.73e-39120
hematopoietic oligopotent progenitor cell2.19e-38161
hematopoietic multipotent progenitor cell2.19e-38161
nongranular leukocyte1.11e-36115
myeloid leukocyte1.10e-2672
classical monocyte3.55e-2642
CD14-positive, CD16-negative classical monocyte3.55e-2642
defensive cell4.58e-2348
phagocyte4.58e-2348
myeloid lineage restricted progenitor cell8.07e-2366
myeloid cell2.30e-22108
common myeloid progenitor2.30e-22108
granulocyte monocyte progenitor cell3.41e-2267
macrophage dendritic cell progenitor3.22e-2161
monopoietic cell3.30e-2059
monocyte3.30e-2059
monoblast3.30e-2059
promonocyte3.30e-2059
nucleate cell1.89e-1555
lymphoid lineage restricted progenitor cell5.24e-1552
lymphocyte9.44e-1553
common lymphoid progenitor9.44e-1553
stuff accumulating cell3.73e-1187
mesenchymal cell1.20e-10354
connective tissue cell2.35e-10361
motile cell2.58e-10386
mature alpha-beta T cell1.72e-0918
alpha-beta T cell1.72e-0918
immature T cell1.72e-0918
mature T cell1.72e-0918
immature alpha-beta T cell1.72e-0918
lymphocyte of B lineage1.29e-0724
pro-B cell1.29e-0724
T cell2.40e-0725
pro-T cell2.40e-0725
B cell5.49e-0714
CD8-positive, alpha-beta T cell5.58e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.53e-2798
blood island6.53e-2798
hemolymphoid system1.18e-24108
bone marrow8.56e-2176
immune system2.26e-1993
bone element4.34e-1882
skeletal element1.17e-1490
skeletal system5.65e-12100
lateral plate mesoderm8.11e-10203
connective tissue6.29e-09371


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)
MA0003.15.21858
MA0004.10.455723
MA0006.11.47431
MA0007.11.1148
MA0009.10.918715
MA0014.13.75123
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.13.21619
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.948176
MA0060.11.06021
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.133123
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0719479
MA0074.10.552456
MA0076.11.74818
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.11.01596
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.279181
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.655057
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.913661
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.10.830366
MA0146.13.51017
MA0147.10.681318
MA0148.10.480298
MA0149.11.26367
MA0062.26.33633
MA0035.20.515566
MA0039.21.46411
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.21.05746
MA0047.20.586412
MA0112.20.458158
MA0065.20.844872
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.11.16939
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.93331
MA0163.13.28366
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.609448
MA0102.21.46209
MA0258.10.603127
MA0259.10.699589
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#90564.752151182721970.0003235895417103970.00331067477926059
E2F1#186963.680541911159490.001366491550819140.00899162116154233
E2F6#187663.762866798773040.001207680027997810.00818540427309128
EGR1#195853.117611934256340.01051390990388360.0389190556621428
ELF1#199773.72583571395660.0002503412725512720.00269790446434654
ELK4#200548.117840829234010.00082327487753990.00626782365763155
GABPB1#255376.18422335665947.95182205325426e-060.000221107652667684
GTF2B#2959415.97191496716216.06953293153323e-050.000996065288869264
GTF2F1#296246.369830438378830.002051908375195520.0119101461010974
HEY1#2346273.53509716271750.0003566123056684080.00356711355154706
HMGN3#932455.111592327094120.001109515975889930.00770713262427456
IRF1#365954.773227345977440.001525548480294670.00971386158599532
MAFF#23764214.07883912248630.008220125695981980.0324440386819343
MXI1#460144.980785814379650.005094415320429170.0236953612563598
MYC#460963.916711403707050.0009649270569246440.00693810787594856
NFKB1#479053.430039640121150.006880907700328230.0291393690420315
NFYA#480049.212790349915260.0005085231351680210.00445550735854135
NFYB#480148.379896626768230.0007296914029278550.00581564716349071
NRF1#489946.105139723855450.002403740277772550.0135545721543268
POLR2A#543082.147453176558070.002210725788971910.0127132861997928
POU2F2#545244.553062028871260.007062473846831130.0294579538355843
RDBP#7936238.40960099750620.001154787820652850.00789660742494356
SIN3A#2594264.056663545111350.000792208907523070.00612779633334335
SIX5#14791236.407518258297120.008979882420728990.0340479194096393
SMARCB1#659836.844768417934030.007473690134633950.030821114470722
SPI1#668866.153242631392047.3612205654473e-050.00114831742290478
TAF1#687283.343046285745296.40776711117462e-050.00104288731389117
TBP#690873.243424351209340.0006354223620492050.0052114713420808
TCF7L2#693445.385088281568670.003825814635011350.0188776459730677
YY1#752884.911170749853862.95299276601526e-060.000101050986726693
ZBTB33#10009311.87427188624290.001564551645953250.00992469687510395
ZNF263#1012744.110920818505340.01019992782316260.0379897386656426



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1010&oldid=3068127"