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Coexpression cluster:C4210: Difference between revisions

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{{Coexpression_clusters
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N-methyltransferase activity!0.0313757618939722!29072$GO:0016278!lysine N-methyltransferase activity!0.0313757618939722!29072$GO:0016279!protein-lysine N-methyltransferase activity!0.0313757618939722!29072$GO:0042054!histone methyltransferase activity!0.0313757618939722!29072$GO:0008276!protein methyltransferase activity!0.0313757618939722!29072$GO:0008170!N-methyltransferase activity!0.0313757618939722!29072$GO:0008757!S-adenosylmethionine-dependent methyltransferase 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|full_id=C4210_granulocyte_Neutrophils_Dendritic_acute_CD4_Eosinophils_CD14
|id=C4210
}}

Latest revision as of 12:41, 17 September 2013


Full id: C4210_granulocyte_Neutrophils_Dendritic_acute_CD4_Eosinophils_CD14



Phase1 CAGE Peaks

Hg19::chr2:24149918..24149974,-p1@ATAD2B
Hg19::chr2:24149977..24150007,-p2@ATAD2B
Hg19::chr3:47205548..47205638,-p1@SETD2


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:0018024histone-lysine N-methyltransferase activity0.0313757618939722
GO:0016278lysine N-methyltransferase activity0.0313757618939722
GO:0016279protein-lysine N-methyltransferase activity0.0313757618939722
GO:0042054histone methyltransferase activity0.0313757618939722
GO:0008276protein methyltransferase activity0.0313757618939722
GO:0008170N-methyltransferase activity0.0313757618939722
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0462323100263678



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
hematopoietic stem cell5.02e-35168
angioblastic mesenchymal cell5.02e-35168
hematopoietic cell1.58e-32177
hematopoietic oligopotent progenitor cell1.67e-31161
hematopoietic multipotent progenitor cell1.67e-31161
leukocyte6.46e-31136
hematopoietic lineage restricted progenitor cell1.64e-23120
nongranular leukocyte2.94e-22115
myeloid cell4.59e-17108
common myeloid progenitor4.59e-17108
nucleate cell1.59e-1455
lymphoid lineage restricted progenitor cell3.04e-1452
lymphocyte5.72e-1453
common lymphoid progenitor5.72e-1453
myeloid leukocyte6.14e-1272
granulocyte monocyte progenitor cell4.49e-1067
myeloid lineage restricted progenitor cell3.00e-0966
macrophage dendritic cell progenitor9.80e-0961
mature alpha-beta T cell1.76e-0818
alpha-beta T cell1.76e-0818
immature T cell1.76e-0818
mature T cell1.76e-0818
immature alpha-beta T cell1.76e-0818
monopoietic cell6.47e-0859
monocyte6.47e-0859
monoblast6.47e-0859
promonocyte6.47e-0859
classical monocyte2.24e-0742
CD14-positive, CD16-negative classical monocyte2.24e-0742
T cell3.97e-0725
pro-T cell3.97e-0725
lymphocyte of B lineage8.08e-0724
pro-B cell8.08e-0724
Uber Anatomy
Ontology termp-valuen
adult organism9.83e-21114
hematopoietic system8.13e-1398
blood island8.13e-1398
hemolymphoid system6.78e-12108
neural tube3.89e-0956
neural rod3.89e-0956
future spinal cord3.89e-0956
neural keel3.89e-0956
immune system1.59e-0893
regional part of nervous system1.80e-0853
regional part of brain1.80e-0853
bone element7.47e-0882
regional part of forebrain7.92e-0841
forebrain7.92e-0841
anterior neural tube7.92e-0841
future forebrain7.92e-0841
central nervous system1.19e-0781
bone marrow1.40e-0776
nervous system1.92e-0789
brain2.54e-0768
future brain2.54e-0768


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.341392
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
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.11.84783
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.94723
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
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
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.76014
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.54885
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
BCLAF1#9774214.43509840674790.006201147435546130.0273913735840383
BRCA1#672213.45615376214920.007119807716084560.0296355505185188
CCNT2#90536.336201576962630.003930750035764890.019048935222739
CTCF#1066435.360256373075030.0064925092527670.0280229439124575
CTCFL#140690213.16431623931620.007433367036996010.0306863283124561
E2F1#186934.907389214879320.008460985347239390.0326325510055886
E2F6#187635.017155731697390.00791769806886330.0323153100400177
EGR1#195834.988179094810140.008056488137383440.0321468466638721
ELF1#199734.258097958807540.01295179875054610.0463545769407588
ELK4#2005210.8237877723120.01091284719516480.0402076782690967
ETS1#211339.728760922202340.001085840092584840.00763766523635963
FOSL2#2355211.28680040304110.0100534586973120.0376834214868666
GABPB1#255337.067683836182170.002832212825417420.0154469411078265
HMGN3#932438.178547723350590.001827766942164210.0108918265247454
IRF1#365937.63716375356390.002244692747297240.0128400408497632
MEF2C#4208227.54090299508270.001729119938369690.0106503631306554
NFKB1#479035.488063424193840.006049381815655430.0270181058606414
NR3C1#290829.982015554115360.01278474365547170.0460565638520165
PAX5#507936.669565531177830.003370290999677260.0173291562482913
RXRA#6256320.07461713913330.0001235730348432220.00165501977250466
SIN3A#2594235.408884726815140.006318961977991520.0277521476038459
SIX5#147912211.3911435703060.009873820081429030.0370846152222234
SMARCB1#6598212.16847718743830.008675002221921740.0329985634125614
SMC3#9126210.02995522995520.0126656379767470.0457695776842836
SP1#666735.69838137814090.005403962701712170.0247125168843207
SP2#6668217.43568699589640.004273568481769740.0203236291001115
TCF7L2#6934310.77017656313730.0008003181298398380.00615360562190553
TFAP2A#7020211.01242291536330.01054990655215560.0390246401643615
USF1#739136.361499277207960.00388404057290560.0190784175239247
YY1#752834.911170749853860.008441455341808260.0330156594556085



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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