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{{Coexpression_clusters
{
|full_id=C3953_Smooth_CD4_Hair_acute_iPS_xeroderma_Nucleus
|gostat_on_coexpression_clusters

Latest revision as of 12:36, 17 September 2013


Full id: C3953_Smooth_CD4_Hair_acute_iPS_xeroderma_Nucleus



Phase1 CAGE Peaks

Hg19::chr1:24018278..24018303,+p1@RPL11
Hg19::chr2:101618729..101618761,+p1@RPL31
Hg19::chr3:197677047..197677074,+p1@RPL35A


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

p.valueFDRnGenesnPathwayName
3.23952687815502e-081.05948726550059e-05392Ribosome (KEGG):03010
3.34751110742684e-081.05948726550059e-05393Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
1.1037505066909e-060.000116445678455893296Metabolism of proteins (Reactome):REACT_17015
6.2031341872007e-081.30886131349935e-053114Regulation of beta-cell development (Reactome):REACT_13698
3.18533613032144e-060.0002520397213116843421Gene Expression (Reactome):REACT_71
1.29326205516739e-060.0001169478401315653312Diabetes pathways (Reactome):REACT_15380
1.23098667822397e-071.55842913463155e-053143Influenza Infection (Reactome):REACT_6167
1.10547371417187e-071.55842913463155e-053138{RPS27A,138} (Static Module):NA



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:0005842cytosolic large ribosomal subunit (sensu Eukaryota)8.11246671004954e-08
GO:0005830cytosolic ribosome (sensu Eukaryota)2.99701452344948e-07
GO:0015934large ribosomal subunit5.54678852341937e-07
GO:0044445cytosolic part2.49698689484997e-06
GO:0033279ribosomal subunit3.28124645425421e-06
GO:0005829cytosol4.4946882578473e-05
GO:0003735structural constituent of ribosome9.91441963952388e-05
GO:0005840ribosome0.000112771658049979
GO:0003723RNA binding0.000152830307734731
GO:0030529ribonucleoprotein complex0.000217462340567173
GO:0006412translation0.000235913035980226
GO:0009059macromolecule biosynthetic process0.000470758868352947
GO:0044249cellular biosynthetic process0.000827081666316246
GO:0009058biosynthetic process0.00155979504619136
GO:0043232intracellular non-membrane-bound organelle0.00229977448464354
GO:0043228non-membrane-bound organelle0.00229977448464354
GO:0032991macromolecular complex0.00509120568496683
GO:0044446intracellular organelle part0.00548130567723766
GO:0044422organelle part0.00548130567723766
GO:0000049tRNA binding0.00588633108744147
GO:0044444cytoplasmic part0.00681719258441986
GO:0019843rRNA binding0.00837260151835178
GO:0010467gene expression0.0104299359727179
GO:0044267cellular protein metabolic process0.0107018979530247
GO:0044260cellular macromolecule metabolic process0.0107018979530247
GO:0019538protein metabolic process0.0114328712142776
GO:0003676nucleic acid binding0.0142031328827836
GO:0005737cytoplasm0.0221219764203332
GO:0005730nucleolus0.0290011854976768
GO:0005515protein binding0.0357886869663508
GO:0006605protein targeting0.0357886869663508



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
native cell4.19e-19722
animal cell9.05e-15679
eukaryotic cell9.05e-15679
hematopoietic oligopotent progenitor cell2.75e-11161
hematopoietic multipotent progenitor cell2.75e-11161
classical monocyte2.85e-1142
CD14-positive, CD16-negative classical monocyte2.85e-1142
hematopoietic cell6.29e-11177
hematopoietic stem cell8.07e-11168
angioblastic mesenchymal cell8.07e-11168
stem cell1.92e-10441
hematopoietic lineage restricted progenitor cell4.07e-10120
nongranular leukocyte4.40e-10115
multi fate stem cell1.80e-09427
somatic stem cell8.06e-09433
somatic cell1.48e-08588
connective tissue cell1.58e-08361
defensive cell1.71e-0848
phagocyte1.71e-0848
mesenchymal cell9.03e-08354
nucleate cell2.87e-0755
leukocyte6.30e-07136
lymphoid lineage restricted progenitor cell6.54e-0752
lymphocyte6.77e-0753
common lymphoid progenitor6.77e-0753
Uber Anatomy
Ontology termp-valuen
connective tissue2.52e-08371


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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
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
MA0055.10.190716
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
MA0073.10.0185922
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
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
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
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.21.20011
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
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
BCL3#602223.03140186915890.002464674760842910.0138540456053645
BCLAF1#9774214.43509840674790.006201147435546130.0273867404017677
E2F4#1874312.66806031528440.0004917987006298980.00437466693595826
ELF1#199734.258097958807540.01295179875054610.0462673727496334
ELK4#2005316.2356816584680.0002336043955745990.00255818490819079
EP300#203336.77394172622320.003216880500103790.0167606776029104
GABPB1#255337.067683836182170.002832212825417420.0154227788348595
GTF2B#2959331.94382993432423.06634405746243e-050.00062817949591471
GTF2F1#2962312.73966087675770.0004835525047438590.00434274142599913
IRF1#365937.63716375356390.002244692747297240.0128168752848383
JUNB#3726220.40708843988080.003131462199438740.0164493904359311
JUND#372736.994663941871030.002921845042734990.0156891812040205
KAT2A#26482410.7266666666677.8689746933917e-060.000222356019481368
MAX#414936.452555509007120.003721913834265510.0186701709383696
MEF2A#4205212.4954872730960.008235029478029740.032485674925626
MYC#460935.22228187160940.007020843755740150.029475013104705
NFKB1#479035.488063424193840.006049381815655430.0269777269501361
POU2F2#545239.106124057742520.001324165192682130.00882824695553967
REST#597839.650028716128020.001112636247114590.00768180187825746
RFX5#5993312.04791082719510.0005717246050312580.00484976819565136
SIN3A#2594235.408884726815140.006318961977991520.0277032184543471
SIX5#147912317.0867153554590.0002004060546325010.00239860278933804
SMC3#9126210.02995522995520.0126656379767470.0457553291128841
SP1#666735.69838137814090.005403962701712170.0246736233542064
TAF7#6879311.43306940492390.0006690181981945830.00543451750806907
TCF12#6938310.63446490218640.0008313523990202070.00629673023433689
YY1#752834.911170749853860.008441455341808260.0329687429207252
ZNF143#7702313.50087655222790.0004062804962997170.00389315797348804
ZZZ3#260092159.6088082901555.21262599582697e-050.000886791735426247



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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