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{{Coexpression_clusters
{
|full_id=C1465_Mast_Preadipocyte_Fibroblast_Smooth_Chondrocyte_basal_Osteoblast
|gostat_on_coexpression_clusters

Latest revision as of 11:45, 17 September 2013


Full id: C1465_Mast_Preadipocyte_Fibroblast_Smooth_Chondrocyte_basal_Osteoblast



Phase1 CAGE Peaks

Hg19::chr1:160312998..160313024,-p2@COPA
Hg19::chr1:160313025..160313072,-p1@COPA
Hg19::chr4:119757222..119757238,-p2@SEC24D
Hg19::chr4:119757239..119757305,-p1@SEC24D
Hg19::chr4:119757322..119757334,-p3@SEC24D
Hg19::chr4:83812268..83812401,-p1@SEC31A


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
0.0001016701891415990.01608930743165812167Protein processing in endoplasmic reticulum (KEGG):04141
2.20782089021958e-060.000465850207836331225SREBP signalling (Wikipathways):WP1982
0.000319276728200750.0404204337902152296Metabolism of proteins (Reactome):REACT_17015
4.83581548478211e-083.06107120186708e-053105Membrane Trafficking (Reactome):REACT_11123
8.833140910259e-070.000279568909809697216{SEC24B,18} (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:0030120vesicle coat1.59360715573632e-07
GO:0030662coated vesicle membrane1.59360715573632e-07
GO:0005798Golgi-associated vesicle2.67292367563503e-07
GO:0030659cytoplasmic vesicle membrane4.8489276073581e-07
GO:0044433cytoplasmic vesicle part4.8489276073581e-07
GO:0012506vesicle membrane4.8489276073581e-07
GO:0030117membrane coat4.8489276073581e-07
GO:0048475coated membrane4.8489276073581e-07
GO:0030135coated vesicle8.82004274168316e-07
GO:0030127COPII vesicle coat3.68578464954729e-06
GO:0012507ER to Golgi transport vesicle membrane3.68578464954729e-06
GO:0030134ER to Golgi transport vesicle4.54798519481905e-06
GO:0016023cytoplasmic membrane-bound vesicle7.87888560646397e-06
GO:0031988membrane-bound vesicle7.87888560646397e-06
GO:0000139Golgi membrane8.20133629517297e-06
GO:0046903secretion8.95670736238786e-06
GO:0044431Golgi apparatus part1.07485746738754e-05
GO:0031410cytoplasmic vesicle1.07485746738754e-05
GO:0031982vesicle1.07485746738754e-05
GO:0030658transport vesicle membrane1.20808507966572e-05
GO:0030660Golgi-associated vesicle membrane1.22723693440234e-05
GO:0006888ER to Golgi vesicle-mediated transport1.84191560341748e-05
GO:0016192vesicle-mediated transport2.45590807920104e-05
GO:0005794Golgi apparatus3.55255879566779e-05
GO:0030133transport vesicle4.05661523916162e-05
GO:0015031protein transport6.34964434528897e-05
GO:0005783endoplasmic reticulum6.7748719125613e-05
GO:0046907intracellular transport6.7748719125613e-05
GO:0045184establishment of protein localization6.7748719125613e-05
GO:0048193Golgi vesicle transport6.7748719125613e-05
GO:0008104protein localization7.27991888716605e-05
GO:0033036macromolecule localization8.23717077444704e-05
GO:0012505endomembrane system8.37282444874029e-05
GO:0051649establishment of cellular localization9.90411355731548e-05
GO:0051641cellular localization0.000103768176789829
GO:0031090organelle membrane0.00024395131137356
GO:0045045secretory pathway0.000401112297492283
GO:0032940secretion by cell0.000597908532731506
GO:0030157pancreatic juice secretion0.00113202077726421
GO:0006886intracellular protein transport0.00179641366272567
GO:0016043cellular component organization and biogenesis0.00218737270485908
GO:0030126COPI vesicle coat0.00307924290153726
GO:0030663COPI coated vesicle membrane0.00307924290153726
GO:0030137COPI-coated vesicle0.00341029397521763
GO:0007589fluid secretion0.00353055334416461
GO:0006810transport0.00356800737070301
GO:0022600digestive system process0.00356800737070301
GO:0044446intracellular organelle part0.00360426233566905
GO:0044422organelle part0.00360426233566905
GO:0051234establishment of localization0.00360426233566905
GO:0051179localization0.00449716529632016
GO:0044444cytoplasmic part0.0047467189745629
GO:0007586digestion0.0157850363922107
GO:0005737cytoplasm0.019776990414091
GO:0050878regulation of body fluid levels0.0199968336228727
GO:0044425membrane part0.0209982178169082
GO:0008565protein transporter activity0.0237513622530376
GO:0005792microsome0.0245486292312923
GO:0042598vesicular fraction0.0251701198432801
GO:0043231intracellular membrane-bound organelle0.0283199098597437
GO:0043227membrane-bound organelle0.0283199098597437
GO:0051082unfolded protein binding0.0283199098597437
GO:0005515protein binding0.0295556769216537
GO:0005179hormone activity0.0297519573752465
GO:0005625soluble fraction0.0315733359434466
GO:0016020membrane0.035777524468533
GO:0006461protein complex assembly0.0443511685631897
GO:0006457protein folding0.0443511685631897
GO:0043229intracellular organelle0.045484256688062
GO:0043226organelle0.045484256688062



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>

Uber Anatomy
Ontology termp-valuen
mesoderm1.00e-22315
mesoderm-derived structure1.00e-22315
presumptive mesoderm1.00e-22315
musculoskeletal system2.23e-21167
somite5.99e-1871
presomitic mesoderm5.99e-1871
presumptive segmental plate5.99e-1871
dermomyotome5.99e-1871
trunk paraxial mesoderm5.99e-1871
dense mesenchyme tissue7.58e-1873
paraxial mesoderm2.36e-1772
presumptive paraxial mesoderm2.36e-1772
splanchnic layer of lateral plate mesoderm4.27e-1783
vasculature1.92e-1678
vascular system1.92e-1678
muscle tissue2.43e-1664
musculature2.43e-1664
musculature of body2.43e-1664
multilaminar epithelium4.01e-1683
skeletal muscle tissue4.79e-1662
striated muscle tissue4.79e-1662
myotome4.79e-1662
unilaminar epithelium2.03e-15148
artery3.19e-1542
arterial blood vessel3.19e-1542
arterial system3.19e-1542
vessel2.54e-1468
epithelial tube open at both ends3.04e-1459
blood vessel3.04e-1459
blood vasculature3.04e-1459
vascular cord3.04e-1459
epithelial vesicle3.25e-1478
trunk mesenchyme3.05e-13122
systemic artery1.68e-1233
systemic arterial system1.68e-1233
cardiovascular system2.32e-12109
lateral plate mesoderm1.23e-11203
connective tissue1.51e-11371
circulatory system2.62e-11112
multi-cellular organism7.52e-11656
mesenchyme1.01e-10160
entire embryonic mesenchyme1.01e-10160
epithelial tube2.44e-10117
anatomical group2.58e-10625
anatomical system4.49e-10624
integument6.33e-0846
integumental system6.33e-0846
aorta2.05e-0721
aortic system2.05e-0721
skin of body4.01e-0741
embryonic structure4.24e-07564
surface structure4.41e-0799
tissue5.62e-07773
germ layer8.67e-07560
germ layer / neural crest8.67e-07560
embryonic tissue8.67e-07560
presumptive structure8.67e-07560
germ layer / neural crest derived structure8.67e-07560
epiblast (generic)8.67e-07560


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)
MA0003.12.14318
MA0004.10.558729
MA0006.11.01439
MA0007.10.539222
MA0009.11.03681
MA0014.11.149
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.13.78197
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.906394
MA0050.11.34656
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.12.04333
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.10.23892
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.0569999
MA0074.10.660398
MA0076.15.34928
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.11.34409
MA0106.10.70837
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.11.72264
MA0114.10.314898
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.11.12205
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.11.19942
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.707171
MA0146.11.05598
MA0147.10.87383
MA0148.10.584698
MA0149.10.612449
MA0062.26.41085
MA0035.20.621793
MA0039.20.82735
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.735746
MA0047.20.695777
MA0112.21.65732
MA0065.20.109623
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.132326
MA0155.10.65596
MA0156.11.88357
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.978497
MA0163.10.508943
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.476723
MA0102.21.58513
MA0258.10.289793
MA0259.10.893594
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#9774310.82632380506090.001772351046991060.0108909491054777
CCNT2#90544.224134384641760.007109805478875810.0296151627012448
CTCF#1066465.360256373075034.21437267579784e-050.000755483810311793
E2F1#186964.907389214879327.15746523583771e-050.00112730887010354
E2F4#187448.445373543522960.0005111193523770840.00443362076768358
ELF1#199764.258097958807540.0001677224776288830.00205306702309926
ELK4#200538.117840829234010.004056113134185760.019409686122393
ETS1#211369.728760922202341.17854759771003e-064.80430650106316e-05
GTF2B#2959315.97191496716210.0005711653715892990.00486755938338758
HEY1#2346264.040111043105710.0002298968555807510.00253218705969184
HMGN3#932468.178547723350593.33956428934731e-060.000111502798853946
MAX#414944.301703672671410.006644923910676370.0283006772819154
NFKB1#479065.488063424193843.65870229532191e-050.00070761335003912
NRF1#489936.105139723855450.009090162079396740.0344060971047047
POLR2A#543062.147453176558070.01019570676818780.0380418498504079
SMARCC1#6599214.55445310654380.007398079383140510.0305660262954273
SMARCC2#6601231.38512480896590.001643869010704610.0102847921649181
SRF#672236.89858913108390.00644245168930370.0280024642907936
TAF1#687263.343046285745290.0007162474284635620.00573299855773344
TAF7#687935.716534702461960.01092729379889660.0402155062746833
TBP#690863.706770687096390.000385416472907960.00377886885223756
TCF12#6938610.63446490218646.9082259011154e-073.11523404527889e-05
ZBTB7A#5134167.35190930787596.32958528301959e-060.000186738858015052
ZEB1#693538.444216008771930.003623843810733590.0183394206400739
ZNF143#770236.750438276113950.006850259204468580.0290413728863606



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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