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Coexpression cluster:C1750: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1750_Monocytederived_Fibroblast_Mesenchymal_Smooth_Macrophage_CD14_Pericytes
|id=C1750
}}

Latest revision as of 11:51, 17 September 2013


Full id: C1750_Monocytederived_Fibroblast_Mesenchymal_Smooth_Macrophage_CD14_Pericytes



Phase1 CAGE Peaks

Hg19::chr15:72668281..72668373,-p1@HEXA
Hg19::chr17:42422629..42422636,+p3@GRN
Hg19::chr17:42422637..42422655,+p2@GRN
Hg19::chr20:44519948..44519986,+p1@CTSA
Hg19::chr20:44519987..44519999,+p3@CTSA


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
5.33094045966131e-050.03374485310965612121Lysosome (KEGG):04142



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:0004186carboxypeptidase C activity0.00430137713279296
GO:0005764lysosome0.00430137713279296
GO:0000323lytic vacuole0.00430137713279296
GO:0005773vacuole0.00430137713279296
GO:0004563beta-N-acetylhexosaminidase activity0.00620624403326304
GO:0006689ganglioside catabolic process0.00620624403326304
GO:0050884neuromuscular process controlling posture0.00620624403326304
GO:0046479glycosphingolipid catabolic process0.00678787958567052
GO:0019377glycolipid catabolic process0.00723976547420677
GO:0019915sequestering of lipid0.00723976547420677
GO:0001573ganglioside metabolic process0.00723976547420677
GO:0007628adult walking behavior0.00723976547420677
GO:0004185serine carboxypeptidase activity0.00918812158171093
GO:0007267cell-cell signaling0.00922311555031341
GO:0008344adult locomotory behavior0.0101338814539278
GO:0030149sphingolipid catabolic process0.0101788223163941
GO:0015929hexosaminidase activity0.0108558122730047
GO:0050885neuromuscular process controlling balance0.0108558122730047
GO:0006687glycosphingolipid metabolic process0.0108558122730047
GO:0007040lysosome organization and biogenesis0.0108558122730047
GO:0007033vacuole organization and biogenesis0.0113264700810796
GO:0050905neuromuscular process0.0113264700810796
GO:0046466membrane lipid catabolic process0.0113264700810796
GO:0042552myelination0.0117218610643795
GO:0030534adult behavior0.0117218610643795
GO:0006664glycolipid metabolic process0.0119745955732875
GO:0007272ensheathment of neurons0.0119745955732875
GO:0008366axon ensheathment0.0119745955732875
GO:0006672ceramide metabolic process0.0119745955732875
GO:0046519sphingoid metabolic process0.0126595217242665
GO:0001508regulation of action potential0.0139992529683599
GO:0044242cellular lipid catabolic process0.0159503329124385
GO:0030203glycosaminoglycan metabolic process0.0159503329124385
GO:0006022aminoglycan metabolic process0.0159503329124385
GO:0006665sphingolipid metabolic process0.0210614992510894
GO:0004180carboxypeptidase activity0.0219788420698607
GO:0046982protein heterodimerization activity0.0307300006956865
GO:0050954sensory perception of mechanical stimulus0.0366217204028624
GO:0007605sensory perception of sound0.0366217204028624
GO:0016042lipid catabolic process0.0394769015844559
GO:0007626locomotory behavior0.047697623954621
GO:0008238exopeptidase activity0.0477278536872717
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0477278536872717



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
mesoderm1.09e-20315
mesoderm-derived structure1.09e-20315
presumptive mesoderm1.09e-20315
lateral plate mesoderm1.99e-17203
musculoskeletal system8.66e-15167
multi-cellular organism6.99e-12656
immune system1.30e-1193
bone marrow3.32e-1176
anatomical group3.50e-11625
anatomical system5.36e-11624
skeletal element1.40e-1090
skeletal system1.55e-10100
bone element4.51e-1082
epithelial tube2.10e-08117
hemolymphoid system3.75e-08108
organ4.93e-08503
splanchnic layer of lateral plate mesoderm3.29e-0783
connective tissue8.91e-07371


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)
MA0003.10.737422
MA0004.15.02437
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.11.7452
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.5062
MA0056.10
MA0057.10.189508
MA0058.16.97782
MA0059.10.522232
MA0060.12.35759
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.11.33654
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.17.70125
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.11.58771
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.11.72991
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.11.99092
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.20.425004
MA0065.22.03954
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.680296
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
ATF3#467522.46317452600871.74638470646713e-079.57431350964413e-06
BCL11A#53335317.02167306216420.000414967457127050.00390439515809838
BCL3#602534.54710280373832.02839878970325e-081.44603372831275e-06
BHLHE40#8553326.92308812818640.0001069419523743840.00148958529794989
CHD2#110648.275218267293490.0004028373567101730.00387795471448555
CTCF#1066444.288205098460020.005152015588243280.0239344938401557
CTCFL#140690311.84788461538460.001201770348538230.00814958076949446
E2F6#187655.017155731697390.0003144978599297790.00322714108795502
ELF1#199754.258097958807540.0007142416939776840.00572967879847418
ELK4#2005516.2356816584688.85705446514576e-073.82240459208825e-05
EP300#203356.77394172622327.00901578206049e-050.00110777027733447
ESRRA#21012193.536125654454.24300082508069e-050.000759442610403773
ETS1#211335.83725655332140.009253279045631430.0349702627192582
FOS#235358.99795530889441.69470025615156e-050.000388995164949918
FOSL1#8061323.82814782982380.0001535927643660730.00195837806343893
FOSL2#2355516.93020060456177.18315284751475e-073.2073591288653e-05
FOXA1#316948.865135799508360.0003075468591372710.00316701700073333
GTF2F1#296237.643796526054590.00428415496412050.0203452555610122
HDAC2#3066410.7324961893010.0001450965797478750.00188573191790546
HEY1#2346254.040111043105710.0009288852205177990.00674067840089344
HMGN3#932458.178547723350592.73180911341838e-050.00058154792498227
HNF4G#3174211.50136901057870.01127438304921050.0413762489028214
IRF1#365957.63716375356393.84754333311872e-050.00072389403380938
IRF3#3661218.79278088459580.004339629777121510.0205871721232248
JUND#372756.994663941871035.97069468343598e-050.000983864597733307
MAFK#7975210.8402932551320.01263683277337880.0456860349632688
MAX#414956.452555509007128.93743970843928e-050.00130657511997437
MEF2A#4205311.24593854578640.001399366787411950.0091024207717063
MEF2C#4208216.52454179704960.005579850077982050.0252438363566977
MXI1#460135.976942977255580.008653004889366880.0329496910941987
MYC#460955.22228187160940.0002573944848850610.00276450253053382
NANOG#79923317.54686708860760.0003794200090681830.0037599626460833
NFE2#4778577.2042606516293.63079662252496e-103.62867721014243e-08
NFKB1#479055.488063424193840.0002008162847462320.0023898190476996
NR2C2#7182319.56876654314450.0002750171700966610.00293086920691073
NR3C1#2908514.9730233311731.32777388277837e-065.24079276430423e-05
POU2F2#545235.463674434645510.01115650094469780.0410099184205015
RXRA#6256520.07461713913333.06418769543848e-071.54078333521377e-05
SIN3A#2594255.408884726815140.0002159522671657270.00247980635849603
SMARCB1#6598310.95162946869440.001511872848343180.00965326700544804
SMARCC2#6601356.49322465613861.17726327391127e-050.000298282870121347
SP1#666755.69838137814090.000166391843712550.00204204439077497
SP2#6668315.69211829630680.0005272235913302770.0045630815161136
SPI1#668858.204323508522732.68916109982495e-050.00057445959522319
SRF#6722513.79717826216781.9987012616697e-067.32172434470438e-05
STAT1#6772520.70658749719922.62418353652031e-071.35475582981041e-05
STAT3#677448.415571997723390.0003771527211598630.00374246584752636
TAF1#687253.343046285745290.002394600090870310.0135293285848204
TAF7#687936.859841642954350.005843286407019040.0262435275248414
TBP#690853.706770687096390.001428755106721120.00918545734631254
TCF12#6938510.63446490218647.34844389925727e-060.000211073743782874
THAP1#55145318.82148676171080.0003085221948150010.00317455660140728
USF1#739156.361499277207969.59569864925045e-050.0013679568266845
USF2#7392512.99219738506962.69963551658264e-069.42022164104158e-05
YY1#752854.911170749853860.00034993140821360.00352697223918357
ZBTB7A#5134157.35190930787594.65425347594289e-050.000815579830157717
ZEB1#6935310.13305921052630.001895556924357070.0111607886809634



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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