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Coexpression cluster:C887: Difference between revisions

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{{Coexpression_clusters
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polysaccharide metabolic process!0.00742663145894526!56052;66005$GO:0005976!polysaccharide metabolic process!0.00742663145894526!56052;66005$GO:0046964!3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity!0.00742663145894526!347734$GO:0004578!chitobiosyldiphosphodolichol beta-mannosyltransferase activity!0.00742663145894526!56052$GO:0046963!3'-phosphoadenosine 5'-phosphosulfate transport!0.00742663145894526!347734$GO:0016020!membrane!0.00742663145894526!51596;977;56052;11018;347734;56926;92579$GO:0015211!purine nucleoside transmembrane transporter activity!0.00960236620985586!347734$GO:0015860!purine nucleoside transport!0.00960236620985586!347734$GO:0015858!nucleoside transport!0.025594252299723!347734$GO:0012505!endomembrane system!0.0287630402966111!56052;347734;56926$GO:0016021!integral to membrane!0.0287630402966111!977;56052;11018;347734;56926$GO:0031224!intrinsic to membrane!0.0287630402966111!977;56052;11018;347734;56926$GO:0006032!chitin catabolic process!0.0287630402966111!66005$GO:0009103!lipopolysaccharide biosynthetic process!0.0287630402966111!56052$GO:0006046!N-acetylglucosamine catabolic process!0.0287630402966111!66005$GO:0006043!glucosamine catabolic process!0.0287630402966111!66005$GO:0008653!lipopolysaccharide metabolic process!0.0287630402966111!56052$GO:0046348!amino sugar catabolic process!0.0287630402966111!66005$GO:0006030!chitin metabolic process!0.0287630402966111!66005$GO:0004568!chitinase activity!0.0287630402966111!66005$GO:0005337!nucleoside transmembrane transporter activity!0.0341983537268676!347734$GO:0044247!cellular polysaccharide catabolic process!0.0341983537268676!66005$GO:0000272!polysaccharide catabolic process!0.0341983537268676!66005$GO:0031090!organelle membrane!0.0341983537268676!56052;347734;56926$GO:0044425!membrane part!0.0341983537268676!977;56052;11018;347734;56926$GO:0005789!endoplasmic reticulum membrane!0.0341983537268676!56052;56926$GO:0042175!nuclear envelope-endoplasmic reticulum network!0.0341983537268676!56052;56926$GO:0015932!nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity!0.0342014318804026!347734$GO:0000030!mannosyltransferase activity!0.0345857875506221!56052$GO:0044262!cellular carbohydrate metabolic process!0.0345857875506221!56052;66005$GO:0044432!endoplasmic reticulum part!0.0366695653368374!56052;56926$GO:0006044!N-acetylglucosamine metabolic process!0.0393858592285063!66005$GO:0010038!response to metal ion!0.0393858592285063!51596$GO:0006041!glucosamine metabolic process!0.0393858592285063!66005$GO:0033692!cellular polysaccharide biosynthetic process!0.0422531577203064!56052$GO:0000271!polysaccharide biosynthetic process!0.0422531577203064!56052$GO:0006040!amino sugar metabolic process!0.0422531577203064!66005$GO:0010035!response to inorganic 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|full_id=C887_Mesenchymal_Alveolar_Smooth_Renal_Fibroblast_leiomyoma_Preadipocyte
|id=C887
}}

Latest revision as of 11:33, 17 September 2013


Full id: C887_Mesenchymal_Alveolar_Smooth_Renal_Fibroblast_leiomyoma_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr11:832944..832994,+p1@CD151
Hg19::chr11:910796..910847,-p1@CHID1
Hg19::chr16:5121814..5121855,+p1@ALG1
Hg19::chr17:42148225..42148317,+p1@G6PC3
Hg19::chr19:10946872..10946894,-p1@TMED1
Hg19::chr19:3185910..3185962,+p1@NCLN
Hg19::chr6:33385655..33385719,-p1@CUTA
Hg19::chr6:44225231..44225280,-p1@SLC35B2
Hg19::chr8:145582231..145582288,+p1@GPR172A


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:0044264cellular polysaccharide metabolic process0.00742663145894526
GO:0005976polysaccharide metabolic process0.00742663145894526
GO:00469643'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity0.00742663145894526
GO:0004578chitobiosyldiphosphodolichol beta-mannosyltransferase activity0.00742663145894526
GO:00469633'-phosphoadenosine 5'-phosphosulfate transport0.00742663145894526
GO:0016020membrane0.00742663145894526
GO:0015211purine nucleoside transmembrane transporter activity0.00960236620985586
GO:0015860purine nucleoside transport0.00960236620985586
GO:0015858nucleoside transport0.025594252299723
GO:0012505endomembrane system0.0287630402966111
GO:0016021integral to membrane0.0287630402966111
GO:0031224intrinsic to membrane0.0287630402966111
GO:0006032chitin catabolic process0.0287630402966111
GO:0009103lipopolysaccharide biosynthetic process0.0287630402966111
GO:0006046N-acetylglucosamine catabolic process0.0287630402966111
GO:0006043glucosamine catabolic process0.0287630402966111
GO:0008653lipopolysaccharide metabolic process0.0287630402966111
GO:0046348amino sugar catabolic process0.0287630402966111
GO:0006030chitin metabolic process0.0287630402966111
GO:0004568chitinase activity0.0287630402966111
GO:0005337nucleoside transmembrane transporter activity0.0341983537268676
GO:0044247cellular polysaccharide catabolic process0.0341983537268676
GO:0000272polysaccharide catabolic process0.0341983537268676
GO:0031090organelle membrane0.0341983537268676
GO:0044425membrane part0.0341983537268676
GO:0005789endoplasmic reticulum membrane0.0341983537268676
GO:0042175nuclear envelope-endoplasmic reticulum network0.0341983537268676
GO:0015932nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity0.0342014318804026
GO:0000030mannosyltransferase activity0.0345857875506221
GO:0044262cellular carbohydrate metabolic process0.0345857875506221
GO:0044432endoplasmic reticulum part0.0366695653368374
GO:0006044N-acetylglucosamine metabolic process0.0393858592285063
GO:0010038response to metal ion0.0393858592285063
GO:0006041glucosamine metabolic process0.0393858592285063
GO:0033692cellular polysaccharide biosynthetic process0.0422531577203064
GO:0000271polysaccharide biosynthetic process0.0422531577203064
GO:0006040amino sugar metabolic process0.0422531577203064
GO:0010035response to inorganic substance0.0422531577203064



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
epithelial vesicle8.93e-2178
mesenchyme3.52e-19160
entire embryonic mesenchyme3.52e-19160
multilaminar epithelium3.72e-1983
unilaminar epithelium5.47e-19148
epithelial tube1.19e-18117
vasculature3.52e-1878
vascular system3.52e-1878
somite7.14e-1871
presomitic mesoderm7.14e-1871
presumptive segmental plate7.14e-1871
dermomyotome7.14e-1871
trunk paraxial mesoderm7.14e-1871
dense mesenchyme tissue1.66e-1773
trunk2.00e-17199
paraxial mesoderm3.69e-1772
presumptive paraxial mesoderm3.69e-1772
organism subdivision1.12e-16264
trunk mesenchyme1.17e-16122
splanchnic layer of lateral plate mesoderm4.73e-1683
artery4.80e-1642
arterial blood vessel4.80e-1642
arterial system4.80e-1642
vessel8.43e-1668
skeletal muscle tissue1.02e-1562
striated muscle tissue1.02e-1562
myotome1.02e-1562
epithelial tube open at both ends4.18e-1559
blood vessel4.18e-1559
blood vasculature4.18e-1559
vascular cord4.18e-1559
muscle tissue1.56e-1464
musculature1.56e-1464
musculature of body1.56e-1464
systemic artery1.98e-1233
systemic arterial system1.98e-1233
cell layer1.24e-11309
epithelium3.43e-11306
cardiovascular system6.99e-11109
circulatory system2.67e-10112
multi-tissue structure2.39e-09342
anatomical cluster7.81e-08373
subdivision of trunk2.67e-07112
surface structure3.83e-0799
urinary system structure6.69e-0747
nephron epithelium8.20e-0715
renal tubule8.20e-0715
nephron tubule8.20e-0715
nephron8.20e-0715
uriniferous tubule8.20e-0715
nephrogenic mesenchyme8.20e-0715


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)
MA0003.16.60424
MA0004.11.87712
MA0006.10.733408
MA0007.10.397529
MA0009.10.870971
MA0014.13.27412
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.13.90501
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.948258
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.12.85007
MA0056.10
MA0057.10.253359
MA0058.13.27605
MA0059.11.55919
MA0060.10.488252
MA0061.12.66787
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.214487
MA0074.11.27017
MA0076.12.44645
MA0077.10.832987
MA0078.10.607575
MA0081.10.865814
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.92658
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.12.91169
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.11.36936
MA0103.10.257174
MA0105.12.98401
MA0106.11.366
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.11.13131
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.11.31371
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.39929
MA0146.14.07186
MA0147.12.52411
MA0148.10.439278
MA0149.10.464973
MA0062.23.36147
MA0035.20.473658
MA0039.23.36072
MA0138.20.608783
MA0002.20.46405
MA0137.20.28622
MA0104.23.66848
MA0047.20.542971
MA0112.21.04513
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.488402
MA0155.10.359913
MA0156.10.785298
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.12.3084
MA0163.12.8522
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.24.84937
MA0102.21.41188
MA0258.11.01999
MA0259.10.624802
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#467512.47954140333821.89229392694668e-050.000429162400513322
BHLHE40#8553314.95727118232580.0008400100540424580.0063361122370461
CCNT2#90553.520111987201460.007045560226413870.0293932757244723
E2F1#186973.816858278239470.0003547577053237570.00355230488842836
E2F4#187445.630249029015310.003536571815964610.0179464566292953
E2F6#187695.017155731697394.96068808485209e-072.32327041656443e-05
ELF1#199783.784975963384486.58614701323904e-050.00106709681649965
ETS1#211377.566814050601823.61164439627206e-060.000118652572853808
GABPB1#255364.711789224121450.0004576307049007980.00421728520154721
HEY1#2346283.591209816093969.88548321897326e-050.00139197786423938
HMGN3#932465.452365148900390.0002014341013823410.0023933533690865
MAX#414964.301703672671410.0007597563851723660.00596737588260636
MXI1#460144.427365168337470.008444657415134930.0327777743999434
MYC#460974.061774789029540.0002355556796573370.00256770688109098
NFKB1#479053.048924124552130.01316873026498510.0466007867768367
NR2C2#7182310.87153696841360.002106061740088360.012176427262682
PAX5#507964.446377020785220.0006322700088175870.0051905083674658
POLR2A#543092.147453176558070.001029412892608020.0072849202528181
RXRA#625636.691539046377760.008273246622947750.0325970348984812
SIN3A#2594295.408884726815142.52149133666339e-071.31146431130372e-05
SIX5#14791235.6955717851530.01288794699034820.0463547989022618
SMARCC2#6601220.92341653931060.003862524075457470.0190497805022999
SP2#6668411.62379133059760.0002304904940995780.00253498280468259
STAT2#6773214.50306026365350.007865683132259650.0322961189121743
TAF1#687282.971596698440260.0004233749951234810.00395818289461116
TAF7#687945.081364179966180.00514192961203820.0239046510906591
TBP#690872.883043867741630.002187802002126050.0126154954339688
THAP1#55145517.42730255713963.71932991889482e-060.000121768996049986
USF1#739164.240999518138640.0008220017441944160.00625904346470695
USF2#739268.661464923379731.42236000274901e-050.000340320403956711
YY1#752873.819799472108550.0003529672812141940.00353607193119705
ZBTB7A#5134175.718151683903472.40589727322203e-050.000524133302707625
ZNF143#770246.000389578767960.002798128726405460.0153218563444167



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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