Personal tools

Coexpression cluster:C562: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C562_Smooth_Fibroblast_Preadipocyte_Hepatic_Alveolar_Adipocyte_Mesenchymal
|

Latest revision as of 11:25, 17 September 2013


Full id: C562_Smooth_Fibroblast_Preadipocyte_Hepatic_Alveolar_Adipocyte_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:66056544..66056560,-p4@YIF1A
Hg19::chr11:66056564..66056579,-p2@YIF1A
Hg19::chr11:68039364..68039457,-p1@C11orf24
Hg19::chr14:24664776..24664904,-p3@TM9SF1
Hg19::chr19:4670345..4670382,-p1@C19orf10
Hg19::chr1:2323260..2323307,+p1@RER1
Hg19::chr2:220363579..220363641,+p1@GMPPA
Hg19::chr2:27255806..27255879,+p1@TMEM214
Hg19::chr3:10362736..10362809,-p1@SEC13
Hg19::chr3:128968437..128968505,+p1@COPG
Hg19::chr6:33168637..33168704,+p1@SLC39A7
Hg19::chr7:6523755..6523829,-p1@DAGLB
p1@KDELR2
Hg19::chr9:136242894..136242905,-p4@SURF4
Hg19::chr9:136242909..136242953,-p1@SURF4
Hg19::chr9:136242956..136242976,-p2@SURF4
Hg19::chrX:54835499..54835584,+p2@MAGED2


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:0005793ER-Golgi intermediate compartment0.00833926739920197
GO:0000139Golgi membrane0.00833926739920197
GO:0012505endomembrane system0.00833926739920197
GO:0044431Golgi apparatus part0.00833926739920197
GO:0044425membrane part0.0139153532669686
GO:0016192vesicle-mediated transport0.0161922944162981
GO:0031090organelle membrane0.0165749186817612
GO:0005794Golgi apparatus0.0180427800933964
GO:0016021integral to membrane0.0214975997088356
GO:0031224intrinsic to membrane0.0214975997088356
GO:0015031protein transport0.0227785891077271
GO:0005783endoplasmic reticulum0.0227785891077271
GO:0046907intracellular transport0.0227785891077271
GO:0045184establishment of protein localization0.0227785891077271
GO:0008104protein localization0.0227785891077271
GO:0016020membrane0.0227785891077271
GO:0033036macromolecule localization0.0248064161649225
GO:0006890retrograde vesicle-mediated transport, Golgi to ER0.0249997241602398
GO:0051649establishment of cellular localization0.0258787183563686
GO:0030126COPI vesicle coat0.0258787183563686
GO:0030663COPI coated vesicle membrane0.0258787183563686
GO:0051641cellular localization0.0258787183563686
GO:0004806triacylglycerol lipase activity0.0265426724499683
GO:0030137COPI-coated vesicle0.0265426724499683
GO:0006810transport0.0272165256352636
GO:0051234establishment of localization0.0291079438701855
GO:0006829zinc ion transport0.0318924360004973
GO:0005789endoplasmic reticulum membrane0.0368909860600387
GO:0051179localization0.0368909860600387
GO:0042175nuclear envelope-endoplasmic reticulum network0.0369405361170417
GO:0044432endoplasmic reticulum part0.0439203538946573
GO:0006886intracellular protein transport0.0439649120519745



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
mesenchyme4.25e-26160
entire embryonic mesenchyme4.25e-26160
trunk mesenchyme8.46e-26122
unilaminar epithelium8.67e-26148
epithelial vesicle2.29e-2478
epithelial tube2.71e-24117
trunk1.29e-23199
organism subdivision1.34e-21264
somite1.49e-2171
presomitic mesoderm1.49e-2171
presumptive segmental plate1.49e-2171
dermomyotome1.49e-2171
trunk paraxial mesoderm1.49e-2171
multilaminar epithelium3.43e-2183
dense mesenchyme tissue3.61e-2173
paraxial mesoderm1.11e-2072
presumptive paraxial mesoderm1.11e-2072
skeletal muscle tissue5.28e-1962
striated muscle tissue5.28e-1962
myotome5.28e-1962
muscle tissue3.83e-1864
musculature3.83e-1864
musculature of body3.83e-1864
vasculature8.27e-1878
vascular system8.27e-1878
splanchnic layer of lateral plate mesoderm5.33e-1783
artery8.56e-1742
arterial blood vessel8.56e-1742
arterial system8.56e-1742
vessel1.68e-1568
epithelial tube open at both ends4.69e-1559
blood vessel4.69e-1559
blood vasculature4.69e-1559
vascular cord4.69e-1559
systemic artery2.65e-1333
systemic arterial system2.65e-1333
cell layer2.56e-12309
cardiovascular system7.50e-12109
epithelium8.43e-12306
circulatory system3.02e-11112
multi-tissue structure1.88e-10342
subdivision of trunk2.51e-10112
surface structure1.24e-0999
multi-cellular organism4.21e-09656
integument8.37e-0946
integumental system8.37e-0946
anatomical group5.73e-08625
anatomical system7.41e-08624
abdominal segment of trunk9.29e-0860
abdomen9.29e-0860
primordium2.14e-07160
skin of body4.27e-0741
anatomical cluster5.50e-07373
mesoderm7.91e-07315
mesoderm-derived structure7.91e-07315
presumptive mesoderm7.91e-07315
adipose tissue8.05e-0714


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)
MA0003.19.15215
MA0004.11.24596
MA0006.10.392773
MA0007.11.19118
MA0009.10.644692
MA0014.13.01311
MA0017.10.89607
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.12.61665
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.859342
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.11.55541
MA0046.10.634468
MA0048.11.32513
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.10.715233
MA0056.10
MA0057.10.0733461
MA0058.10.968374
MA0059.10.964661
MA0060.10.464905
MA0061.10.175447
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.10.0313753
MA0069.10.630852
MA0070.10.620368
MA0071.10.289163
MA0072.10.616162
MA0073.10.0227426
MA0074.10.850035
MA0076.13.04253
MA0077.10.608956
MA0078.10.402443
MA0081.10.499456
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.10.846467
MA0089.10
MA0090.10.189305
MA0091.10.240316
MA0092.10.607109
MA0093.11.29113
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.10.118522
MA0105.10.16519
MA0106.10.355999
MA0107.10.0842574
MA0108.20.492699
MA0109.10
MA0111.10.578093
MA0113.10.968027
MA0114.10.985949
MA0115.10.874839
MA0116.10.607827
MA0117.11.6287
MA0119.10.918526
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.12.81858
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.87256
MA0139.11.44384
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.546187
MA0145.10.113672
MA0146.17.97869
MA0147.11.53356
MA0148.10.257816
MA0149.10.279141
MA0062.25.93075
MA0035.20.286421
MA0039.28.15564
MA0138.20.403517
MA0002.20.196222
MA0137.20.430142
MA0104.22.25595
MA0047.20.345656
MA0112.21.20168
MA0065.20.667633
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.542249
MA0155.11.88309
MA0156.11.9909
MA0157.10.442323
MA0158.10
MA0159.10.29763
MA0160.10.26995
MA0161.10
MA0162.11.14234
MA0163.11.10514
MA0164.10.380804
MA0080.20.793571
MA0018.20.939567
MA0099.20.292649
MA0079.22.43496
MA0102.21.16862
MA0258.10.520754
MA0259.12.80337
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#46745.615793631502190.004641412127675220.0219123244373145
BRCA1#67245.046057660805940.006778976696404470.0287730450782649
CCNT2#905124.752151182721972.31381839264867e-071.21985299904005e-05
CHD2#110663.879008562793820.002773171528270150.0151923657805815
CTCFL#14069067.404927884615388.67296992239919e-050.0012991914884186
E2F1#186992.760406433369620.001696428202141060.0105996568952085
E2F4#187453.958768848526390.006382759939409180.0277846392677541
E2F6#1876134.076439032004132.37289564027328e-071.2459670576898e-05
EBF1#187973.896579245373940.001021158414795670.00724368428192929
ELF1#1997153.991966836382074.54061180224701e-093.66757119887761e-07
ELK4#20051111.16203114019681.57457980886855e-101.65941009746137e-08
ESR1#209935.769113118028970.01399042242294870.0491157930495255
ETS1#2113159.120713364564692.17334805334434e-143.66100479585854e-12
GABPB1#2553125.300762877136636.68540345520611e-084.06886277073585e-06
HEY1#23462164.040111043105711.98084199021544e-102.05031869788018e-08
HMGN3#932484.08927386167530.0002572852935955120.00276816923640896
IRF1#3659115.250550080575184.46896063357945e-072.12731895902645e-05
JUND#3727114.808831460036331.10371712893257e-064.57788376602813e-05
MAX#414993.629562473816510.0002071788170627830.00243501558352689
MXI1#460195.60338404117716.10807177715345e-060.000181640349753454
MYC#4609134.243104020682641.44725283711898e-078.17909302250373e-06
NFKB1#479082.744031712096920.003856163139355890.0190246975346587
NFYA#480044.606395174957630.009320267223685850.0352055911090646
NFYB#480177.33240954842221.90141463325496e-050.000430669795884872
NRF1#489986.105139723855451.42402144556288e-050.00034063988949414
PAX5#5079125.002174148383371.2934425150475e-077.37770851059781e-06
POLR2A#5430162.147453176558074.88536678567824e-060.000151042872033585
POU2F2#5452105.691327536089081.08661015877248e-064.51589647322081e-05
REST#597874.221887563306010.0006272813656043830.0051633542356838
RXRA#625645.018654284783320.006909951752017850.0292576198422522
SIN3A#25942155.070829431389191.3297899225369e-101.42297059139172e-08
SIX5#14791299.611277387445696.29588488815385e-083.88614611012943e-06
SP1#6667134.629934869739484.9106978951726e-083.16195053929674e-06
SPI1#668894.614931973544033.01826774164688e-050.000620643561074736
SRF#672286.89858913108395.75315050227476e-060.000172857677015844
TAF1#6872153.134105892886211.57946317760101e-078.84016906781733e-06
TAF7#687975.001967864654210.0002195065578727680.00248752662735178
TBP#6908153.475097519152863.48271765686805e-082.32564929261919e-06
TCF12#693863.987924338319910.002406057678715160.0135669073484144
TCF7L2#693464.03881621117650.002254045226455730.0128037762104759
THAP1#55145611.76342922606926.36151165140569e-060.000187627764857712
YY1#7528133.990326234256263.08644499595592e-071.54973667756077e-05
ZNF263#1012763.0831906138790.008734686727107120.0331832944269885



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C562&oldid=3067679"