Personal tools

Coexpression cluster:C1986: 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=C1986_Preadipocyte_Mesenchymal_basal_Fibroblast_Ewing_hepatic_Adipocyte
|

Latest revision as of 11:56, 17 September 2013


Full id: C1986_Preadipocyte_Mesenchymal_basal_Fibroblast_Ewing_hepatic_Adipocyte



Phase1 CAGE Peaks

Hg19::chr7:134464377..134464413,+p1@CALD1
Hg19::chr7:134464414..134464425,+p6@CALD1
Hg19::chr7:134464465..134464476,+p7@CALD1
Hg19::chr7:134655216..134655252,+p42@CALD1
Hg19::chr7:41740181..41740234,-p3@INHBA


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:0048180activin complex0.00274327425429597
GO:0043509activin A complex0.00274327425429597
GO:0043511inhibin complex0.00274327425429597
GO:0043512inhibin A complex0.00274327425429597
GO:0045077negative regulation of interferon-gamma biosynthetic process0.00274327425429597
GO:0045650negative regulation of macrophage differentiation0.00274327425429597
GO:0032278positive regulation of gonadotropin secretion0.00274327425429597
GO:0046881positive regulation of follicle-stimulating hormone secretion0.00274327425429597
GO:0045578negative regulation of B cell differentiation0.00274327425429597
GO:0032276regulation of gonadotropin secretion0.00274327425429597
GO:0046880regulation of follicle-stimulating hormone secretion0.00274327425429597
GO:0046887positive regulation of hormone secretion0.00274327425429597
GO:0048184follistatin binding0.00274327425429597
GO:0046882negative regulation of follicle-stimulating hormone secretion0.00274327425429597
GO:0042541hemoglobin biosynthetic process0.00274327425429597
GO:0045620negative regulation of lymphocyte differentiation0.00274327425429597
GO:0032277negative regulation of gonadotropin secretion0.00274327425429597
GO:0017106activin inhibitor activity0.00274327425429597
GO:0032925regulation of activin receptor signaling pathway0.00274327425429597
GO:0045649regulation of macrophage differentiation0.00274327425429597
GO:0032274gonadotropin secretion0.00274327425429597
GO:0020027hemoglobin metabolic process0.00274327425429597
GO:0032924activin receptor signaling pathway0.00274327425429597
GO:0046884follicle-stimulating hormone secretion0.00274327425429597
GO:0045648positive regulation of erythrocyte differentiation0.00274327425429597
GO:0050869negative regulation of B cell activation0.00316526985601304
GO:0045577regulation of B cell differentiation0.0039187901672028
GO:0017022myosin binding0.0039187901672028
GO:0002762negative regulation of myeloid leukocyte differentiation0.00425655424855442
GO:0030225macrophage differentiation0.00457171996631325
GO:0005160transforming growth factor beta receptor binding0.00457171996631325
GO:0046888negative regulation of hormone secretion0.00457171996631325
GO:0045646regulation of erythrocyte differentiation0.00457171996631325
GO:0045072regulation of interferon-gamma biosynthetic process0.00469189024750552
GO:0042326negative regulation of phosphorylation0.00469189024750552
GO:0045639positive regulation of myeloid cell differentiation0.00469189024750552
GO:0042095interferon-gamma biosynthetic process0.00469189024750552
GO:0045936negative regulation of phosphate metabolic process0.00469189024750552
GO:0002761regulation of myeloid leukocyte differentiation0.00527475089124858
GO:0045619regulation of lymphocyte differentiation0.00535186357924799
GO:0042036negative regulation of cytokine biosynthetic process0.00535186357924799
GO:0051048negative regulation of secretion0.00548549865239052
GO:0001541ovarian follicle development0.00548549865239052
GO:0032609interferon-gamma production0.00548549865239052
GO:0045638negative regulation of myeloid cell differentiation0.00548549865239052
GO:0046883regulation of hormone secretion0.00554377340373417
GO:0051250negative regulation of lymphocyte activation0.00554377340373417
GO:0051047positive regulation of secretion0.00587706040487411
GO:0005523tropomyosin binding0.00587706040487411
GO:0022601menstrual cycle phase0.00658201692404939
GO:0022602menstrual cycle process0.00659246796298695
GO:0050864regulation of B cell activation0.00659246796298695
GO:0008585female gonad development0.0069853226122356
GO:0030183B cell differentiation0.00710061156532613
GO:0046545development of primary female sexual characteristics0.00710061156532613
GO:0046660female sex differentiation0.00710061156532613
GO:0002573myeloid leukocyte differentiation0.0072164862557348
GO:0030218erythrocyte differentiation0.00751867023133696
GO:0042698menstrual cycle0.00751867023133696
GO:0045637regulation of myeloid cell differentiation0.00751867023133696
GO:0000082G1/S transition of mitotic cell cycle0.00751867023133696
GO:0046879hormone secretion0.00751867023133696
GO:0017148negative regulation of translation0.00892179721406047
GO:0031327negative regulation of cellular biosynthetic process0.00963864524147757
GO:0045597positive regulation of cell differentiation0.00991186012605939
GO:0009890negative regulation of biosynthetic process0.0104817334367983
GO:0008406gonad development0.0104817334367983
GO:0048608reproductive structure development0.0104817334367983
GO:0030308negative regulation of cell growth0.0105283196439338
GO:0045792negative regulation of cell size0.010573569048139
GO:0051046regulation of secretion0.0108572593869365
GO:0045137development of primary sexual characteristics0.0108572593869365
GO:0042035regulation of cytokine biosynthetic process0.0108572593869365
GO:0048609reproductive process in a multicellular organism0.0108572593869365
GO:0032504multicellular organism reproduction0.0108572593869365
GO:0042113B cell activation0.0108572593869365
GO:0045926negative regulation of growth0.0108572593869365
GO:0042325regulation of phosphorylation0.0111023468893183
GO:0030098lymphocyte differentiation0.0111023468893183
GO:0045596negative regulation of cell differentiation0.0111239770299129
GO:0042089cytokine biosynthetic process0.0111239770299129
GO:0042107cytokine metabolic process0.0111239770299129
GO:0051094positive regulation of developmental process0.0111239770299129
GO:0051174regulation of phosphorus metabolic process0.0111239770299129
GO:0019220regulation of phosphate metabolic process0.0111239770299129
GO:0003001generation of a signal involved in cell-cell signaling0.0111538065677599
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0117226808852989
GO:0051249regulation of lymphocyte activation0.0117226808852989
GO:0030099myeloid cell differentiation0.0117226808852989
GO:0051093negative regulation of developmental process0.0117226808852989
GO:0050865regulation of cell activation0.0120450365843769
GO:0007548sex differentiation0.0120628609213449
GO:0051329interphase of mitotic cell cycle0.012521706120398
GO:0003006reproductive developmental process0.0126796167943465
GO:0002521leukocyte differentiation0.0128430095254642
GO:0051325interphase0.0128430095254642
GO:0007050cell cycle arrest0.0142618136123162
GO:0051248negative regulation of protein metabolic process0.0145349377240317
GO:0001816cytokine production0.0156311719386937
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.019028151025804
GO:0005516calmodulin binding0.0191102653726784
GO:0045595regulation of cell differentiation0.019324669846072
GO:0046649lymphocyte activation0.0205955677522962
GO:0030097hemopoiesis0.0211016001926894
GO:0001558regulation of cell growth0.0211016001926894
GO:0003012muscle system process0.0211016001926894
GO:0006936muscle contraction0.0211016001926894
GO:0048534hemopoietic or lymphoid organ development0.0219172624202018
GO:0045321leukocyte activation0.0225925424131273
GO:0002520immune system development0.0226352337476506
GO:0006417regulation of translation0.0226771413179177
GO:0031326regulation of cellular biosynthetic process0.0241143574865719
GO:0016049cell growth0.0241143574865719
GO:0040008regulation of growth0.0241143574865719
GO:0008361regulation of cell size0.0243210210561916
GO:0001501skeletal development0.0243210210561916
GO:0001775cell activation0.0243210210561916
GO:0006917induction of apoptosis0.0243210210561916
GO:0012502induction of programmed cell death0.0243210210561916
GO:0032501multicellular organismal process0.0243210210561916
GO:0005179hormone activity0.0243210210561916
GO:0009889regulation of biosynthetic process0.0243210210561916
GO:0045893positive regulation of transcription, DNA-dependent0.0247880963368237
GO:0045786negative regulation of progression through cell cycle0.0248079815534451
GO:0050793regulation of developmental process0.0258084567133596
GO:0008083growth factor activity0.0274410651209666
GO:0043065positive regulation of apoptosis0.0275441036420166
GO:0043068positive regulation of programmed cell death0.0275441036420166
GO:0051239regulation of multicellular organismal process0.0293187191323811
GO:0045941positive regulation of transcription0.0293187191323811
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0301332864785564
GO:0051179localization0.0307047454263562
GO:0007167enzyme linked receptor protein signaling pathway0.0308048393720118
GO:0022414reproductive process0.0310822373624248
GO:0005125cytokine activity0.0313554509768971
GO:0000278mitotic cell cycle0.0327235991619901
GO:0000074regulation of progression through cell cycle0.0351611490324562
GO:0051726regulation of cell cycle0.0354965159760112
GO:0042802identical protein binding0.0355710461104435
GO:0031325positive regulation of cellular metabolic process0.0355710461104435
GO:0022403cell cycle phase0.0357037107339966
GO:0031324negative regulation of cellular metabolic process0.036122093213212
GO:0006928cell motility0.036122093213212
GO:0051674localization of cell0.036122093213212
GO:0046903secretion0.036122093213212
GO:0009893positive regulation of metabolic process0.0365248623183854
GO:0051246regulation of protein metabolic process0.0389616696652158
GO:0006357regulation of transcription from RNA polymerase II promoter0.0389616696652158
GO:0009892negative regulation of metabolic process0.0397965356152556
GO:0003779actin binding0.0397965356152556
GO:0000902cell morphogenesis0.0428340666047415
GO:0032989cellular structure morphogenesis0.0428340666047415
GO:0005615extracellular space0.0469705347814123



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
multi-cellular organism1.31e-17656
splanchnic layer of lateral plate mesoderm2.86e-1483
anatomical system8.88e-14624
vasculature1.72e-1378
vascular system1.72e-1378
anatomical group1.75e-13625
muscle tissue3.71e-1264
musculature3.71e-1264
musculature of body3.71e-1264
multilaminar epithelium3.87e-1283
dense mesenchyme tissue7.40e-1273
somite9.95e-1271
presomitic mesoderm9.95e-1271
presumptive segmental plate9.95e-1271
dermomyotome9.95e-1271
trunk paraxial mesoderm9.95e-1271
paraxial mesoderm1.60e-1172
presumptive paraxial mesoderm1.60e-1172
skeletal muscle tissue2.24e-1162
striated muscle tissue2.24e-1162
myotome2.24e-1162
epithelial tube open at both ends4.88e-1159
blood vessel4.88e-1159
blood vasculature4.88e-1159
vascular cord4.88e-1159
anatomical cluster4.89e-11373
vessel9.90e-1168
surface structure1.75e-1099
epithelial vesicle2.21e-1078
artery2.64e-1042
arterial blood vessel2.64e-1042
arterial system2.64e-1042
multi-tissue structure8.33e-10342
trunk mesenchyme1.04e-09122
cardiovascular system2.15e-09109
embryonic structure2.59e-09564
circulatory system3.48e-09112
mesenchyme8.17e-09160
entire embryonic mesenchyme8.17e-09160
unilaminar epithelium1.09e-08148
systemic artery1.15e-0833
systemic arterial system1.15e-0833
cell layer2.01e-08309
germ layer2.17e-08560
germ layer / neural crest2.17e-08560
embryonic tissue2.17e-08560
presumptive structure2.17e-08560
germ layer / neural crest derived structure2.17e-08560
epiblast (generic)2.17e-08560
epithelium3.52e-08306
epithelial tube5.41e-08117
integument7.91e-0846
integumental system7.91e-0846
developing anatomical structure8.77e-08581
organism subdivision1.06e-07264
embryo1.32e-07592
skin of body4.07e-0741


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)
MA0003.10.00991994
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.13.57633
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.11.55172
MA0061.10.291022
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
MA0076.10.540943
MA0077.11.07324
MA0078.11.95181
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.11.43794
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.994489
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.11.57313
MA0149.13.99004
MA0062.20.284987
MA0035.20.691506
MA0039.20.311551
MA0138.20.837782
MA0002.20.30855
MA0137.21.20193
MA0104.20.320919
MA0047.21.80892
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.11.20729
MA0157.12.04894
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.340387
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
FOS#235335.398773185336640.01153895317278740.0421974414514776
FOXA1#316936.648851849631270.006389025166568720.0278107531101267
FOXA2#3170314.77827825159910.0006289192851194480.00517479722828252
GTF2F1#296237.643796526054590.00428415496412050.0203489567171994
JUN#372537.50769751540180.004511206552906030.0213390960269465
MXI1#460135.976942977255580.008653004889366880.0329569008293128
NR3C1#290838.983813998703820.002687995788940450.0147994934999817
RFX5#599337.228746496317060.00502918278958660.0234703436865648
SRF#672238.278306957300690.003404846073776150.0173640665608236
STAT3#677436.311678998292540.007411172122460540.0306164868991597
TAF7#687936.859841642954350.005843286407019040.0262525591096387
TRIM28#10155311.15431502715750.001433159271529250.0092030079414193



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:C1986&oldid=3069103"