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Coexpression cluster:C4290

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Full id: C4290_Lymphatic_Hepatocyte_liver_adipose_breast_Renal_vagina



Phase1 CAGE Peaks

  Short description
Hg19::chr3:145940083..145940098,- p6@PLSCR4
Hg19::chr3:145940126..145940135,- p15@PLSCR4
Hg19::chr3:145940214..145940228,- p14@PLSCR4


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism9.91e-19114
anatomical conduit4.02e-16240
tube4.51e-13192
anatomical cluster1.04e-12373
blood vessel endothelium4.01e-1218
endothelium4.01e-1218
cardiovascular system endothelium4.01e-1218
lymphatic vessel1.97e-118
lymph vasculature1.97e-118
lymphatic part of lymphoid system1.97e-118
liver2.68e-1119
digestive gland2.68e-1119
liver bud2.68e-1119
endocrine gland2.06e-1035
endothelial tube1.11e-099
arterial system endothelium1.11e-099
endothelium of artery1.11e-099
simple squamous epithelium1.65e-0922
hepatic diverticulum1.88e-0922
liver primordium1.88e-0922
epithelial tube5.36e-09117
lymphoid system5.76e-0910
digestive tract diverticulum6.03e-0923
endocrine system1.52e-0845
squamous epithelium4.18e-0825
epithelial sac4.67e-0825
epithelium of foregut-midgut junction4.67e-0825
anatomical boundary4.67e-0825
hepatobiliary system4.67e-0825
foregut-midgut junction4.67e-0825
septum transversum4.67e-0825
sac1.15e-0726
epithelium1.23e-07306
abdomen element1.64e-0754
abdominal segment element1.64e-0754
vessel1.77e-0768
cell layer1.89e-07309
trunk region element2.45e-07101
vasculature8.12e-0778
vascular system8.12e-0778


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.12.76432
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.12.78037
MA0041.10.847069
MA0042.13.15728
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.12.32521
MA0115.15.50024
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.12.18164
MA0139.11.12079
MA0140.10.894983
MA0141.11.6959
MA0142.11.12317
MA0143.11.00455
MA0144.14.49708
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.22.70092
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.13.156
MA0154.10.312019
MA0155.10.256269
MA0156.12.7096
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.13.79952
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066435.360256373075030.0064925092527670.0280426457340667
ELF1#199734.258097958807540.01295179875054610.0463752368934546
EP300#203336.77394172622320.003216880500103790.0167933511221803
FOS#235338.99795530889440.001372499272417130.00899883555226144
FOXA1#3169311.08141974938550.000734755275698670.00582710200005265
FOXA2#3170324.63046375266526.68983856509345e-050.0010747270418394
GATA2#2624312.7449317335540.0004829527704283790.00437915474828699
HDAC2#3066313.41562023662630.0004140761399857210.00392464815173507
HNF4A#3172323.13229036295378.07584663437677e-050.00123128955714989
HNF4G#3174328.75342252644684.20470658818262e-050.000758830743672377
JUN#3725312.51282919233630.0005103313992726250.0044530454514691
NR3C1#2908314.9730233311730.0002978331194675480.0030953719936383
RXRA#6256320.07461713913330.0001235730348432220.00165608163556927
SP1#666735.69838137814090.005403962701712170.0247265919213195
TCF7L2#6934310.77017656313730.0008003181298398380.00615859307120121



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.