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Coexpression cluster:C4341

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Full id: C4341_CD8_CD4_CD133_CD19_CD34_skeletal_neuroectodermal



Phase1 CAGE Peaks

  Short description
Hg19::chr3:61728802..61728813,- p1@RPL10AP6
Hg19::chr5:149829294..149829310,- p1@RPS14
Hg19::chr6:33239845..33239859,+ p1@RPS18


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


p.valueFDRnGenesnPathwayName
3.0758227865789e-050.00943346997452502292Ribosome (KEGG):03010
3.14334971571015e-050.00943346997452502293Cytoplasmic Ribosomal Proteins (Wikipathways):WP477
0.000319276728200750.03207087027504722296Metabolism of proteins (Reactome):REACT_17015
4.73033289875392e-050.009433469974525022114Regulation of beta-cell development (Reactome):REACT_13698
0.0003546541736577090.03207087027504722312Diabetes pathways (Reactome):REACT_15380
7.45139808414298e-050.009433469974525022143Influenza Infection (Reactome):REACT_6167
6.93847325306698e-050.009433469974525022138{RPS27A,138} (Static Module):NA



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


GO IDGO nameFDR corrected p-value
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)7.194409102925e-05
GO:0005830cytosolic ribosome (sensu Eukaryota)0.000177936588775551
GO:0015935small ribosomal subunit0.000310347059341862
GO:0044445cytosolic part0.000575648910173879
GO:0033279ribosomal subunit0.000622361272308287
GO:0042257ribosomal subunit assembly0.000622361272308287
GO:0000028ribosomal small subunit assembly and maintenance0.000622361272308287
GO:0042274ribosomal small subunit biogenesis and assembly0.000968103285525504
GO:0030490maturation of SSU-rRNA0.000968103285525504
GO:0005829cytosol0.00206506472197114
GO:0042255ribosome assembly0.00277209174988996
GO:0003735structural constituent of ribosome0.00323014220823884
GO:0005840ribosome0.00355109640920681
GO:0003723RNA binding0.00436735624453293
GO:0030529ribonucleoprotein complex0.00553112840447372
GO:0006412translation0.00583360297203652
GO:0009059macromolecule biosynthetic process0.00870856932178837
GO:0019843rRNA binding0.00870856932178837
GO:0044249cellular biosynthetic process0.0126687003930597
GO:0006364rRNA processing0.0153350836109307
GO:0016072rRNA metabolic process0.0153350836109307
GO:0009058biosynthetic process0.0175449323810289
GO:0042254ribosome biogenesis and assembly0.0209909472866491
GO:0043234protein complex0.0210206369465923
GO:0043232intracellular non-membrane-bound organelle0.0210206369465923
GO:0043228non-membrane-bound organelle0.0210206369465923
GO:0022618protein-RNA complex assembly0.0223825016040295
GO:0045892negative regulation of transcription, DNA-dependent0.0314909289356775
GO:0032991macromolecular complex0.0333293770674674
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0341701770605187
GO:0044446intracellular organelle part0.0341701770605187
GO:0044422organelle part0.0341701770605187
GO:0016481negative regulation of transcription0.0382526883561942
GO:0044444cytoplasmic part0.0395208036809799
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0395208036809799
GO:0031324negative regulation of cellular metabolic process0.0458487231224755



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



Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell2.00e-1652
lymphocyte3.01e-1653
common lymphoid progenitor3.01e-1653
nucleate cell2.77e-1455
native cell8.51e-11722
animal cell1.23e-09679
eukaryotic cell1.23e-09679
T cell4.03e-0925
pro-T cell4.03e-0925
mature alpha-beta T cell4.13e-0918
alpha-beta T cell4.13e-0918
immature T cell4.13e-0918
mature T cell4.13e-0918
immature alpha-beta T cell4.13e-0918
lymphocyte of B lineage2.78e-0824
pro-B cell2.78e-0824
somatic cell6.54e-08588
B cell2.65e-0714


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
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.13.88968
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
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
MA0076.14.21544
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
MA0114.10.549955
MA0115.11.57693
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
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.24.02533
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
BCL3#602223.03140186915890.002464674760842910.013860013318311
BCLAF1#9774214.43509840674790.006201147435546130.0273948494996405
ELK4#2005210.8237877723120.01091284719516480.0402105153900584
JUNB#3726220.40708843988080.003131462199438740.0164535282309797
NR2C2#7182221.74307393682720.002762207975496010.0151402455522634
RDBP#79362102.4256026600170.0001264379392731220.00168367358660533
RFX5#5993312.04791082719510.0005717246050312580.0048584496358714
SIX5#147912211.3911435703060.009873820081429030.0370872827003908
SP2#6668217.43568699589640.004273568481769740.0203254801524454
STAT1#6772213.80439166479950.006770931708444080.0287611069548213
THAP1#55145220.91276306856750.002983447413736940.0158746823131889
TRIM28#10155212.39368336350830.008368344129438470.0329319677657193
WRNIP1#56897273.21330956625070.000247093641135960.00268590890784747
ZZZ3#26009179.80440414507770.0124784379082580.0451665480245566



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.