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Coexpression cluster:C1766

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Full id: C1766_CD14_CD14CD16_Hair_CD8_CD19_xeroderma_CD4



Phase1 CAGE Peaks

  Short description
Hg19::chr16:67970711..67970770,- p1@PSMB10
Hg19::chr6:32806506..32806579,- p1@TAP2
Hg19::chr6:32811771..32811831,- p1@PSMB8
Hg19::chr6:32821924..32821931,+ p3@PSMB9
Hg19::chr6:32821956..32821975,+ p1@PSMB9


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
1.46259452862696e-089.05665559813991e-06345Proteasome (KEGG):03050
4.292253837981e-089.05665559813991e-06364Proteasome Degradation (Wikipathways):WP183
2.67613900622899e-074.23498997735737e-053117Cell Cycle Checkpoints (Reactome):REACT_1538
1.34823063570187e-069.48255547110314e-053200DNA Replication (Reactome):REACT_383
5.28055171391627e-060.00033425892349093315Cell Cycle, Mitotic (Reactome):REACT_152
7.41609277987709e-077.82397788277033e-053164Metabolism of RNA (Reactome):REACT_21257
4.292253837981e-089.05665559813991e-06364Signaling by Wnt (Reactome):REACT_11045
5.33165031389329e-076.7498692973889e-053147Apoptosis (Reactome):REACT_578
1.23011302483476e-069.48255547110314e-053194HIV Infection (Reactome):REACT_6185
1.24930054759413e-069.48255547110314e-053195Metabolism of amino acids and derivatives (Reactome):REACT_13
6.99828407380497e-060.0004027194380653223346{CDC2,351} (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:0004298threonine endopeptidase activity4.45890006046998e-07
GO:0005839proteasome core complex (sensu Eukaryota)4.45890006046998e-07
GO:0000502proteasome complex (sensu Eukaryota)1.67734810946468e-06
GO:0005829cytosol2.45545651619859e-06
GO:0006955immune response3.17272568259787e-05
GO:0006511ubiquitin-dependent protein catabolic process3.17272568259787e-05
GO:0043632modification-dependent macromolecule catabolic process3.17272568259787e-05
GO:0019941modification-dependent protein catabolic process3.17272568259787e-05
GO:0051603proteolysis involved in cellular protein catabolic process3.17272568259787e-05
GO:0044257cellular protein catabolic process3.17272568259787e-05
GO:0002376immune system process3.18547758936163e-05
GO:0030163protein catabolic process4.79337041589452e-05
GO:0043285biopolymer catabolic process9.17363901730058e-05
GO:0044265cellular macromolecule catabolic process0.000130138439451392
GO:0009057macromolecule catabolic process0.000207011545222337
GO:0004175endopeptidase activity0.000372993694047045
GO:0043234protein complex0.000372993694047045
GO:0044248cellular catabolic process0.000372993694047045
GO:0009056catabolic process0.000612888261624961
GO:0004409homoaconitate hydratase activity0.000747674555516307
GO:0032991macromolecular complex0.00103080130692212
GO:0016787hydrolase activity0.00103483066727459
GO:0008233peptidase activity0.00103483066727459
GO:0006508proteolysis0.00119483757108028
GO:0046967cytosol to ER transport0.00119622646674452
GO:0044444cytoplasmic part0.00149521705842028
GO:0015440peptide-transporting ATPase activity0.00149521705842028
GO:0042825TAP complex0.00149521705842028
GO:0046980tapasin binding0.00149521705842028
GO:0015433peptide antigen-transporting ATPase activity0.00149521705842028
GO:0046978TAP1 binding0.00175900121882525
GO:0046977TAP binding0.00175900121882525
GO:0042824MHC class I peptide loading complex0.00175900121882525
GO:0046979TAP2 binding0.00175900121882525
GO:0042301phosphate binding0.00249169833156373
GO:0015198oligopeptide transporter activity0.00249169833156373
GO:0019538protein metabolic process0.00303212289754489
GO:0015197peptide transporter activity0.00314713046787477
GO:0042288MHC class I protein binding0.00344958683718131
GO:0002483antigen processing and presentation of endogenous peptide antigen0.00583164475744578
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.00583164475744578
GO:0006857oligopeptide transport0.00604832873003494
GO:0042605peptide antigen binding0.00611274679452986
GO:0019883antigen processing and presentation of endogenous antigen0.00611274679452986
GO:0005737cytoplasm0.00663599333603718
GO:0042287MHC protein binding0.00746948551180881
GO:0043231intracellular membrane-bound organelle0.011881802746805
GO:0043227membrane-bound organelle0.011881802746805
GO:0015833peptide transport0.011881802746805
GO:0005788endoplasmic reticulum lumen0.0190872887198677
GO:0006959humoral immune response0.0219186774220755
GO:0043229intracellular organelle0.0241778826458626
GO:0043226organelle0.0241778826458626
GO:0016836hydro-lyase activity0.0248247132780344
GO:0043170macromolecule metabolic process0.0264901850198828
GO:0016835carbon-oxygen lyase activity0.0264901850198828
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0264901850198828
GO:0046982protein heterodimerization activity0.0264901850198828
GO:0048002antigen processing and presentation of peptide antigen0.0264901850198828
GO:0044267cellular protein metabolic process0.0329518394413252
GO:0044260cellular macromolecule metabolic process0.0336207880593579
GO:0042803protein homodimerization activity0.03784391734532
GO:0005634nucleus0.0395329301440715
GO:0044238primary metabolic process0.0395329301440715
GO:0003823antigen binding0.0404041470685052
GO:0044424intracellular part0.040719536022715
GO:0042277peptide binding0.0460001800729374



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


Cell Type
Ontology termp-valuen
leukocyte4.94e-51136
nongranular leukocyte2.76e-48115
hematopoietic cell3.46e-41177
hematopoietic lineage restricted progenitor cell4.07e-41120
hematopoietic stem cell8.96e-41168
angioblastic mesenchymal cell8.96e-41168
hematopoietic oligopotent progenitor cell1.81e-37161
hematopoietic multipotent progenitor cell1.81e-37161
lymphocyte2.51e-2553
common lymphoid progenitor2.51e-2553
lymphoid lineage restricted progenitor cell4.49e-2552
nucleate cell6.17e-2355
myeloid leukocyte6.28e-2172
macrophage dendritic cell progenitor6.86e-2161
monopoietic cell1.03e-2059
monocyte1.03e-2059
monoblast1.03e-2059
promonocyte1.03e-2059
granulocyte monocyte progenitor cell3.23e-1867
defensive cell1.58e-1748
phagocyte1.58e-1748
myeloid lineage restricted progenitor cell3.65e-1666
connective tissue cell5.59e-16361
mesenchymal cell6.46e-16354
classical monocyte6.50e-1642
CD14-positive, CD16-negative classical monocyte6.50e-1642
myeloid cell2.48e-14108
common myeloid progenitor2.48e-14108
lymphocyte of B lineage9.12e-1324
pro-B cell9.12e-1324
multi fate stem cell2.87e-12427
T cell3.35e-1225
pro-T cell3.35e-1225
motile cell8.44e-12386
somatic stem cell2.15e-11433
stem cell1.13e-10441
mature alpha-beta T cell4.04e-1018
alpha-beta T cell4.04e-1018
immature T cell4.04e-1018
mature T cell4.04e-1018
immature alpha-beta T cell4.04e-1018
native cell4.54e-09722
B cell1.15e-0814
somatic cell1.33e-08588
CD8-positive, alpha-beta T cell3.66e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system4.87e-29108
hematopoietic system4.24e-2798
blood island4.24e-2798
immune system9.23e-2293
bone marrow2.14e-1776
connective tissue2.38e-15371
bone element8.44e-1482
skeletal element4.86e-1290
lateral plate mesoderm2.89e-11203
skeletal system2.29e-10100
blood1.01e-0815
haemolymphatic fluid1.01e-0815
organism substance1.01e-0815


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)
MA0003.11.80249
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.660087
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.569896
MA0050.16.28581
MA0051.17.0616
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
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
MA0139.12.96863
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.6031
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.527987
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.11.35623
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.20.230892
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
ELF1#199754.258097958807540.0007142416939776840.00573099940667912
GATA3#2625210.89460654288240.0125158291218830.0452830554167652
GTF2F1#296237.643796526054590.00428415496412050.0203461807238316
IRF1#365957.63716375356393.84754333311872e-050.000724154943535027
MEF2C#4208216.52454179704960.005579850077982050.0252449299209135
NANOG#79923211.69791139240510.01091164951956080.0402231315887834
NFKB1#479055.488063424193840.0002008162847462320.00239036379788143
PAX5#507945.335652424942260.002223389586187790.0127783724957003
PRDM1#639379.09857346647654.30606791165081e-060.000136196676748909
RAD21#588536.21302033727380.007751055068811640.031893169976031
REST#597835.790017229676810.009468788694433940.0356968856245889
RFX5#599349.638328661756080.000221480125815720.00249634824736326
SIN3A#2594255.408884726815140.0002159522671657270.00248035179044555
SMARCB1#6598414.60217262492594.30486693344344e-050.000768408815009228
SMC3#912639.02695970695970.002650964449467550.014637276031612
STAT1#6772416.56526999775942.61308619905866e-050.000563626826814306
STAT2#6773452.21101694915252.71660181075469e-071.3976314113961e-05
STAT3#677436.311678998292540.007411172122460540.0306128541883268
TAF1#687253.343046285745290.002394600090870310.0135322568524649
TBP#690853.706770687096390.001428755106721120.00918715395830854
YY1#752843.928936599883080.007193866269917620.0298403447201496
ZEB1#6935310.13305921052630.001895556924357070.0111614179186406
ZNF143#770238.100525931336740.003624870512090980.0183304048521895



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.