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Coexpression cluster:C3402: Difference between revisions

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{{Coexpression_clusters
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amino acid ADP-ribosylation!0.0320481603041205!10038$GO:0006284!base-excision repair!0.0320481603041205!10038$GO:0003950!NAD+ ADP-ribosyltransferase 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|full_id=C3402_CD8_CD4_diffuse_non_cord_CD19_b
|gostat_on_coexpression_clusters=GO:0006471!protein amino acid ADP-ribosylation!0.0320481603041205!10038$GO:0006284!base-excision repair!0.0320481603041205!10038$GO:0003950!NAD+ ADP-ribosyltransferase activity!0.0320481603041205!10038
|id=C3402
|ontology_enrichment_celltype=CL:0000542!9.53e-29!53;CL:0000051!9.53e-29!53;CL:0000838!4.17e-28!52;CL:0000037!3.32e-23!172;CL:0000566!3.32e-23!172;CL:0000988!1.30e-20!182;CL:0000738!1.57e-20!140;CL:0002032!2.16e-20!165;CL:0000837!2.16e-20!165;CL:0002031!4.24e-16!124;CL:0002087!3.62e-15!119;CL:0000945!2.68e-14!24;CL:0000826!2.68e-14!24;CL:0000084!4.20e-13!25;CL:0000827!4.20e-13!25;CL:0000791!3.18e-12!18;CL:0000789!3.18e-12!18;CL:0002420!3.18e-12!18;CL:0002419!3.18e-12!18;CL:0000790!3.18e-12!18;CL:0000236!3.16e-09!14;CL:0000625!3.27e-08!11
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.99e-11!115;UBERON:0000178!7.35e-07!15;UBERON:0000179!7.35e-07!15;UBERON:0000463!7.35e-07!15
}}

Latest revision as of 12:25, 17 September 2013


Full id: C3402_CD8_CD4_diffuse_non_cord_CD19_b



Phase1 CAGE Peaks

Hg19::chr14:20811696..20811707,+p4@PARP2
Hg19::chr1:186344883..186344903,+p3@C1orf27
Hg19::chr1:186344904..186344925,+p2@C1orf27


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:0006471protein amino acid ADP-ribosylation0.0320481603041205
GO:0006284base-excision repair0.0320481603041205
GO:0003950NAD+ ADP-ribosyltransferase activity0.0320481603041205



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
adult organism2.82e-10114
blood9.72e-0715
haemolymphatic fluid9.72e-0715
organism substance9.72e-0715


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0057.10.886807
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
MA0088.10.715722
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
MA0139.15.09957
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
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
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.12.02335
MA0161.10
MA0162.10.149099
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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#467322.46317452600878.81932387510763e-050.00129419891273341
BCLAF1#9774321.65264761012189.8473954032885e-050.00139055182331537
BDP1#558141350.0511363636360.002854021475323210.0154705532185229
BRCA1#672320.18423064322380.0001215704860271640.00164040051552855
BRF2#552901358.1918604651160.002789217733358720.0152770668583098
CCNT2#90536.336201576962630.003930750035764890.0189574510729739
CHD2#1106310.34402283411690.0009033701102746880.00659216538198562
CTCFL#140690213.16431623931620.007433367036996010.0306705681090718
E2F1#186934.907389214879320.008460985347239390.0324301544583211
E2F4#1874312.66806031528440.0004917987006298980.00436240568159385
EBF1#187938.9064668465690.00141523283560980.00913507429655453
EGR1#195834.988179094810140.008056488137383440.0319673099266817
ELF1#199734.258097958807540.01295179875054610.0460923743383747
ELK4#2005210.8237877723120.01091284719516480.040180745574328
EP300#203336.77394172622320.003216880500103790.0167148150522557
GTF2F1#2962312.73966087675770.0004835525047438590.00433156703344574
HDAC2#3066313.41562023662630.0004140761399857210.00390409840064717
HMGN3#932438.178547723350590.001827766942164210.0108497301166698
IRF1#365937.63716375356390.002244692747297240.0127791477696907
JUND#372736.994663941871030.002921845042734990.0156385268497002
MEF2C#4208341.31135449262411.41744912101957e-050.000340236655366957
MYC#460935.22228187160940.007020843755740150.0293734687740154
NFKB1#479035.488063424193840.006049381815655430.0269042025058654
POLR3A#111281113.0440366972480.00882009881003120.0334955928737446
REST#597839.650028716128020.001112636247114590.00766204780511675
RFX5#5993312.04791082719510.0005717246050312580.00483641228129431
SIN3A#2594235.408884726815140.006318961977991520.0275897186462984
SIX5#147912211.3911435703060.009873820081429030.0370632892026153
SMARCB1#6598318.25271578115740.000164397760679890.00202733944121467
SMC3#9126210.02995522995520.0126656379767470.0457221169214158
SP1#666735.69838137814090.005403962701712170.0245865589459428
SP2#6668217.43568699589640.004273568481769740.0203106811680341
SPI1#668838.204323508522730.001810593189410520.0108932854489801
SREBF2#67211145.6477541371160.006850215514569990.0290459038661108
SRF#6722313.79717826216780.0003806615025800190.00374349403653057
STAT1#6772320.70658749719920.0001125992441046670.00154591198304815
STAT2#6773243.50918079096040.0006968990898868230.00560692119626299
STAT3#6774310.51946499715420.0008589184530415310.00641893268817205
TAF7#6879311.43306940492390.0006690181981945830.00541598260609597
TRIM28#10155318.59052504526250.0001555969297255280.0019671211407341
USF1#739136.361499277207960.00388404057290560.0189855524381582
USF2#7392312.99219738506960.0004558979393427810.0042091164150478
WRNIP1#56897273.21330956625070.000247093641135960.0026847911763003
YY1#752834.911170749853860.008441455341808260.0328520328828109



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.

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