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Coexpression cluster:C3709: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3709_schwannoma_CD14_corpus_Macrophage_prostate_optic_clear
|id=C3709
}}

Latest revision as of 12:31, 17 September 2013


Full id: C3709_schwannoma_CD14_corpus_Macrophage_prostate_optic_clear



Phase1 CAGE Peaks

Hg19::chr18:21166386..21166479,-p1@NPC1
Hg19::chr18:21166649..21166681,-p4@NPC1
Hg19::chr18:21166757..21166776,-p5@NPC1


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

No GOStat results

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
organ7.30e-18503
anatomical system2.91e-13624
anatomical group3.13e-13625
multi-cellular organism1.18e-10656
developing anatomical structure3.48e-09581
bone marrow3.99e-0976
embryo1.28e-08592
bone element1.61e-0882
immune system1.03e-0793
germ layer4.44e-07560
germ layer / neural crest4.44e-07560
embryonic tissue4.44e-07560
presumptive structure4.44e-07560
germ layer / neural crest derived structure4.44e-07560
epiblast (generic)4.44e-07560
embryonic structure5.86e-07564


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)
MA0003.11.54338
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.14.7105
MA0017.10.686276
MA0019.12.26702
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.11.90116
MA0051.13.54769
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.990225
MA0074.10.935474
MA0076.11.74184
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
MA0101.11.55947
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
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
MA0144.10.531867
MA0145.11.37817
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.22.15877
MA0138.21.04628
MA0002.20.476938
MA0137.21.60005
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.711948
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
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
CTCFL#140690213.16431623931620.007433367036996010.0306778400370199
E2F1#186934.907389214879320.008460985347239390.032508897383575
E2F4#1874312.66806031528440.0004917987006298980.00436759902169098
E2F6#187635.017155731697390.00791769806886330.032193275271121
EGR1#195834.988179094810140.008056488137383440.0320440080958256
ELF1#199734.258097958807540.01295179875054610.0461915349579389
FOSL2#2355211.28680040304110.0100534586973120.0376712533326838
FOXA1#3169311.08141974938550.000734755275698670.00580989599020997
FOXA2#3170324.63046375266526.68983856509345e-050.00107208846079453
GABPB1#255337.067683836182170.002832212825417420.015401097327594
HNF4A#3172215.42152690863580.005444210486686610.0246750813270435
IRF1#365937.63716375356390.002244692747297240.0127979837228397
JUND#372736.994663941871030.002921845042734990.015666627703984
NRF1#4899312.21027944771090.0005492172401020010.00470894830793965
PAX5#507936.669565531177830.003370290999677260.017281511278245
SIN3A#2594235.408884726815140.006318961977991520.0276486685667375
SMC3#9126210.02995522995520.0126656379767470.0457410894101968
SP1#666735.69838137814090.005403962701712170.0246305516541903
SREBF1#6720231.33723296032550.00133816265136180.00887511076049884
SREBF2#67212291.2955082742321.56525677906814e-050.000366369011091657
TFAP2A#7020316.5186343730450.0002218033880766340.00248177887800895
TFAP2C#7022310.80922860986020.0007916746575753130.00615603525891655
USF1#739136.361499277207960.00388404057290560.0190149211734725
YY1#752834.911170749853860.008441455341808260.0329108987025203
ZBTB7A#5134137.35190930787590.002516255860282270.0140097689408263
ZEB1#6935211.25895467836260.01010222676646330.0378105813239198



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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