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Coexpression cluster:C4240: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4240_Dendritic_left_mature_heart_medial_occipital_Macrophage
|id=C4240
}}

Latest revision as of 12:42, 17 September 2013


Full id: C4240_Dendritic_left_mature_heart_medial_occipital_Macrophage



Phase1 CAGE Peaks

Hg19::chr2:63816087..63816124,+p1@MDH1
Hg19::chr2:63816126..63816152,+p2@MDH1
Hg19::chr2:63816295..63816356,+p4@MDH1


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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
central nervous system1.11e-1681
brain1.26e-1568
future brain1.26e-1568
neural tube3.59e-1556
neural rod3.59e-1556
future spinal cord3.59e-1556
neural keel3.59e-1556
regional part of nervous system1.40e-1453
regional part of brain1.40e-1453
nervous system1.42e-1489
regional part of forebrain2.19e-1341
forebrain2.19e-1341
anterior neural tube2.19e-1341
future forebrain2.19e-1341
cerebral hemisphere7.07e-1232
brain grey matter1.09e-1134
gray matter1.09e-1134
telencephalon2.34e-1134
regional part of telencephalon1.16e-1032
neural plate3.85e-1082
presumptive neural plate3.85e-1082
regional part of cerebral cortex1.00e-0922
neurectoderm1.40e-0986
cerebral cortex5.28e-0925
pallium5.28e-0925
neocortex1.01e-0820
structure with developmental contribution from neural crest1.20e-08132
ecto-epithelium3.05e-08104
adult organism3.69e-08114
organ system subdivision4.45e-08223
pre-chordal neural plate7.10e-0861
ectoderm-derived structure8.61e-07171
ectoderm8.61e-07171
presumptive ectoderm8.61e-07171
Disease
Ontology termp-valuen
disease of cellular proliferation1.67e-07239
cancer5.71e-07235


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
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.12.16573
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
MA0076.10.734647
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
MA0139.10.440097
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
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.11.29138
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-050.0012985779870187
BCL11A#53335218.91297006907140.003639406248379680.018392332777244
BCLAF1#9774321.65264761012189.8473954032885e-050.00139394433250752
CEBPB#105137.971147625824820.001974187055288560.0115521135066832
CHD2#1106310.34402283411690.0009033701102746880.00661713220276183
E2F1#186934.907389214879320.008460985347239390.0326385775533846
E2F4#1874312.66806031528440.0004917987006298980.00437951607222766
ELF1#199734.258097958807540.01295179875054610.0463625208975968
EP300#203336.77394172622320.003216880500103790.0167874772672933
ESR1#2099330.76860329615453.43136389821584e-050.000678213879950348
ETS1#211339.728760922202340.001085840092584840.00763817966117517
FOXA2#3170324.63046375266526.68983856509345e-050.0010740661797076
GABPB1#255337.067683836182170.002832212825417420.0154493614997268
GTF2F1#2962312.73966087675770.0004835525047438590.00434909921141439
HNF4G#3174328.75342252644684.20470658818262e-050.000758437567121252
IRF4#3662321.91451268674419.49854535978121e-050.00136981300584119
JUNB#3726330.61063265982113.4847716247536e-050.000681291770343769
JUND#372736.994663941871030.002921845042734990.0157142270157165
MYC#460935.22228187160940.007020843755740150.0295296162460531
NFKB1#479035.488063424193840.006049381815655430.0270192613199862
NFYA#4800318.42558069983050.0001598135507814160.00200009196285924
NFYB#4801211.17319550235760.01025467135054530.0381419431311513
NR2C2#7182332.61461090524092.88098172333076e-050.000605649859506726
PBX3#5090321.91451268674419.49854535978121e-050.00137000218040352
POU2F2#545239.106124057742520.001324165192682130.00883783797025364
SIN3A#2594235.408884726815140.006318961977991520.0277568165385034
SIX5#147912317.0867153554590.0002004060546325010.00240025320410135
SMARCC2#6601394.15537442689761.19621075407887e-064.8592397878352e-05
SP1#666735.69838137814090.005403962701712170.0247168459579626
SRF#6722313.79717826216780.0003806615025800190.0037580023317851
TAF7#6879311.43306940492390.0006690181981945830.00544425678675737
TCF7L2#6934310.77017656313730.0008003181298398380.00615496503404587
TRIM28#10155318.59052504526250.0001555969297255280.00197501066402581
WRNIP1#568973109.8199643493767.53682839543883e-073.32969044327934e-05
YY1#752834.911170749853860.008441455341808260.0330230795386415
ZEB1#6935316.88843201754390.0002075486917327580.00243251911299265
ZNF143#7702313.50087655222790.0004062804962997170.00389923991481769
ZNF263#1012738.221841637010680.001799043925565870.0109704179682475



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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