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{{Coexpression_clusters
{
|full_id=C3659_breast_MCF7_cerebellum_occipital_pons_frontal_paracentral
|

Latest revision as of 12:30, 17 September 2013


Full id: C3659_breast_MCF7_cerebellum_occipital_pons_frontal_paracentral



Phase1 CAGE Peaks

Hg19::chr17:57184170..57184257,-p1@TRIM37
Hg19::chr17:57184260..57184271,-p6@TRIM37
Hg19::chr20:49411484..49411518,+p2@BCAS4


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:0005777peroxisome0.0499682941000963
GO:0042579microbody0.0499682941000963



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 system2.75e-3081
nervous system6.47e-2889
brain1.25e-2668
future brain1.25e-2668
neural tube1.33e-2656
neural rod1.33e-2656
future spinal cord1.33e-2656
neural keel1.33e-2656
regional part of nervous system1.12e-2553
regional part of brain1.12e-2553
regional part of forebrain3.24e-2341
forebrain3.24e-2341
anterior neural tube3.24e-2341
future forebrain3.24e-2341
brain grey matter5.62e-2034
gray matter5.62e-2034
telencephalon6.40e-2034
neurectoderm7.34e-2086
neural plate8.88e-2082
presumptive neural plate8.88e-2082
cerebral hemisphere9.77e-2032
regional part of telencephalon5.52e-1932
pre-chordal neural plate3.94e-1861
ectoderm-derived structure1.22e-16171
ectoderm1.22e-16171
presumptive ectoderm1.22e-16171
ecto-epithelium6.87e-16104
cerebral cortex1.74e-1525
pallium1.74e-1525
regional part of cerebral cortex1.30e-1422
organ system subdivision2.09e-13223
neocortex2.17e-1320
structure with developmental contribution from neural crest2.24e-12132
adult organism9.93e-12114
anatomical cluster5.85e-09373
Disease
Ontology termp-valuen
cell type cancer6.64e-12143
carcinoma1.31e-11106


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.12.72668
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
MA0048.13.37768
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.11.59304
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
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.11.52002
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.11.37817
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.24.04548
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
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
MA0162.12.76014
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.21.22771
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#467214.97544968400580.005768294540793880.0259547160202478
BCL3#602223.03140186915890.002464674760842910.0138503183937408
BRCA1#672213.45615376214920.007119807716084560.0296225638618499
CCNT2#90536.336201576962630.003930750035764890.0189855063120404
CEBPB#105137.971147625824820.001974187055288560.0115146946200872
CTCF#1066435.360256373075030.0064925092527670.0279179501749726
CTCFL#140690319.74647435897440.0001298372005551160.00171602978850618
E2F6#187635.017155731697390.00791769806886330.0321757380783663
EGR1#195834.988179094810140.008056488137383440.032028151367675
ELF1#199734.258097958807540.01295179875054610.0461726143401244
ETS1#211339.728760922202340.001085840092584840.00761509894100643
GABPB1#255337.067683836182170.002832212825417420.0153962874908271
HDAC2#3066313.41562023662630.0004140761399857210.00390903895724204
HMGN3#932438.178547723350590.001827766942164210.0108614595546338
HNF4A#3172323.13229036295378.07584663437677e-050.00122752633772038
IRF1#365937.63716375356390.002244692747297240.0127937931584248
NFE2#4778251.4695071010860.0004987653528392110.00440623876545207
PAX5#507936.669565531177830.003370290999677260.0172781180893036
POU2F2#545239.106124057742520.001324165192682130.00881530396217038
SETDB1#9869226.8800174520070.001814468907964410.0108927584226531
SIN3A#2594235.408884726815140.006318961977991520.0276359325803793
SMARCB1#6598318.25271578115740.000164397760679890.00202925632048777
SMC3#9126315.04493284493280.0002935825420371870.00308807202213936
SP1#666735.69838137814090.005403962701712170.0246230295625896
SP2#6668217.43568699589640.004273568481769740.02031437889343
STAT1#6772213.80439166479950.006770931708444080.0287505828873878
TCF12#6938310.63446490218640.0008313523990202070.00628852127191072
TFAP2A#7020211.01242291536330.01054990655215560.0390066800155975
TFAP2C#7022310.80922860986020.0007916746575753130.00615008253217109
TRIM28#10155212.39368336350830.008368344129438470.0329034520192163
USF1#739136.361499277207960.00388404057290560.0190077931396696
YY1#752834.911170749853860.008441455341808260.0328949350562708
ZBTB33#10009221.10981668665410.002928597060603240.0156338043555685
ZEB1#6935316.88843201754390.0002075486917327580.00242598520602994



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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