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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:26, 17 September 2013


Full id: C596_testis_medulla_pituitary_caudate_amygdala_hippocampus_putamen



Phase1 CAGE Peaks

Hg19::chr13:26042916..26042952,+p4@ATP8A2
Hg19::chr14:24025106..24025172,-p2@ZFHX2
Hg19::chr14:74111671..74111730,+p1@DNAL1
Hg19::chr15:40074996..40075059,-p1@FSIP1
Hg19::chr16:81110786..81110863,-p1@C16orf46
Hg19::chr1:42921677..42921722,-p1@ZMYND12
Hg19::chr1:45140360..45140399,+p2@C1orf228
Hg19::chr2:120301997..120302038,+p1@PCDP1
Hg19::chr2:120302041..120302052,+p2@PCDP1
Hg19::chr2:207630033..207630061,-p2@MDH1B
Hg19::chr2:27712537..27712579,-p2@IFT172
Hg19::chr3:27410847..27410917,-p1@NEK10
Hg19::chr5:114515949..114516006,-p2@TRIM36
Hg19::chr5:137475071..137475122,-p1@NME5
Hg19::chr6:163148973..163149044,+p1@PACRG


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><br>

Uber Anatomy
Ontology termp-valuen
nervous system9.91e-4389
central nervous system6.31e-4281
neural tube8.15e-4056
neural rod8.15e-4056
future spinal cord8.15e-4056
neural keel8.15e-4056
regional part of nervous system8.82e-3853
regional part of brain8.82e-3853
neurectoderm2.17e-3686
adult organism5.11e-36114
neural plate8.27e-3682
presumptive neural plate8.27e-3682
brain4.51e-3568
future brain4.51e-3568
regional part of forebrain1.20e-3141
forebrain1.20e-3141
anterior neural tube1.20e-3141
future forebrain1.20e-3141
ectoderm-derived structure9.80e-29171
ectoderm9.80e-29171
presumptive ectoderm9.80e-29171
pre-chordal neural plate1.03e-2761
telencephalon2.16e-2634
brain grey matter2.45e-2634
gray matter2.45e-2634
ecto-epithelium7.10e-26104
cerebral hemisphere3.95e-2532
regional part of telencephalon6.26e-2532
structure with developmental contribution from neural crest8.74e-25132
organ system subdivision4.01e-23223
cerebral cortex1.06e-1925
pallium1.06e-1925
anatomical cluster6.87e-19373
regional part of cerebral cortex1.65e-1822
neocortex6.07e-1720
multi-tissue structure3.95e-14342
tube5.10e-12192
anatomical conduit1.40e-10240
epithelium1.17e-09306
organ part1.27e-09218
cell layer2.07e-09309
posterior neural tube2.74e-0915
chordal neural plate2.74e-0915
basal ganglion2.58e-089
nuclear complex of neuraxis2.58e-089
aggregate regional part of brain2.58e-089
collection of basal ganglia2.58e-089
cerebral subcortex2.58e-089
neural nucleus4.64e-089
nucleus of brain4.64e-089
segmental subdivision of nervous system4.91e-0813
segmental subdivision of hindbrain1.99e-0712
hindbrain1.99e-0712
presumptive hindbrain1.99e-0712


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)
MA0003.11.89076
MA0004.10.256222
MA0006.10.842675
MA0007.10.67744
MA0009.10.669377
MA0014.10.956537
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.12.05529
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.229721
MA0056.10
MA0057.10.0873069
MA0058.10.182945
MA0059.10.182001
MA0060.11.32216
MA0061.10.43901
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.341559
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.098235
MA0074.10.894848
MA0076.11.07748
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.11.62113
MA0084.11.15904
MA0087.10.63829
MA0088.10.426561
MA0089.10
MA0090.10.593146
MA0091.11.32108
MA0092.10.228476
MA0093.10.431889
MA0095.10
MA0098.10
MA0100.11.66251
MA0101.10.861002
MA0103.10.411001
MA0105.10.376193
MA0106.10.37688
MA0107.10.315431
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.660297
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.11.12143
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.406749
MA0140.10.30631
MA0141.11.61764
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.11.79586
MA0146.10.62917
MA0147.10.0991954
MA0148.10.276339
MA0149.10.298252
MA0062.21.14324
MA0035.20.305721
MA0039.21.80801
MA0138.21.08869
MA0002.20.0612545
MA0137.20.465392
MA0104.20.236755
MA0047.20.366327
MA0112.20.448515
MA0065.20.287056
MA0150.10.201098
MA0151.10
MA0152.10.838393
MA0153.10.763487
MA0154.10.912675
MA0155.10.6552
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.10.786431
MA0161.10
MA0162.10.76493
MA0163.10.153816
MA0164.11.03839
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.20.34639
MA0102.21.1957
MA0258.10.569952
MA0259.10.693919
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#46745.990179873602330.00360721410305840.0182596856198777
BRCA1#67245.382461504859670.005289673768002730.0244966405931375
CHD2#110674.82721065592120.0002511849755939860.00270643842629323
E2F1#186992.944433528927590.0009058368633748020.00659725914741987
ELF1#1997102.838731972538360.0004638915348213510.00427045993875778
ETS1#211363.891504368880930.002591331521227080.0143307425335152
FOSL2#235544.514720161216450.009808741154451470.0368693581943407
FOXA1#316953.693806583128480.008293763036037370.0326754052480556
GABPB1#255362.827073534472870.01273088928445650.0459227487990657
HEY1#2346292.424066625863430.003896879222507080.0189949672883141
HMGN3#932473.816655604230280.001069817901824620.00755549850207337
HSF1#3297443.81084444444441.76670144256977e-066.63714143742966e-05
IRF1#365963.054865501425560.008746772827476030.0332280011395595
JUND#372762.797865576748410.01337976808190040.0472771119770477
MAX#414973.011192570869990.004354689183513060.020648296723732
MXI1#4601106.64104775250621.93197229432088e-071.05144999711609e-05
NFKB1#4790103.658708949462564.91132197708818e-050.00085219065619723
NR2C2#718236.522922181048170.00994133198947190.0372952610240474
NRF1#489954.070093149236970.005493687985816360.0248755811641307
POLR2A#5430121.717962541246460.008857472838871370.0336179672863643
PPARGC1A#10891246.67348484848480.0008344464478183190.00629642024157918
RFX5#599375.622358386024389.57153219667447e-050.00136899650929675
SIN3A#25942124.327107781452114.13656523923942e-071.98995272695037e-05
SIX5#147912910.25202921327542.9069232749672e-081.97782514602149e-06
SP1#666772.659244643132420.008824589092176910.03350898997229
SREBF1#6720928.2035096642933.94371509408989e-125.20047551403604e-10
TAF1#6872122.674437028596238.87480614411867e-050.00129978387166682
TBP#690892.224062412257830.00725695134502010.030031649622481
THAP1#5514536.273828920570270.01105094501602920.0406490912030809
USF1#739172.968699662697050.004726377572875510.0222731769395156
YY1#7528103.27411383323590.0001326837928134460.00174328376369902
ZBTB33#1000948.443926674661640.001025437384919650.00726564823905175
ZEB1#693544.503581871345030.009893096304177240.0371196366054237



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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