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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.0275087243397802

Latest revision as of 12:15, 17 September 2013


Full id: C2931_Mast_malignant_pituitary_occipital_pineal_cerebellum_small



Phase1 CAGE Peaks

Hg19::chr8:92082244..92082289,-p1@uc003yet.2
Hg19::chr8:92082301..92082316,-p3@uc003yet.2
Hg19::chr8:92082319..92082348,-p2@uc003yet.2
Hg19::chr8:92082349..92082360,-p2@ENST00000522817


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
adult organism7.97e-29114
nervous system5.29e-1689
neural tube1.76e-1556
neural rod1.76e-1556
future spinal cord1.76e-1556
neural keel1.76e-1556
central nervous system2.77e-1581
regional part of nervous system4.50e-1453
regional part of brain4.50e-1453
regional part of forebrain1.11e-1241
forebrain1.11e-1241
anterior neural tube1.11e-1241
future forebrain1.11e-1241
brain2.40e-1268
future brain2.40e-1268
organ system subdivision1.69e-11223
neural plate1.33e-1082
presumptive neural plate1.33e-1082
neurectoderm1.93e-1086
ectoderm-derived structure9.29e-10171
ectoderm9.29e-10171
presumptive ectoderm9.29e-10171
brain grey matter1.39e-0934
gray matter1.39e-0934
telencephalon8.80e-0934
regional part of telencephalon1.42e-0832
cerebral hemisphere3.75e-0832
ecto-epithelium4.17e-08104
pre-chordal neural plate2.91e-0761
structure with developmental contribution from neural crest6.21e-07132
Disease
Ontology termp-valuen
cancer5.07e-08235
disease of cellular proliferation1.17e-07239


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.14.37647
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.539587
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.869502
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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#467422.46317452600873.92475754624726e-060.000127614493577994
BRCA1#672420.18423064322386.02116732184487e-060.000179824047448143
CCNT2#90546.336201576962630.0006203100587215640.0051391846916406
CEBPB#105147.971147625824820.0002476385788090830.00268875408381763
E2F1#186944.907389214879320.001724022357361790.0106864010315454
E2F4#1874412.66806031528443.88145892637771e-050.000728568815262332
ELF1#199744.258097958807540.003041525565781240.0161335714645044
ELK4#2005416.2356816584681.43847748454449e-050.000343861638838045
EP300#203346.77394172622320.0004748459821442640.00435632813854223
FOXA1#3169411.08141974938556.62943068949433e-050.00107394309257034
FOXA2#3170424.63046375266522.71504128667089e-069.45817868374318e-05
GABPB1#255347.067683836182170.0004006876864423170.00391024306525408
GATA1#2623413.56030814380042.95627390049268e-050.000615653618930319
GTF2F1#2962412.73966087675773.79492332235515e-050.000719829271455594
HEY1#2346244.040111043105710.00375304636917980.0186711956247687
HMGN3#932448.178547723350590.0002234570284440470.00248695956880519
IRF1#365947.63716375356390.0002938853996185490.00308194570245623
JUND#372746.994663941871030.000417684217818580.00392818748534486
MAFF#23764456.31535648994529.92458849374232e-085.83622802757857e-06
MAFK#7975427.10073313782991.85228494563408e-066.85995700131483e-05
MAX#414946.452555509007120.0005767613195645490.00486797926733489
MYC#460945.22228187160940.001344309395272740.00890174543069296
NFKB1#479045.488063424193840.001102199566301980.00769572272396124
NFYB#4801416.75979325353651.26678572070404e-050.000312106237047911
NR2C2#7182432.61461090524098.82887529809196e-073.82605355708476e-05
NRF1#4899412.21027944771094.49717228915276e-050.000796068096113263
PAX5#507946.669565531177830.0005052774169483260.00445096728649344
PBX3#5090421.91451268674414.33289161192893e-060.000136920685948032
POU2F2#545249.106124057742520.000145395665174930.00188867884019956
RAD21#5885410.35503389545638.6948481184721e-050.00130153539149363
REST#597849.650028716128020.0001152825614219170.00157632828388892
RXRA#6256420.07461713913336.1537798808435e-060.000182687497718992
SETDB1#9869440.32002617801053.77887289069054e-071.85461327928021e-05
SIN3A#2594245.408884726815140.001168172384885160.0079844735409045
SP1#666745.69838137814090.0009482606065333980.00686030683608628
SP2#6668426.15353049384462.13562021071447e-067.76338458708002e-05
SPI1#668848.204323508522730.000220661881527680.00249953429987737
SRF#6722413.79717826216782.75840773062708e-050.000586134984697785
TAF1#687243.343046285745290.008005664898701650.0323494403913759
TAF7#6879411.43306940492395.85061525419808e-050.00097251696089956
TBP#690843.706770687096390.005296377814784350.0245168160002776
TCF7L2#6934410.77017656313737.42969445082454e-050.00115847993244202
USF1#739146.361499277207960.0006105011399140830.00509347567914099
YY1#752844.911170749853860.00171871838055440.0107126539118358
ZEB1#6935312.66632401315790.000793336075912850.00613606061114287



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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