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{{Coexpression_clusters
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|full_id=C2889_B_papillotubular_clear_small_Prostate_splenic_Intestinal
|id=C2889
}}

Latest revision as of 12:15, 17 September 2013


Full id: C2889_B_papillotubular_clear_small_Prostate_splenic_Intestinal



Phase1 CAGE Peaks

Hg19::chr7:20256965..20257034,-p1@MACC1
Hg19::chr7:20257037..20257051,-p2@MACC1
Hg19::chr7:20257073..20257093,-p3@MACC1
Hg19::chr7:20257095..20257125,-p4@MACC1


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>disease_data<br>

Cell Type
Ontology termp-valuen
endo-epithelial cell1.09e-1342
lymphocyte of B lineage8.28e-1124
pro-B cell8.28e-1124
epithelial cell of alimentary canal1.42e-0820
endodermal cell1.59e-0758
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.38e-12160
endoderm9.38e-12160
presumptive endoderm9.38e-12160
digestive system2.88e-10145
digestive tract2.88e-10145
primitive gut2.88e-10145
subdivision of digestive tract4.19e-09118
orifice1.59e-0736
respiratory system2.58e-0774
gastrointestinal system5.26e-0725
endo-epithelium8.33e-0782
Disease
Ontology termp-valuen
squamous cell carcinoma6.33e-0914
carcinoma7.79e-09106
adenocarcinoma1.48e-0725


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
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
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
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
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.12.85665
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.12.23207
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
MA0125.12.94475
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
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.21.37305
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.11.84959
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
MA0163.10.0725493
MA0164.12.08227
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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-060.000127574775403834
BCLAF1#9774421.65264761012184.54636978835329e-060.000141906250545675
CTCF#1066445.360256373075030.001211145381643620.00819878224743831
CTCFL#140690419.74647435897446.5732084880439e-060.000193543648515031
EBF1#187948.9064668465690.00015887907472010.00200062354529691
ELF1#199744.258097958807540.003041525565781240.0161262000489708
EP300#203346.77394172622320.0004748459821442640.00435365108674961
ESR1#2099430.76860329615451.11467714392546e-064.61784078676838e-05
ETS1#211349.728760922202340.0001115955317418140.00154821011418481
GATA3#2625320.42738726790450.0001924415576258320.00232109987722419
HEY1#2346244.040111043105710.00375304636917980.0186614173372105
IRF4#3662421.91451268674414.33289161192893e-060.000136755172879494
JUND#372735.245997956403270.01043432751748420.0387205348066562
MAX#414946.452555509007120.0005767613195645490.00486561998820694
MYC#460945.22228187160940.001344309395272740.00889948839584745
NFKB1#479045.488063424193840.001102199566301980.00769366531914265
PAX5#507946.669565531177830.0005052774169483260.00444946611708821
POU2F2#545249.106124057742520.000145395665174930.00188797437215025
SIX5#147912417.0867153554591.17257016123224e-050.000297743873252938
SP1#666745.69838137814090.0009482606065333980.00685745668783697
SPI1#668848.204323508522730.000220661881527680.00249899221913569
TAF1#687243.343046285745290.008005664898701650.0323331774761399
TBP#690843.706770687096390.005296377814784350.0245026977895133
TCF12#6938410.63446490218647.8163066689251e-050.00120295793132312
WRNIP1#568974109.8199643493766.85077246696163e-095.3634769541005e-07
YY1#752844.911170749853860.00171871838055440.0107094582033722
ZEB1#6935416.88843201754391.22862303393937e-050.000305296600146548
ZNF143#7702413.50087655222793.00867915035614e-050.000621978309152899



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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