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Coexpression cluster:C3176: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3176_oral_cervical_Esophageal_Hep2_iPS_giant_choriocarcinoma
|full_id=C3176_oral_cervical_Esophageal_Hep2_iPS_giant_choriocarcinoma
|id=C3176
|id=C3176

Revision as of 16:03, 12 September 2012


Full id: C3176_oral_cervical_Esophageal_Hep2_iPS_giant_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr11:62623512..62623526,+p9@SLC3A2
Hg19::chr11:62623544..62623614,+p3@SLC3A2
Hg19::chr11:62623621..62623640,+p5@SLC3A2


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
epithelial cell4.83e-47254
embryonic cell4.98e-14248
endodermal cell4.92e-1259
endo-epithelial cell2.18e-1143
squamous epithelial cell7.22e-1062
animal cell2.69e-09679
eukaryotic cell2.69e-09679
epithelial cell of lung8.99e-0819
respiratory epithelial cell4.05e-0713
Disease
Ontology termp-valuen
cancer2.18e-44235
disease of cellular proliferation1.40e-42239
cell type cancer1.60e-32143
carcinoma1.45e-31106
organ system cancer6.02e-17137
hematologic cancer3.61e-0851
immune system cancer3.61e-0851
disease of anatomical entity2.70e-0739


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)

{{{tfbs_overrepresentation_jaspar}}}



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
BCL3#602334.54710280373832.42397750207122e-050.000526315564113963
BCLAF1#9774321.65264761012189.8473954032885e-050.00138848674027818
CCNT2#90536.336201576962630.003930750035764890.0189233706548008
CEBPB#105137.971147625824820.001974187055288560.0114967169547943
CTCFL#140690319.74647435897440.0001298372005551160.00171212972080503
E2F1#186934.907389214879320.008460985347239390.0323778707562778
E2F4#1874312.66806031528440.0004917987006298980.00435685507634965
E2F6#187635.017155731697390.00791769806886330.032058481376057
EBF1#187938.9064668465690.00141523283560980.0091254863319289
EGR1#195834.988179094810140.008056488137383440.0319200138308114
ELF1#199734.258097958807540.01295179875054610.0460233714303114
EP300#203336.77394172622320.003216880500103790.0166932218299881
ESR1#2099330.76860329615453.43136389821584e-050.000674004540465984
ETS1#211339.728760922202340.001085840092584840.00760131734227949
FOSL2#2355316.93020060456170.0002060162053171620.00242380606816707
FOXA1#3169311.08141974938550.000734755275698670.00579629173190523
GABPB1#255337.067683836182170.002832212825417420.0153658948194166
GATA1#2623313.56030814380040.0004009615963782630.00386917011587817
GTF2B#2959331.94382993432423.06634405746243e-050.000625969325678888
GTF2F1#2962312.73966087675770.0004835525047438590.00432785500410866
HDAC2#3066313.41562023662630.0004140761399857210.00389952191018654
HDAC8#558693776.5840336134452.10837623426304e-091.80785472520688e-07
HMGN3#932438.178547723350590.001827766942164210.0108355651741323
HNF4G#3174328.75342252644684.20470658818262e-050.00075504702779093
IRF1#365937.63716375356390.002244692747297240.012765926041983
JUN#3725312.51282919233630.0005103313992726250.00443120227873576
JUND#372736.994663941871030.002921845042734990.015620115398147
MAX#414936.452555509007120.003721913834265510.0185844788170231
MEF2A#4205318.74323090964410.0001518243905622470.00194843788718733
MXI1#460139.96157162875930.001011470541259020.00718374511108813
MYC#460935.22228187160940.007020843755740150.0293288228873143
NANOG#79923329.24477848101273.99627955670032e-050.000734155568376825
NFKB1#479035.488063424193840.006049381815655430.0268664478416924
NRF1#4899312.21027944771090.0005492172401020010.00469661011536992
PAX5#507936.669565531177830.003370290999677260.0172375035120124
POU2F2#545239.106124057742520.001324165192682130.00879791898711934
REST#597839.650028716128020.001112636247114590.00765498135786566
RFX5#5993312.04791082719510.0005717246050312580.0048317159754701
SIN3A#2594235.408884726815140.006318961977991520.0275540090192249
SIX5#147912317.0867153554590.0002004060546325010.00239065767444475
SP1#666735.69838137814090.005403962701712170.024553400356918
SRF#6722313.79717826216780.0003806615025800190.00373997240526384
TAF7#6879311.43306940492390.0006690181981945830.00540759938094916
TCF12#6938310.63446490218640.0008313523990202070.00627851711629701
TCF7L2#6934310.77017656313730.0008003181298398380.00611936636374133
TFAP2C#7022310.80922860986020.0007916746575753130.00613092907923092
THAP1#55145331.36914460285133.23800758564397e-050.000645247613503283
TRIM28#10155318.59052504526250.0001555969297255280.00196569344908726
USF1#739136.361499277207960.00388404057290560.0189589322019858
USF2#7392312.99219738506960.0004558979393427810.00420539877115534
YY1#752834.911170749853860.008441455341808260.0328080215258676
ZBTB7A#5134137.35190930787590.002516255860282270.0139658418340872
ZEB1#6935316.88843201754390.0002075486917327580.00242029676372013
ZNF143#7702313.50087655222790.0004062804962997170.003878213029252



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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