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Coexpression cluster:C2929: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000142033596866835!BHLHE40#8553;4:44.8718135469774:2.46312701995675e-07:1.28881023465563e-05!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513836946564256!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268847458755112!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129410288606036!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820409991655716!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000728437895439285!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999678714311106!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161319327898343!ELK4#2005;4:16.235681658468:1.43847748454449e-05:0.000343782951964169!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000304540721913269!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390987772440896!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000615408191934532!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.00071969855976657!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186694169921776!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248642963921456!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00308132689998611!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136879270132561!JUNB#3726;4:30.6106326598211:1.13787152942193e-06:4.66397820491748e-05!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00392783378576937!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486758589527288!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142819313284307!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00890118106466046!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000795933192182385!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00445021657519533!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188844395911012!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00130116240528028!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00798395103102027!SIRT6#51548;4:153.638403990025:1.78585744852249e-09:1.55557269446405e-07!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297961204547283!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685983164686164!SRF#6722;4:13.7971782621678:2.75840773062708e-05:0.000586015754635804!STAT1#6772;4:20.7065874971992:5.43610708103893e-06:0.000165667227148125!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00123585559852277!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323469373396588!TAF7#6879;4:11.4330694049239:5.85061525419808e-05:0.000972207488517412!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245146429089817!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120313522799686!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115830699917848!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00509306881951329!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000683466719019033!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107113753996134!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.00062234787439898!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00250135827332355
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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.54039,0.581696,0.741427,1.32255,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,2.06579,0.316693,1.72987,1.33003,0.806311,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,2.13139,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.314427,2.53981,0.822818,0.694903,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,1.90242,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,4.57517,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,2.84439,0.109222,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,1.88833,0.632569,1.28386,0.594299,1.14697,0.575476,1.70537,1.46636,0.489254,1.27972,2.74919,0.988625,0.444962,1.31973,2.14757,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,1.00204,1.24902,0.383416,0.824835,1.65997,0.917558,1.28873,3.77839,0.600782,1.44595,4.4486,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.4289
}}
}}

Revision as of 15:48, 26 November 2012


Full id: C2929_CD14_Eosinophils_Wilms_cord_Mast_anaplastic_Neural



Phase1 CAGE Peaks

Hg19::chr8:8860373..8860388,+p2@ERI1
Hg19::chr8:8860460..8860479,+p3@ERI1
Hg19::chr8:8860484..8860495,+p4@ERI1
Hg19::chr8:8860501..8860512,+p5@ERI1


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><br>disease_data<br>

Cell Type
Ontology termp-valuen
myeloid cell2.72e-10108
common myeloid progenitor2.72e-10108
native cell3.88e-09722
animal cell1.45e-08679
eukaryotic cell1.45e-08679
myeloid leukocyte3.06e-0772
neural cell4.71e-0725
hematopoietic oligopotent progenitor cell8.70e-07161
hematopoietic multipotent progenitor cell8.70e-07161
Disease
Ontology termp-valuen
disease of cellular proliferation1.59e-07239
cancer5.25e-07235


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
BCLAF1#9774421.65264761012184.54636978835329e-060.000142033596866835
BHLHE40#8553444.87181354697742.46312701995675e-071.28881023465563e-05
CCNT2#90546.336201576962630.0006203100587215640.00513836946564256
CEBPB#105147.971147625824820.0002476385788090830.00268847458755112
CHD2#1106410.34402283411698.73193255208051e-050.00129410288606036
CTCF#1066445.360256373075030.001211145381643620.00820409991655716
E2F4#1874412.66806031528443.88145892637771e-050.000728437895439285
E2F6#187645.017155731697390.00157802193473060.00999678714311106
ELF1#199744.258097958807540.003041525565781240.0161319327898343
ELK4#2005416.2356816584681.43847748454449e-050.000343782951964169
FOSL2#2355416.93020060456171.2165416097647e-050.000304540721913269
GABPB1#255347.067683836182170.0004006876864423170.00390987772440896
GATA1#2623413.56030814380042.95627390049268e-050.000615408191934532
GTF2F1#2962412.73966087675773.79492332235515e-050.00071969855976657
HEY1#2346244.040111043105710.00375304636917980.0186694169921776
HMGN3#932448.178547723350590.0002234570284440470.00248642963921456
IRF1#365947.63716375356390.0002938853996185490.00308132689998611
IRF4#3662421.91451268674414.33289161192893e-060.000136879270132561
JUNB#3726430.61063265982111.13787152942193e-064.66397820491748e-05
JUND#372746.994663941871030.000417684217818580.00392783378576937
MAX#414946.452555509007120.0005767613195645490.00486758589527288
MXI1#460149.96157162875930.0001015224754950450.00142819313284307
MYC#460945.22228187160940.001344309395272740.00890118106466046
NRF1#4899412.21027944771094.49717228915276e-050.000795933192182385
PAX5#507946.669565531177830.0005052774169483260.00445021657519533
POU2F2#545249.106124057742520.000145395665174930.00188844395911012
RAD21#5885410.35503389545638.6948481184721e-050.00130116240528028
SIN3A#2594245.408884726815140.001168172384885160.00798395103102027
SIRT6#515484153.6384039900251.78585744852249e-091.55557269446405e-07
SIX5#147912417.0867153554591.17257016123224e-050.000297961204547283
SP1#666745.69838137814090.0009482606065333980.00685983164686164
SRF#6722413.79717826216782.75840773062708e-050.000586015754635804
STAT1#6772420.70658749719925.43610708103893e-060.000165667227148125
STAT3#6774410.51946499715428.16377768286615e-050.00123585559852277
TAF1#687243.343046285745290.008005664898701650.0323469373396588
TAF7#6879411.43306940492395.85061525419808e-050.000972207488517412
TBP#690843.706770687096390.005296377814784350.0245146429089817
TCF12#6938410.63446490218647.8163066689251e-050.00120313522799686
TCF7L2#6934410.77017656313737.42969445082454e-050.00115830699917848
USF1#739146.361499277207960.0006105011399140830.00509306881951329
USF2#7392412.99219738506963.50833029870167e-050.000683466719019033
YY1#752844.911170749853860.00171871838055440.0107113753996134
ZNF143#7702413.50087655222793.00867915035614e-050.00062234787439898
ZNF263#1012748.221841637010680.0002187871180958320.00250135827332355



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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