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Coexpression cluster:C593: Difference between revisions

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|tf_chipseq_enrich=BRCA1#672;5:6.72807688107459:0.000588957275188037:0.00493304265485311!CCNT2#905;7:2.95689406924923:0.0048359224775451:0.0226738005671081!CHD2#1106;7:4.8272106559212:0.000251184975593986:0.00270615923932951!CTCFL#140690;5:6.58215811965812:0.000651042219508022:0.00533246007083353!E2F1#1869;12:3.92591137190346:1.24796592318433e-06:5.02453018702575e-05!E2F6#1876;12:4.01372458535791:9.71551435172565e-07:4.12470976983689e-05!EGR1#1958;9:2.99290745688608:0.000798992306608397:0.00617112538898642!ELF1#1997;9:2.55485877528452:0.00264558951804961:0.0146145521884895!GABPB1#2553;7:3.29825245688501:0.00256014028915444:0.0141642470550935!GATA1#2623;5:4.52010271460015:0.00349167803009598:0.0177350141905065!GTF2F1#2962;5:4.24655362558588:0.00457735060258693:0.0216343358638537!HEY1#23462;10:2.69340736207047:0.000729505226786442:0.00581549472409352!IRF1#3659;6:3.05486550142556:0.00874677282747603:0.0332267925409657!NFKB1#4790;9:3.2928380545163:0.000380404893577693:0.00376614908335962!NRF1#4899;5:4.07009314923697:0.00549368798581636:0.0248745027118128!PAX5#5079;10:4.44637702078522:8.29479623652792e-06:0.000229240599139121!PBX3#5090;5:7.30483756224804:0.000403662994078613:0.00388339714798971!POLR2A#5430;14:2.0042896314542:0.000191108900166577:0.00230689117250314!POU2F2#5452;7:4.24952456027984:0.000554860687628875:0.00473595091167637!RFX5#5993;5:4.0159702757317:0.0058175499794261:0.0261504305027667!SIN3A#25942;9:3.24533083608908:0.000426242415214441:0.00398285153463192!TBP#6908;10:2.47118045806426:0.00151496764704519:0.0096671171314079!YY1#7528;10:3.2741138332359:0.000132683792813446:0.00174306448272245!ZEB1#6935;5:5.62947733918129:0.00132162503983572:0.00884519048608799
|tf_chipseq_enrich=BRCA1#672;5:6.72807688107459:0.000588957275188037:0.00493304265485311!CCNT2#905;7:2.95689406924923:0.0048359224775451:0.0226738005671081!CHD2#1106;7:4.8272106559212:0.000251184975593986:0.00270615923932951!CTCFL#140690;5:6.58215811965812:0.000651042219508022:0.00533246007083353!E2F1#1869;12:3.92591137190346:1.24796592318433e-06:5.02453018702575e-05!E2F6#1876;12:4.01372458535791:9.71551435172565e-07:4.12470976983689e-05!EGR1#1958;9:2.99290745688608:0.000798992306608397:0.00617112538898642!ELF1#1997;9:2.55485877528452:0.00264558951804961:0.0146145521884895!GABPB1#2553;7:3.29825245688501:0.00256014028915444:0.0141642470550935!GATA1#2623;5:4.52010271460015:0.00349167803009598:0.0177350141905065!GTF2F1#2962;5:4.24655362558588:0.00457735060258693:0.0216343358638537!HEY1#23462;10:2.69340736207047:0.000729505226786442:0.00581549472409352!IRF1#3659;6:3.05486550142556:0.00874677282747603:0.0332267925409657!NFKB1#4790;9:3.2928380545163:0.000380404893577693:0.00376614908335962!NRF1#4899;5:4.07009314923697:0.00549368798581636:0.0248745027118128!PAX5#5079;10:4.44637702078522:8.29479623652792e-06:0.000229240599139121!PBX3#5090;5:7.30483756224804:0.000403662994078613:0.00388339714798971!POLR2A#5430;14:2.0042896314542:0.000191108900166577:0.00230689117250314!POU2F2#5452;7:4.24952456027984:0.000554860687628875:0.00473595091167637!RFX5#5993;5:4.0159702757317:0.0058175499794261:0.0261504305027667!SIN3A#25942;9:3.24533083608908:0.000426242415214441:0.00398285153463192!TBP#6908;10:2.47118045806426:0.00151496764704519:0.0096671171314079!YY1#7528;10:3.2741138332359:0.000132683792813446:0.00174306448272245!ZEB1#6935;5:5.62947733918129:0.00132162503983572:0.00884519048608799
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|tfbs_overrepresentation_for_novel_motifs=0.172755,0.217977,1.54147,0.277483,0.138858,0.276158,0.338925,0.241,0.510737,2.55774,0.252096,0.3759,0.177832,0.329255,0.427489,0.153757,0.534852,0.104074,0.19463,0.351904,0.968262,0.379112,1.36406,0.135481,0.581509,1.80933,1.3983,0.739386,0.434999,0.310781,1.23363,0.568576,0.0851517,0.180835,3.12369,1.46657,0.740892,0.27709,0.100329,2.86113,0.370199,0.222502,0.246674,0.136946,1.03632,1.05727,0.901103,1.26597,0.223066,0.8571,0.407934,0.349819,0.698571,0.639823,0.784252,0.882989,0.143846,0.304469,0.310516,0.303639,0.606437,0.90555,0.512045,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,0.609701,0.0712089,1.83181,0.782342,0.388726,0.641622,0.139392,0.494371,0.556046,0.570606,0.0546605,0.50868,0.356776,0.0697103,0.733386,1.21291,0.34732,0.0308053,1.92947,1.32629,0.95934,0.70782,0.584068,0.0892066,0.139351,0.0967938,0.427968,0.623577,1.10949,0.0255063,0.33179,0.578851,0.618385,1.33072,1.18153,0.694065,1.30008,0.326366,0.581061,0.403142,0.175484,0.61581,1.51877,0.719501,2.10817,0.364707,2.98912,0.234099,0.476505,0.630394,0.77444,0.428661,0.273941,0.366411,1.02031,0.495057,0.887148,0.588683,0.815183,0.321662,0.708473,0.237246,0.828971,0.363559,0.971853,0.283882,0.230408,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,0.620293,0.469857,0.297516,0.454976,1.61933,0.627312,2.72322,0.633819,3.98085,0.708834,0.0630438,0.341434,1.09904,0.41656,0.406462,0.200711,3.04962,0.893382,0.691354,0.555323,0.536459,0.48429,0.356103,0.0806293,0.337803,0.371261
}}
}}

Revision as of 14:20, 26 November 2012


Full id: C593_Dendritic_CD8_Natural_CD4_CD19_Basophils_Peripheral



Phase1 CAGE Peaks


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




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><br>



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



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
BRCA1#67256.728076881074590.0005889572751880370.00493304265485311
CCNT2#90572.956894069249230.00483592247754510.0226738005671081
CHD2#110674.82721065592120.0002511849755939860.00270615923932951
CTCFL#14069056.582158119658120.0006510422195080220.00533246007083353
E2F1#1869123.925911371903461.24796592318433e-065.02453018702575e-05
E2F6#1876124.013724585357919.71551435172565e-074.12470976983689e-05
EGR1#195892.992907456886080.0007989923066083970.00617112538898642
ELF1#199792.554858775284520.002645589518049610.0146145521884895
GABPB1#255373.298252456885010.002560140289154440.0141642470550935
GATA1#262354.520102714600150.003491678030095980.0177350141905065
GTF2F1#296254.246553625585880.004577350602586930.0216343358638537
HEY1#23462102.693407362070470.0007295052267864420.00581549472409352
IRF1#365963.054865501425560.008746772827476030.0332267925409657
NFKB1#479093.29283805451630.0003804048935776930.00376614908335962
NRF1#489954.070093149236970.005493687985816360.0248745027118128
PAX5#5079104.446377020785228.29479623652792e-060.000229240599139121
PBX3#509057.304837562248040.0004036629940786130.00388339714798971
POLR2A#5430142.00428963145420.0001911089001665770.00230689117250314
POU2F2#545274.249524560279840.0005548606876288750.00473595091167637
RFX5#599354.01597027573170.00581754997942610.0261504305027667
SIN3A#2594293.245330836089080.0004262424152144410.00398285153463192
TBP#6908102.471180458064260.001514967647045190.0096671171314079
YY1#7528103.27411383323590.0001326837928134460.00174306448272245
ZEB1#693555.629477339181290.001321625039835720.00884519048608799



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.