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Coexpression cluster:C2430: Difference between revisions

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|tf_chipseq_enrich=BRCA1#672;3:15.1381729824178:0.000468218442143119:0.00430157159385866!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129044050347635!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160853700913828!ELK4#2005;3:12.176761243851:0.000891263257762061:0.00663785519342594!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390222130588858!GATA1#2623;3:10.1702311078503:0.00151515816849827:0.00966360940212465!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.0254729284457163!GTF2F1#2962;3:9.55474565756824:0.00182036231930478:0.0108986941220977!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.018596783686045!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307422849066122!IRF3#3661;2:23.4909761057448:0.00264110142537554:0.0145936189495157!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767775765390598!NR2C2#7182;3:24.4609581789307:0.000112590606343803:0.00155540348359001!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227592817704673!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00795998928068251!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.00601585526130973!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683898829402262!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328071757239433!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249439400853657!SRF#6722;3:10.3478836966259:0.00143989377840126:0.00923716623602269!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322073819859592!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244097084240882!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499319087413563!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106820536150155!ZBTB33#10009;2:15.8323625149906:0.00573424893032464:0.0258382614563023
|tf_chipseq_enrich=BRCA1#672;3:15.1381729824178:0.000468218442143119:0.00430157159385866!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129044050347635!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160853700913828!ELK4#2005;3:12.176761243851:0.000891263257762061:0.00663785519342594!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390222130588858!GATA1#2623;3:10.1702311078503:0.00151515816849827:0.00966360940212465!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.0254729284457163!GTF2F1#2962;3:9.55474565756824:0.00182036231930478:0.0108986941220977!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.018596783686045!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307422849066122!IRF3#3661;2:23.4909761057448:0.00264110142537554:0.0145936189495157!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767775765390598!NR2C2#7182;3:24.4609581789307:0.000112590606343803:0.00155540348359001!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227592817704673!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00795998928068251!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.00601585526130973!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00683898829402262!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328071757239433!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249439400853657!SRF#6722;3:10.3478836966259:0.00143989377840126:0.00923716623602269!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322073819859592!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244097084240882!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499319087413563!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106820536150155!ZBTB33#10009;2:15.8323625149906:0.00573424893032464:0.0258382614563023
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|tfbs_overrepresentation_for_novel_motifs=1.44014,1.03954,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,1.96835,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.28263,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,1.37313,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,0.359498
}}
}}

Revision as of 15:29, 26 November 2012


Full id: C2430_MCF7_CD14_CD19_Natural_Neutrophils_CD8_CD4



Phase1 CAGE Peaks

Hg19::chr17:65713775..65713818,-p@chr17:65713775..65713818
-
Hg19::chr1:145507436..145507501,-p1@ENST00000421764
Hg19::chr1:149899786..149899836,+p@chr1:149899786..149899836
+
Hg19::chr9:135905830..135905859,-p@chr9:135905830..135905859
-


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><br>


Cell Type
Ontology termp-valuen
leukocyte1.36e-44136
hematopoietic stem cell7.57e-39168
angioblastic mesenchymal cell7.57e-39168
hematopoietic cell7.97e-38177
hematopoietic lineage restricted progenitor cell5.76e-37120
hematopoietic oligopotent progenitor cell1.26e-35161
hematopoietic multipotent progenitor cell1.26e-35161
nongranular leukocyte4.96e-35115
classical monocyte9.34e-2342
CD14-positive, CD16-negative classical monocyte9.34e-2342
myeloid leukocyte8.75e-2172
nucleate cell4.45e-1955
defensive cell6.62e-1948
phagocyte6.62e-1948
lymphoid lineage restricted progenitor cell7.81e-1952
lymphocyte1.56e-1853
common lymphoid progenitor1.56e-1853
myeloid cell4.70e-17108
common myeloid progenitor4.70e-17108
myeloid lineage restricted progenitor cell4.84e-1766
granulocyte monocyte progenitor cell1.83e-1667
macrophage dendritic cell progenitor8.27e-1661
monopoietic cell4.24e-1559
monocyte4.24e-1559
monoblast4.24e-1559
promonocyte4.24e-1559
native cell3.06e-14722
mature alpha-beta T cell1.66e-1018
alpha-beta T cell1.66e-1018
immature T cell1.66e-1018
mature T cell1.66e-1018
immature alpha-beta T cell1.66e-1018
T cell9.44e-1025
pro-T cell9.44e-1025
lymphocyte of B lineage1.54e-0824
pro-B cell1.54e-0824
B cell5.34e-0814
CD8-positive, alpha-beta T cell1.46e-0711
stuff accumulating cell1.49e-0787
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.00e-1998
blood island1.00e-1998
hemolymphoid system1.04e-18108
bone marrow2.18e-1476
immune system7.08e-1493
bone element1.91e-1382
skeletal element6.23e-1290
skeletal system5.39e-09100
lateral plate mesoderm9.51e-08203


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
BRCA1#672315.13817298241780.0004682184421431190.00430157159385866
CHD2#1106410.34402283411698.73193255208051e-050.00129044050347635
ELF1#199744.258097958807540.003041525565781240.0160853700913828
ELK4#2005312.1767612438510.0008912632577620610.00663785519342594
GABPB1#255347.067683836182170.0004006876864423170.00390222130588858
GATA1#2623310.17023110785030.001515158168498270.00966360940212465
GTF2B#2959215.97191496716210.005636585723537220.0254729284457163
GTF2F1#296239.554745657568240.001820362319304780.0108986941220977
HEY1#2346244.040111043105710.00375304636917980.018596783686045
IRF1#365947.63716375356390.0002938853996185490.00307422849066122
IRF3#3661223.49097610574480.002641101425375540.0145936189495157
NFKB1#479045.488063424193840.001102199566301980.00767775765390598
NR2C2#7182324.46095817893070.0001125906063438030.00155540348359001
POU2F2#545236.829593043306890.004860473775203740.0227592817704673
SIN3A#2594245.408884726815140.001168172384885160.00795998928068251
SIX5#147912312.81503651659420.0007664471136930380.00601585526130973
SP1#666745.69838137814090.0009482606065333980.00683898829402262
SP2#6668213.07676524692230.008330036536614940.0328071757239433
SPI1#668848.204323508522730.000220661881527680.00249439400853657
SRF#6722310.34788369662590.001439893778401260.00923716623602269
TAF1#687243.343046285745290.008005664898701650.0322073819859592
TBP#690843.706770687096390.005296377814784350.0244097084240882
TRIM28#10155313.94289378394690.0005972858184258420.00499319087413563
YY1#752844.911170749853860.00171871838055440.0106820536150155
ZBTB33#10009215.83236251499060.005734248930324640.0258382614563023



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.