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Coexpression cluster:C875: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;3:11.5157009345794:0.00178591501782776:0.0109549617377489!BRCA1#672;4:8.97076917476612:0.000620269035673191:0.00514006806448245!CHD2#1106;6:6.89601522274457:5.28898897155739e-05:0.00089758972895756!CTCF#10664;6:3.57350424871668:0.00210388362937215:0.0121645076879809!E2F4#1874;4:5.63024902901531:0.00353657181596461:0.017945584680183!E2F6#1876;6:3.34477048779826:0.00300955536409489:0.0159842835979814!EBF1#1879;6:5.93764456437934:0.000124243650792417:0.00165593193531256!EGR1#1958;6:3.32545272987342:0.00310493641438398:0.016325653435123!ELF1#1997;9:4.25809795880754:2.17161853202127e-06:7.82074716778515e-05!FOS#2353;5:4.99886406049689:0.00145028992150504:0.00929757713535482!FOSL2#2355;3:5.64340020152056:0.0132155804190592:0.0467570718312314!FOXA1#3169;4:4.92507544417131:0.00575815054200309:0.0259280626220687!FOXA2#3170;3:8.21015458422175:0.0046728123675689:0.0220515950863734!GABPB1#2553;5:3.92649102010121:0.00433797609228731:0.0205830668803051!GATA1#2623;4:6.02680361946686:0.00275314489424295:0.0151000787527486!GTF2F1#2962;4:5.66207150078118:0.0034642002070655:0.0176022966539707!HEY1#23462;7:3.14230858908222:0.00125876346284377:0.0084564516464647!IRF3#3661;3:15.6606507371632:0.000735147872062502:0.00579282545724579!IRF4#3662;5:12.1747292704134:2.1331797509613e-05:0.000470015105507695!MAFF#23764;2:12.5145236644323:0.0104448206301486:0.0386975991270384!MAX#4149;7:5.01865428478332:5.77474544696214e-05:0.000962202679858454!MXI1#4601;5:5.53420646042183:0.00090661270204698:0.00660152854975141!MYC#4609;6:3.4815212477396:0.00242366981145926:0.0136544207271007!NFKB1#4790;6:3.65870894946256:0.00185064964860272:0.0109333634263163!NFYA#4800;3:6.14186023327684:0.0104816316305809:0.0388147050266368!NFYB#4801;3:5.58659775117882:0.0135850027711194:0.047947149620254!NRF1#4899;5:6.78348858206162:0.000350041984902588:0.00352400567391955!PAX5#5079;8:5.92850269438029:1.99061202941177e-06:7.30233683666089e-05!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728393313625267!POU2F2#5452;7:7.08254093379974:5.66141070992737e-06:0.000170444529586078!REST#5978;5:5.36112706451557:0.00105037221365292:0.00742368705567415!RFX5#5993;4:5.35462703430893:0.00424944502767474:0.0202199548610562!RXRA#6256;3:6.69153904637776:0.00827324662294775:0.0325958051929244!SIN3A#25942;6:3.60592315121009:0.00200305799133432:0.0116453670428059!SP1#6667;6:3.7989209187606:0.00150699787113838:0.00962390550714326!SP2#6668;3:8.7178434979482:0.00394553175057863:0.0189430143198033!SPI1#6688;8:7.29273200757576:3.90517100687164e-07:1.89786949644796e-05!SRF#6722;4:6.13207922763014:0.00258257360325073:0.0142860913426856!STAT1#6772;3:6.90219583239973:0.00759156108216665:0.0312862066080184!TAF1#6872;9:3.34304628574529:1.91655056102793e-05:0.000433440069387606!TBP#6908;8:3.29490727741901:0.000191885322027247:0.00231492562633749!TCF12#6938;6:7.08964326812428:4.5123563262149e-05:0.000793777972635268!TCF7L2#6934;5:5.98343142396519:0.000630515439732144:0.00518384649375623!TFAP2A#7020;3:5.50621145768165:0.0141316266277055:0.0495848464092368!TFAP2C#7022;4:4.80410160438232:0.00629930343474712:0.0277849882347138!TRIM28#10155;4:8.26245557567223:0.000846928597179193:0.00638368762707836!USF2#7392;4:5.77430994891982:0.00322324100537492:0.0166996759281849!YY1#7528;7:3.81979947210855:0.000352967281214194:0.00353573277217813!ZBTB33#10009;3:10.5549083433271:0.00229172162882116:0.0130036463757716
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|tfbs_overrepresentation_for_novel_motifs=0.312007,0.479568,0.823567,1.12193,0.267236,0.439064,0.511871,0.164003,0.161941,1.65033,0.410439,0.553754,0.799936,0.500805,0.734361,0.287179,0.728104,0.218596,0.137566,0.473089,0.305279,0.33045,1.9325,0.262652,0.347482,0.575764,0.36063,0.429643,0.270022,0.329945,0.389837,0.764231,0.190489,0.807612,0.23642,0.452714,0.233607,1.9611,0.611187,0.884996,0.235191,0.97787,0.366128,0.731232,0.513344,0.333541,0.51292,1.0341,0.615516,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,1.28186,0.162346,0.700946,3.33727,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.253077,0.988898,0.784625,0.741954,0.105027,0.684401,0.750836,0.341765,0.436045,0.699894,0.532172,0.166331,0.937974,0.89521,0.468577,0.320664,0.614883,1.54397,1.17124,0.911274,0.78075,0.571859,0.267904,0.598862,0.136404,0.82268,0.619373,0.290348,0.613956,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,1.64174,0.252953,0.846745,3.1686,0.300169,1.89062,1.12352,0.232218,0.0867932,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,2.6976,1.03718,0.539846,1.18405,0.307751,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.193834,0.50389,0.347165,0.912334,0.155464,0.514733,1.31376,0.599133,0.254737,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,0.333592
}}
}}

Revision as of 14:32, 26 November 2012


Full id: C875_Eosinophils_Neutrophils_Mast_CD19_CD14_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:70660801..70660814,-p@chr10:70660801..70660814
-
Hg19::chr11:102187888..102187900,-p@chr11:102187888..102187900
-
Hg19::chr19:2270812..2270826,-p@chr19:2270812..2270826
-
Hg19::chr1:225655463..225655481,-p@chr1:225655463..225655481
-
Hg19::chr1:66801524..66801541,-p@chr1:66801524..66801541
-
Hg19::chr20:34330506..34330528,+p@chr20:34330506..34330528
+
Hg19::chr20:34330534..34330580,+p@chr20:34330534..34330580
+
Hg19::chr2:208031542..208031595,-p2@KLF7
Hg19::chr5:130971280..130971333,+p@chr5:130971280..130971333
+


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
leukocyte9.62e-59136
hematopoietic cell4.39e-50177
hematopoietic stem cell6.33e-50168
angioblastic mesenchymal cell6.33e-50168
hematopoietic lineage restricted progenitor cell1.44e-46120
hematopoietic oligopotent progenitor cell4.34e-46161
hematopoietic multipotent progenitor cell4.34e-46161
nongranular leukocyte7.03e-45115
classical monocyte7.63e-3142
CD14-positive, CD16-negative classical monocyte7.63e-3142
myeloid leukocyte2.30e-3072
defensive cell3.77e-2548
phagocyte3.77e-2548
granulocyte monocyte progenitor cell1.02e-2467
myeloid cell4.57e-24108
common myeloid progenitor4.57e-24108
myeloid lineage restricted progenitor cell3.45e-2366
macrophage dendritic cell progenitor2.06e-2261
monopoietic cell2.31e-2159
monocyte2.31e-2159
monoblast2.31e-2159
promonocyte2.31e-2159
lymphoid lineage restricted progenitor cell3.94e-2152
lymphocyte1.30e-2053
common lymphoid progenitor1.30e-2053
nucleate cell1.23e-1955
mesenchymal cell1.95e-19354
connective tissue cell3.01e-19361
motile cell9.32e-17386
stem cell4.01e-16441
multi fate stem cell4.28e-16427
somatic stem cell2.62e-15433
stuff accumulating cell1.43e-1287
mature alpha-beta T cell9.24e-1118
alpha-beta T cell9.24e-1118
immature T cell9.24e-1118
mature T cell9.24e-1118
immature alpha-beta T cell9.24e-1118
lymphocyte of B lineage1.32e-1024
pro-B cell1.32e-1024
T cell1.03e-0925
pro-T cell1.03e-0925
B cell3.39e-0914
native cell8.40e-09722
CD8-positive, alpha-beta T cell2.02e-0811
granulocyte4.01e-088
intermediate monocyte9.59e-089
CD14-positive, CD16-positive monocyte9.59e-089
blood cell6.63e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.33e-3198
blood island1.33e-3198
hemolymphoid system6.72e-30108
bone marrow1.09e-2276
immune system4.88e-2293
bone element8.82e-2282
skeletal element2.97e-1990
connective tissue7.06e-18371
skeletal system5.46e-16100
lateral plate mesoderm3.23e-14203
blood1.82e-0915
haemolymphatic fluid1.82e-0915
organism substance1.82e-0915
musculoskeletal system8.14e-08167


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#602311.51570093457940.001785915017827760.0109549617377489
BRCA1#67248.970769174766120.0006202690356731910.00514006806448245
CHD2#110666.896015222744575.28898897155739e-050.00089758972895756
CTCF#1066463.573504248716680.002103883629372150.0121645076879809
E2F4#187445.630249029015310.003536571815964610.017945584680183
E2F6#187663.344770487798260.003009555364094890.0159842835979814
EBF1#187965.937644564379340.0001242436507924170.00165593193531256
EGR1#195863.325452729873420.003104936414383980.016325653435123
ELF1#199794.258097958807542.17161853202127e-067.82074716778515e-05
FOS#235354.998864060496890.001450289921505040.00929757713535482
FOSL2#235535.643400201520560.01321558041905920.0467570718312314
FOXA1#316944.925075444171310.005758150542003090.0259280626220687
FOXA2#317038.210154584221750.00467281236756890.0220515950863734
GABPB1#255353.926491020101210.004337976092287310.0205830668803051
GATA1#262346.026803619466860.002753144894242950.0151000787527486
GTF2F1#296245.662071500781180.00346420020706550.0176022966539707
HEY1#2346273.142308589082220.001258763462843770.0084564516464647
IRF3#3661315.66065073716320.0007351478720625020.00579282545724579
IRF4#3662512.17472927041342.1331797509613e-050.000470015105507695
MAFF#23764212.51452366443230.01044482063014860.0386975991270384
MAX#414975.018654284783325.77474544696214e-050.000962202679858454
MXI1#460155.534206460421830.000906612702046980.00660152854975141
MYC#460963.48152124773960.002423669811459260.0136544207271007
NFKB1#479063.658708949462560.001850649648602720.0109333634263163
NFYA#480036.141860233276840.01048163163058090.0388147050266368
NFYB#480135.586597751178820.01358500277111940.047947149620254
NRF1#489956.783488582061620.0003500419849025880.00352400567391955
PAX5#507985.928502694380291.99061202941177e-067.30233683666089e-05
POLR2A#543092.147453176558070.001029412892608020.00728393313625267
POU2F2#545277.082540933799745.66141070992737e-060.000170444529586078
REST#597855.361127064515570.001050372213652920.00742368705567415
RFX5#599345.354627034308930.004249445027674740.0202199548610562
RXRA#625636.691539046377760.008273246622947750.0325958051929244
SIN3A#2594263.605923151210090.002003057991334320.0116453670428059
SP1#666763.79892091876060.001506997871138380.00962390550714326
SP2#666838.71784349794820.003945531750578630.0189430143198033
SPI1#668887.292732007575763.90517100687164e-071.89786949644796e-05
SRF#672246.132079227630140.002582573603250730.0142860913426856
STAT1#677236.902195832399730.007591561082166650.0312862066080184
TAF1#687293.343046285745291.91655056102793e-050.000433440069387606
TBP#690883.294907277419010.0001918853220272470.00231492562633749
TCF12#693867.089643268124284.5123563262149e-050.000793777972635268
TCF7L2#693455.983431423965190.0006305154397321440.00518384649375623
TFAP2A#702035.506211457681650.01413162662770550.0495848464092368
TFAP2C#702244.804101604382320.006299303434747120.0277849882347138
TRIM28#1015548.262455575672230.0008469285971791930.00638368762707836
USF2#739245.774309948919820.003223241005374920.0166996759281849
YY1#752873.819799472108550.0003529672812141940.00353573277217813
ZBTB33#10009310.55490834332710.002291721628821160.0130036463757716



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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