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Coexpression cluster:C2680: Difference between revisions

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|full_id=C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature
|full_id=C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature
|id=C2680
|id=C2680
|ontology_enrichment_celltype=CL:0000037!7.67e-47!172;CL:0000566!7.67e-47!172;CL:0002032!8.36e-46!165;CL:0000837!8.36e-46!165;CL:0000988!1.25e-45!182;CL:0000738!6.34e-43!140;CL:0002031!4.33e-35!124;CL:0002087!1.29e-33!119;CL:0000763!2.16e-29!112;CL:0000049!2.16e-29!112;CL:0000766!1.16e-23!76;CL:0002057!2.01e-21!42;CL:0000557!1.40e-20!71;CL:0000839!3.45e-19!70;CL:0002009!9.88e-19!65;CL:0000860!3.18e-18!45;CL:0002194!1.30e-17!63;CL:0000576!1.30e-17!63;CL:0000040!1.30e-17!63;CL:0000559!1.30e-17!63;CL:0000542!2.14e-14!53;CL:0000051!2.14e-14!53;CL:0000838!3.00e-14!52;CL:0000791!1.61e-10!18;CL:0000789!1.61e-10!18;CL:0002420!1.61e-10!18;CL:0002419!1.61e-10!18;CL:0000790!1.61e-10!18;CL:0000134!3.30e-10!358;CL:0000084!3.48e-09!25;CL:0000827!3.48e-09!25;CL:0002320!8.02e-09!365;CL:0000625!1.46e-07!11;CL:0000048!3.86e-07!430
|ontology_enrichment_celltype=CL:0000037!4.94e-48!168;CL:0000566!4.94e-48!168;CL:0002032!3.32e-47!161;CL:0000837!3.32e-47!161;CL:0000988!2.09e-46!177;CL:0000738!9.30e-45!136;CL:0002031!7.70e-37!120;CL:0002087!1.98e-35!115;CL:0000763!7.12e-31!108;CL:0000049!7.12e-31!108;CL:0000766!6.91e-26!72;CL:0000557!1.36e-22!67;CL:0000473!1.31e-21!48;CL:0000234!1.31e-21!48;CL:0000860!3.56e-21!42;CL:0002057!3.56e-21!42;CL:0000839!4.64e-21!66;CL:0002009!1.09e-20!61;CL:0002194!1.52e-19!59;CL:0000576!1.52e-19!59;CL:0000040!1.52e-19!59;CL:0000559!1.52e-19!59;CL:0000542!2.57e-14!53;CL:0000051!2.57e-14!53;CL:0000838!3.74e-14!52;CL:0002242!4.23e-14!55;CL:0000134!5.35e-11!354;CL:0000791!1.30e-10!18;CL:0000789!1.30e-10!18;CL:0002420!1.30e-10!18;CL:0002419!1.30e-10!18;CL:0000790!1.30e-10!18;CL:0002320!1.71e-09!361;CL:0000084!4.07e-09!25;CL:0000827!4.07e-09!25;CL:0000625!1.18e-07!11;CL:0000048!1.26e-07!427
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.34e-28!112;UBERON:0002390!3.88e-26!102;UBERON:0003061!3.88e-26!102;UBERON:0003081!1.09e-24!216;UBERON:0002405!3.69e-16!115;UBERON:0002371!3.81e-16!80;UBERON:0001474!1.30e-12!86;UBERON:0000178!6.24e-10!15;UBERON:0000179!6.24e-10!15;UBERON:0000463!6.24e-10!15;UBERON:0001009!4.70e-09!113;UBERON:0004535!1.76e-08!110;UBERON:0004765!2.96e-08!101;UBERON:0001434!2.96e-08!101;UBERON:0002384!3.69e-08!375
|ontology_enrichment_uberon=UBERON:0002193!6.01e-30!108;UBERON:0002390!1.20e-27!98;UBERON:0003061!1.20e-27!98;UBERON:0003081!5.51e-25!203;UBERON:0002405!1.01e-21!93;UBERON:0002371!2.14e-17!76;UBERON:0001474!1.61e-13!82;UBERON:0000926!4.05e-10!315;UBERON:0004120!4.05e-10!315;UBERON:0006603!4.05e-10!315;UBERON:0004765!5.11e-10!90;UBERON:0000178!5.17e-10!15;UBERON:0000179!5.17e-10!15;UBERON:0000463!5.17e-10!15;UBERON:0002384!1.02e-08!371;UBERON:0001009!1.31e-08!112;UBERON:0004535!4.66e-08!109;UBERON:0001434!8.38e-08!100
|tf_chipseq_enrich=BCL11A#53335;3:21.2770913277053:0.000170483911460614:0.00208198891826883!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512860688907706!CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00268317517711814!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129171997706337!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818498851517266!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.010662353939747!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998044164242288!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199797371278658!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101547372701049!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161114774074167!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434563963627452!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390586347623195!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000627386340276494!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186365733050005!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.67282608436001e-05!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136590059480304!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485855585207307!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224452168655542!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768493360738449!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443604836947485!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444459430208592!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188492774021903!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129651805060695!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00797247309057184!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241870675700569!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438744260547943!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00684939411340629!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032274516959604!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244615222481874!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120171831620178!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000326958440910335!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114696456459312!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230512387570661!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347004701900291!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249371470335159
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}}
}}

Revision as of 14:18, 19 October 2012


Full id: C2680_Neutrophils_Eosinophils_CD14_Whole_migratory_CD8_immature



Phase1 CAGE Peaks

Hg19::chr2:201983381..201983425,+p2@CFLAR
Hg19::chr2:201983432..201983453,+p5@CFLAR
Hg19::chr2:201983467..201983478,+p19@CFLAR
Hg19::chr2:201983487..201983498,+p23@CFLAR


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
hematopoietic stem cell4.94e-48168
angioblastic mesenchymal cell4.94e-48168
hematopoietic oligopotent progenitor cell3.32e-47161
hematopoietic multipotent progenitor cell3.32e-47161
hematopoietic cell2.09e-46177
leukocyte9.30e-45136
hematopoietic lineage restricted progenitor cell7.70e-37120
nongranular leukocyte1.98e-35115
myeloid cell7.12e-31108
common myeloid progenitor7.12e-31108
myeloid leukocyte6.91e-2672
granulocyte monocyte progenitor cell1.36e-2267
defensive cell1.31e-2148
phagocyte1.31e-2148
classical monocyte3.56e-2142
CD14-positive, CD16-negative classical monocyte3.56e-2142
myeloid lineage restricted progenitor cell4.64e-2166
macrophage dendritic cell progenitor1.09e-2061
monopoietic cell1.52e-1959
monocyte1.52e-1959
monoblast1.52e-1959
promonocyte1.52e-1959
lymphocyte2.57e-1453
common lymphoid progenitor2.57e-1453
lymphoid lineage restricted progenitor cell3.74e-1452
nucleate cell4.23e-1455
mesenchymal cell5.35e-11354
mature alpha-beta T cell1.30e-1018
alpha-beta T cell1.30e-1018
immature T cell1.30e-1018
mature T cell1.30e-1018
immature alpha-beta T cell1.30e-1018
connective tissue cell1.71e-09361
T cell4.07e-0925
pro-T cell4.07e-0925
CD8-positive, alpha-beta T cell1.18e-0711
multi fate stem cell1.26e-07427
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.01e-30108
hematopoietic system1.20e-2798
blood island1.20e-2798
lateral plate mesoderm5.51e-25203
immune system1.01e-2193
bone marrow2.14e-1776
bone element1.61e-1382
mesoderm4.05e-10315
mesoderm-derived structure4.05e-10315
presumptive mesoderm4.05e-10315
skeletal element5.11e-1090
blood5.17e-1015
haemolymphatic fluid5.17e-1015
organism substance5.17e-1015
connective tissue1.02e-08371
circulatory system1.31e-08112
cardiovascular system4.66e-08109
skeletal system8.38e-08100


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
BCL11A#53335321.27709132770530.0001704839114606140.00208198891826883
CCNT2#90546.336201576962630.0006203100587215640.00512860688907706
CEBPB#105147.971147625824820.0002476385788090830.00268317517711814
CHD2#1106410.34402283411698.73193255208051e-050.00129171997706337
CTCF#1066445.360256373075030.001211145381643620.00818498851517266
E2F1#186944.907389214879320.001724022357361790.010662353939747
E2F6#187645.017155731697390.00157802193473060.00998044164242288
EBF1#187948.9064668465690.00015887907472010.00199797371278658
EGR1#195844.988179094810140.001615011500076050.0101547372701049
ELF1#199744.258097958807540.003041525565781240.0161114774074167
EP300#203346.77394172622320.0004748459821442640.00434563963627452
GABPB1#255347.067683836182170.0004006876864423170.00390586347623195
HDAC2#3066413.41562023662633.0859005065161e-050.000627386340276494
HEY1#2346244.040111043105710.00375304636917980.0186365733050005
HNF4G#3174428.75342252644681.46167379934821e-065.67282608436001e-05
IRF4#3662421.91451268674414.33289161192893e-060.000136590059480304
MAX#414946.452555509007120.0005767613195645490.00485855585207307
MEF2A#4205418.74323090964418.0978922767748e-060.000224452168655542
NFKB1#479045.488063424193840.001102199566301980.00768493360738449
NR3C1#2908414.9730233311731.98868032687801e-050.000443604836947485
PAX5#507946.669565531177830.0005052774169483260.00444459430208592
POU2F2#545249.106124057742520.000145395665174930.00188492774021903
RAD21#5885410.35503389545638.6948481184721e-050.00129651805060695
SIN3A#2594245.408884726815140.001168172384885160.00797247309057184
SMARCB1#6598418.25271578115749.00423392720929e-060.000241870675700569
SMC3#9126415.04493284493281.95092670935632e-050.000438744260547943
SP1#666745.69838137814090.0009482606065333980.00684939411340629
TAF1#687243.343046285745290.008005664898701650.032274516959604
TBP#690843.706770687096390.005296377814784350.0244615222481874
TCF12#6938410.63446490218647.8163066689251e-050.00120171831620178
TFAP2A#7020416.5186343730451.34240829060362e-050.000326958440910335
TFAP2C#7022410.80922860986027.32289634782688e-050.00114696456459312
TRIM28#10155418.59052504526258.36730015875654e-060.000230512387570661
ZBTB7A#5134147.35190930787590.000342223540015990.00347004701900291
ZNF263#1012748.221841637010680.0002187871180958320.00249371470335159



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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