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Coexpression cluster:C4535: Difference between revisions

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|full_id=C4535_Neutrophils_CD4_CD8_Peripheral_Eosinophils_CD34_Natural
|full_id=C4535_Neutrophils_CD4_CD8_Peripheral_Eosinophils_CD34_Natural
|id=C4535
|id=C4535
|ontology_enrichment_celltype=CL:0000037!3.62e-36!172;CL:0000566!3.62e-36!172;CL:0000988!2.24e-33!182;CL:0000738!2.01e-32!140;CL:0002032!2.45e-32!165;CL:0000837!2.45e-32!165;CL:0002031!2.56e-26!124;CL:0002087!1.06e-24!119;CL:0000763!3.63e-19!112;CL:0000049!3.63e-19!112;CL:0000860!2.07e-18!45;CL:0002057!4.03e-18!42;CL:0000766!5.55e-17!76;CL:0000557!3.81e-14!71;CL:0000839!1.84e-13!70;CL:0000542!2.43e-12!53;CL:0000051!2.43e-12!53;CL:0002009!5.36e-12!65;CL:0000838!5.49e-12!52;CL:0002194!4.16e-11!63;CL:0000576!4.16e-11!63;CL:0000040!4.16e-11!63;CL:0000559!4.16e-11!63;CL:0000094!9.49e-07!8
|ontology_enrichment_celltype=CL:0000037!3.02e-30!168;CL:0000566!3.02e-30!168;CL:0000988!1.38e-28!177;CL:0000738!3.20e-28!136;CL:0002032!1.50e-26!161;CL:0000837!1.50e-26!161;CL:0002031!4.27e-22!120;CL:0002087!2.99e-21!115;CL:0000763!8.50e-15!108;CL:0000049!8.50e-15!108;CL:0000860!1.96e-14!42;CL:0002057!1.96e-14!42;CL:0000766!6.67e-14!72;CL:0002242!3.41e-12!55;CL:0000542!1.43e-11!53;CL:0000051!1.43e-11!53;CL:0000557!3.20e-11!67;CL:0000838!3.46e-11!52;CL:0000473!5.48e-11!48;CL:0000234!5.48e-11!48;CL:0000839!1.55e-10!66;CL:0002009!1.34e-09!61;CL:0002194!7.87e-09!59;CL:0000576!7.87e-09!59;CL:0000040!7.87e-09!59;CL:0000559!7.87e-09!59
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!8.91e-16!102;UBERON:0003061!8.91e-16!102;UBERON:0002193!5.54e-12!112;UBERON:0001474!2.69e-11!86;UBERON:0002371!4.35e-11!80;UBERON:0004765!7.85e-08!101;UBERON:0001434!7.85e-08!101;UBERON:0002405!3.13e-07!115
|ontology_enrichment_uberon=UBERON:0002390!3.37e-12!98;UBERON:0003061!3.37e-12!98;UBERON:0002193!4.61e-09!108;UBERON:0001474!5.01e-09!82;UBERON:0002371!1.20e-08!76;UBERON:0004765!2.70e-07!90;UBERON:0002405!6.26e-07!93
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019093233011732!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327292436268134!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438624803544714!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0323976049449151!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.032214539782541!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464564656286116!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764641989275624!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00389254770070175!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.00085401929494252!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109092554390609!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128625845404903!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.0047306968527021!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173573559699834!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.006451246624754!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00545190321482866!TAL1#6886;3:29.8686166774402:3.75103522793067e-05:0.000722127867594195!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330949793326744!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140780653448342
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.123526,0.0906475,0.0558058,0.00477066,1.15329e-05,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.016278,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.001389,0.144567,0.038848,0.000119282,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.022113,0.000434303,0.0774373,0.109194,0.128564,0.131452,0.323837,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.0122266,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,1.93633e-06,0.057571,0.047591,0.392974,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0121461,6.33791e-09,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.00232088,0.153469,0.0376916,0.13262,0.00102818,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.0122477,0.194941,0.218271,0.101607,5.85104e-05,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.0128248,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.000260208,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0125264,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.00309372,0.178389,0.0257622,0.231073,0.000211542,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.643768,0.432035,0.0411943,0.390366,0.48809,0.50058,0.443185,0.522904,0.0608227,6.79659e-10,0.227104,0.518585,0.0734371,0.38649,0.284625,0.504757,0.192225,0.375373,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.0186777,0.390974,0.0115792,0.683217,0.161598,0.000101989,0.644754,0.496032,4.65435e-05,0.37357,0.00500957,0.477353,0.78384,0.0508568,0.43491,0.20342,0.200493,0.20558,0.300504,0.00348292,0.000277336,0.349197,0.383291,0.156104,0.141318,0.00217346,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.0442318,0.194707,0.616388,0.408413,0.516511,0.322213,0.656109,0.33942,0.0700181,0.387276,0.0391112,0.802166,0.537348,0.222037,0.416621,0.416292,0.462712,0.0115406,0.579431,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.170369,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.019895,0.0524515,0.241132,0.0795725,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.201728,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.24107,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.000574807,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,5.91485e-06,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.0199603,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,2.70035e-05,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.0240944,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.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}}
}}

Revision as of 16:01, 19 October 2012


Full id: C4535_Neutrophils_CD4_CD8_Peripheral_Eosinophils_CD34_Natural



Phase1 CAGE Peaks

Hg19::chr5:98264458..98264477,-p@chr5:98264458..98264477
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Hg19::chr5:98264490..98264505,-p@chr5:98264490..98264505
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Hg19::chr5:98264529..98264538,-p@chr5:98264529..98264538
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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 cell3.02e-30168
angioblastic mesenchymal cell3.02e-30168
hematopoietic cell1.38e-28177
leukocyte3.20e-28136
hematopoietic oligopotent progenitor cell1.50e-26161
hematopoietic multipotent progenitor cell1.50e-26161
hematopoietic lineage restricted progenitor cell4.27e-22120
nongranular leukocyte2.99e-21115
myeloid cell8.50e-15108
common myeloid progenitor8.50e-15108
classical monocyte1.96e-1442
CD14-positive, CD16-negative classical monocyte1.96e-1442
myeloid leukocyte6.67e-1472
nucleate cell3.41e-1255
lymphocyte1.43e-1153
common lymphoid progenitor1.43e-1153
granulocyte monocyte progenitor cell3.20e-1167
lymphoid lineage restricted progenitor cell3.46e-1152
defensive cell5.48e-1148
phagocyte5.48e-1148
myeloid lineage restricted progenitor cell1.55e-1066
macrophage dendritic cell progenitor1.34e-0961
monopoietic cell7.87e-0959
monocyte7.87e-0959
monoblast7.87e-0959
promonocyte7.87e-0959
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.37e-1298
blood island3.37e-1298
hemolymphoid system4.61e-09108
bone element5.01e-0982
bone marrow1.20e-0876
skeletal element2.70e-0790
immune system6.26e-0793


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
CCNT2#90536.336201576962630.003930750035764890.019093233011732
E2F1#186934.907389214879320.008460985347239390.0327292436268134
E2F4#1874312.66806031528440.0004917987006298980.00438624803544714
E2F6#187635.017155731697390.00791769806886330.0323976049449151
EGR1#195834.988179094810140.008056488137383440.032214539782541
ELF1#199734.258097958807540.01295179875054610.0464564656286116
ETS1#211339.728760922202340.001085840092584840.00764641989275624
GATA1#2623313.56030814380040.0004009615963782630.00389254770070175
GATA3#2625327.2365163572064.94721007899563e-050.00085401929494252
HMGN3#932438.178547723350590.001827766942164210.0109092554390609
IRF1#365937.63716375356390.002244692747297240.0128625845404903
NRF1#4899312.21027944771090.0005492172401020010.0047306968527021
PAX5#507936.669565531177830.003370290999677260.0173573559699834
STAT3#6774310.51946499715420.0008589184530415310.006451246624754
TAF7#6879311.43306940492390.0006690181981945830.00545190321482866
TAL1#6886329.86861667744023.75103522793067e-050.000722127867594195
YY1#752834.911170749853860.008441455341808260.0330949793326744
ZBTB7A#5134137.35190930787590.002516255860282270.0140780653448342



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.