Personal tools

Coexpression cluster:C901: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.315925797665145,0.315405114428282,0.322622574948882,0.144064671875115,0.247398438714038,0.117149360021774,0,0,0,0.142181656843797,0.475724818903348,0,0.191449731291012,0.343067067616665,0.401241286650242,0.326249274299738,0.294836650975188,0.248641786604834,0.272396181407098,0,0,0.285493430983262,0,0,0.109812129893149,0,0,0.308401558284621,0,0,0.138771381856642,0,0,0.115971073434934,0,0,0.220030274432855,0.0789870938765965,0,0.110660147363526,0,0,0.097343627213097,0,0.0853579634813876,0,0,0,0.0832356854652995,0,0.0826628337153937,0.0880145622338434,0,0,0.108907434678255,0,0,0.440903172569491,0.320619227153203,0.564491809947528,0.432475563704395,0.415237844311434,0.43524812648554,0.365879000610354,0.586830403682648,0.585016602270098,0.524908502418249,0.565365176504752,0,0.428381961848574,0,0.772156192325488,1.1451763594241,1.06015657806008,0.426814503483428,0.55719166837821,0.527273946548287,0.469566853250347,0.565121534581417,0.778751640134203,0.71676636286113,0.768968656837043,0.623485295623849,0.57185391767143,0.123484395618314,0,0.334295354160308,0.58177275453673,0.18613148201837,0.310768747319633,0.225272069414753,0.776836710419881,0.573917706747164,0.70314645200003,0.509196861711859,0,0.462533370184438,0.343329990739072,0.381629919597668,0.352048786074314,0.495682411305515,0,0.604668888456243,0.744017711919828,0.650869283733341,0,0,0,0,0,0,0,0,0,0,0,0.027549189648299,0,0,0,0.0697160876101768,0.221359407009807,0.092892723212638,0,0.13718235424895,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.050375285110278,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.393978959673908,0,0.160136301416294,0,0,0,0,0,0,0,0,0.150650916833568,0.0584715597507662,0.139478375171065,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.399114709370023,0,0,0,0,0,0,0,0.087841834467317,0.597197151070492,0.847422856990977,0.759569066761349,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.308316812342537,0.399673618657105,0.21494058611927,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390744040629657,0,0,0,0,0.178242227335072,0.246655432029025,0.432799636342854,0.385497356176373,0.349100046305231,0.361150902956099,0.499704364577129,0.253610608288505,0,0,0,0.137229487140467,0.110097374326945,0.0298469850284923,0,0.0790289888064564,0,0.0833856393724342,0,0,0.226523616575823,0,0,0,0.120960725232206,0.147243178344539,0.26756886175468,0,0.116355582210209,0.160574230329875,0.125057592200758,0.143257247232019,0,0,0,0,0,0,0.0593771573651105,0,0.192349114301995,0,0,0,0,0,0,0,0.123723537352191,0,0.0789089986057754,0.424506527225336,0,0,0.523565859468153,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0321956448428329,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.070745145653078,0,0,0.0959109874126932,0.0431350293094685,0,0,0,0.238000702387805,0,0,0,0,0,0.0978631351411755,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0402022792589852,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.364445320695129,0,0,0,0,0,0,0,0,0,0.0329341673988529,0,0.0283286403579212,0,0,0,0,0,0,0,1.15452925018239,0.94141301182329,0,0,0.0329432353726146,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0440642112897698,0,0,0,0.078316005475075,0.536034444148841,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0773171348687735,0.0541780982062256,0.0657907963604995,0,0,0,0,0,0.0690072669026771,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.128948885815716,0,0,0,0,0,0.032817368032432,0,0,0,0,0,0.0299826682885844,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0904423417827262,0,0,0,0,0,0,0,0,0.0390109377342095,0.161728830628106,0.322085411133589,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0317229404497622,0,0,0.0427459664864042,0,0,0.0527623387552046,0.074166758861158,0,0,0,0.0855462791577618,0,0.394757184679813,0.0300822291072195,0,0,0,0,0,0,0,0,0,0.146917605400546,0.358367776881315
|full_id=C901_immature_CD4_Natural_CD19_CD8_lymphoma_tonsil
|full_id=C901_immature_CD4_Natural_CD19_CD8_lymphoma_tonsil
|id=C901
|id=C901

Revision as of 18:41, 12 September 2012


Full id: C901_immature_CD4_Natural_CD19_CD8_lymphoma_tonsil



Phase1 CAGE Peaks

Hg19::chr13:52377773..52377786,+p@chr13:52377773..52377786
+
Hg19::chr6:149771109..149771126,-p@chr6:149771109..149771126
-
Hg19::chr6:149802219..149802228,-p@chr6:149802219..149802228
-
Hg19::chr6:149805982..149805989,-p9@ZC3H12D
Hg19::chr6:149806011..149806038,-p2@ZC3H12D
Hg19::chr6:149806045..149806063,-p5@ZC3H12D
Hg19::chr6:149806066..149806087,-p4@ZC3H12D
Hg19::chr6:149806091..149806098,-p7@ZC3H12D
Hg19::chr6:149806105..149806172,-p1@ZC3H12D


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>disease_data<br>

Cell Type
Ontology termp-valuen
leukocyte3.64e-66140
hematopoietic stem cell9.13e-64172
angioblastic mesenchymal cell9.13e-64172
hematopoietic cell9.66e-61182
hematopoietic oligopotent progenitor cell8.12e-60165
hematopoietic multipotent progenitor cell8.12e-60165
nongranular leukocyte1.08e-57119
hematopoietic lineage restricted progenitor cell2.69e-55124
lymphocyte1.55e-3253
common lymphoid progenitor1.55e-3253
lymphoid lineage restricted progenitor cell5.41e-3252
myeloid cell1.06e-26112
common myeloid progenitor1.06e-26112
myeloid leukocyte1.83e-2576
granulocyte monocyte progenitor cell1.04e-2471
macrophage dendritic cell progenitor8.50e-2465
monopoietic cell2.74e-2263
monocyte2.74e-2263
monoblast2.74e-2263
promonocyte2.74e-2263
myeloid lineage restricted progenitor cell2.29e-2170
lymphocyte of B lineage6.30e-1724
pro-B cell6.30e-1724
CD14-positive, CD16-negative classical monocyte3.93e-1642
classical monocyte9.04e-1645
mesenchymal cell1.10e-15358
connective tissue cell1.41e-14365
mature alpha-beta T cell2.93e-1418
alpha-beta T cell2.93e-1418
immature T cell2.93e-1418
mature T cell2.93e-1418
immature alpha-beta T cell2.93e-1418
T cell6.91e-1425
pro-T cell6.91e-1425
B cell3.60e-1114
motile cell2.71e-10390
CD8-positive, alpha-beta T cell4.92e-0911
dendritic cell3.55e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.94e-34102
blood island4.94e-34102
hemolymphoid system7.86e-30112
bone marrow3.66e-2280
bone element2.15e-2086
immune system1.38e-18115
skeletal element2.19e-14101
skeletal system2.19e-14101
connective tissue2.17e-13375
blood1.85e-0915
haemolymphatic fluid1.85e-0915
organism substance1.85e-0915
adult organism3.58e-09115
Disease
Ontology termp-valuen
hematologic cancer1.45e-0751
immune system cancer1.45e-0751


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
BATF#10538616.23853452820243.60599433803205e-071.77980360429929e-05
BHLHE40#8553629.91454236465169.67850629002477e-097.35137104308289e-07
CTCF#1066474.169088290169470.0001982812163300480.00238135832018099
EBF1#187976.927251991775896.58055964035478e-060.000192781786333524
ELF1#199762.838731972538360.007207863124148630.0298580841195843
EP300#203364.515961150815470.0005799248109934980.0048663640796521
FOSL2#2355611.28680040304113.04906898154755e-060.000103155722502055
GATA2#262445.664414103801770.003458945869346950.0175781639651952
HNF4A#3172615.42152690863584.88730097228247e-072.30024707635966e-05
HNF4G#3174619.16894835096451.35455066501517e-077.70522423221786e-06
JUN#372568.341886128224221.76795022778297e-050.000403591155933172
JUND#372775.44029417701083.36301553174088e-050.000667864573339962
MEF2A#4205612.4954872730961.68150394512489e-066.36054293824333e-05
MYC#460974.061774789029540.0002355556796573370.00256824299276883
NFKB1#479074.268493774372980.0001696536641662860.00207281925969382
PAX5#507975.187439857582764.62776729125731e-050.000812711263042917
PBX3#5090512.17472927041342.1331797509613e-050.000470114285736754
POLR2A#543081.908847268051620.0116612289598830.0425819758519359
POU2F2#545266.070749371828350.0001095272295875280.0015239694019307
RAD21#588566.903355930304225.2568380699896e-050.000893440050759388
SMC3#9126610.02995522995526.06947327596995e-060.000180646828004852
SP1#666763.79892091876060.001506997871138380.00962508259930411
SPI1#668865.469549005681820.0001978832720239980.00237739917714417
TAF1#687272.600147111135230.004212151627688650.0200525528236017
TCF12#693867.089643268124284.5123563262149e-050.000793911695339552
YY1#752863.27411383323590.003375958902549820.0172420055662086



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C901&oldid=2140291"