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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:33, 17 September 2013


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
leukocyte2.20e-65136
nongranular leukocyte3.13e-59115
hematopoietic lineage restricted progenitor cell1.22e-57120
hematopoietic stem cell2.26e-57168
angioblastic mesenchymal cell2.26e-57168
hematopoietic cell1.50e-55177
hematopoietic oligopotent progenitor cell8.79e-55161
hematopoietic multipotent progenitor cell8.79e-55161
lymphocyte2.17e-5253
common lymphoid progenitor2.17e-5253
lymphoid lineage restricted progenitor cell2.28e-5152
nucleate cell7.46e-5055
lymphocyte of B lineage8.80e-2824
pro-B cell8.80e-2824
T cell3.37e-2025
pro-T cell3.37e-2025
mature alpha-beta T cell4.55e-2018
alpha-beta T cell4.55e-2018
immature T cell4.55e-2018
mature T cell4.55e-2018
immature alpha-beta T cell4.55e-2018
B cell6.33e-1914
granulocyte monocyte progenitor cell8.19e-1467
myeloid cell1.15e-13108
common myeloid progenitor1.15e-13108
mesenchymal cell2.22e-13354
macrophage dendritic cell progenitor6.60e-1361
myeloid leukocyte9.45e-1372
connective tissue cell1.28e-12361
myeloid lineage restricted progenitor cell1.00e-1166
monopoietic cell3.91e-1159
monocyte3.91e-1159
monoblast3.91e-1159
promonocyte3.91e-1159
CD8-positive, alpha-beta T cell1.21e-1011
CD4-positive, alpha-beta T cell1.35e-106
motile cell5.32e-10386
conventional dendritic cell2.93e-088
dendritic cell3.55e-0810
multi fate stem cell5.84e-07427
Langerhans cell7.69e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.64e-2698
blood island3.64e-2698
hemolymphoid system1.98e-23108
immune system2.32e-1493
blood2.65e-1315
haemolymphatic fluid2.65e-1315
organism substance2.65e-1315
connective tissue4.65e-12371
bone marrow7.24e-1276
bone element2.60e-1082
skeletal element1.36e-0890
hemopoietic organ3.00e-087
immune organ3.00e-087
skeletal system6.91e-07100
Disease
Ontology termp-valuen
hematologic cancer2.43e-0751
immune system cancer2.43e-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)
MA0003.10.0149552
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.12.25785
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.11.28049
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.11.8363
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.0725989
MA0058.10.325084
MA0059.10.323879
MA0060.10.488252
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.11.18425
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.78251
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.11.47707
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.11.31682
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.12.25779
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.12.2317
MA0139.14.07339
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.319685
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.21.95022
MA0035.20.473658
MA0039.20.679176
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.378721
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.10.156896
MA0156.13.04199
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.101664
MA0164.10.583138
MA0080.22.09
MA0018.20.556211
MA0099.22.0981
MA0079.20.48507
MA0102.21.41188
MA0258.10.532421
MA0259.10.218904
MA0442.10



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.

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