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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:28, 17 September 2013


Full id: C675_Eosinophils_CD14_Natural_CD8_Neutrophils_Basophils_CD4



Phase1 CAGE Peaks

Hg19::chr10:27444086..27444105,-p4@YME1L1
Hg19::chr12:49412702..49412735,+p@chr12:49412702..49412735
+
Hg19::chr12:50064927..50064942,+p@chr12:50064927..50064942
+
Hg19::chr17:75954523..75954527,-p@chr17:75954523..75954527
-
Hg19::chr19:41304544..41304552,-p@chr19:41304544..41304552
-
Hg19::chr19:54372647..54372650,-p7@ENST00000455835
Hg19::chr1:174968433..174968454,-p4@BC038430
Hg19::chr21:45559862..45559873,-p1@AK127364
Hg19::chr2:135810397..135810416,+p@chr2:135810397..135810416
+
Hg19::chr6:138029264..138029275,-p@chr6:138029264..138029275
-
Hg19::chr7:130598148..130598162,-p2@LOC646329
Hg19::chr9:134609727..134609746,-p@chr9:134609727..134609746
-


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

GO IDGO nameFDR corrected p-value
GO:0005618cell wall0.00541614540821025
GO:0030312external encapsulating structure0.00812373980212789
GO:0005739mitochondrion0.0132731077032574



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
leukocyte2.34e-87136
nongranular leukocyte3.66e-73115
hematopoietic lineage restricted progenitor cell6.24e-73120
hematopoietic stem cell4.02e-69168
angioblastic mesenchymal cell4.02e-69168
hematopoietic cell2.15e-67177
classical monocyte5.42e-6542
CD14-positive, CD16-negative classical monocyte5.42e-6542
hematopoietic oligopotent progenitor cell2.53e-60161
hematopoietic multipotent progenitor cell2.53e-60161
defensive cell5.25e-5548
phagocyte5.25e-5548
myeloid leukocyte3.98e-5472
granulocyte monocyte progenitor cell9.09e-4967
macrophage dendritic cell progenitor8.27e-4861
myeloid lineage restricted progenitor cell2.36e-4566
monopoietic cell2.64e-4559
monocyte2.64e-4559
monoblast2.64e-4559
promonocyte2.64e-4559
myeloid cell9.15e-35108
common myeloid progenitor9.15e-35108
stuff accumulating cell5.37e-2487
lymphoid lineage restricted progenitor cell4.30e-2352
lymphocyte1.81e-2253
common lymphoid progenitor1.81e-2253
mesenchymal cell1.19e-21354
nucleate cell2.72e-2155
connective tissue cell1.02e-20361
motile cell1.90e-17386
stem cell4.44e-14441
intermediate monocyte5.89e-149
CD14-positive, CD16-positive monocyte5.89e-149
multi fate stem cell1.66e-13427
somatic stem cell5.74e-13433
T cell1.30e-1125
pro-T cell1.30e-1125
mature alpha-beta T cell1.53e-1118
alpha-beta T cell1.53e-1118
immature T cell1.53e-1118
mature T cell1.53e-1118
immature alpha-beta T cell1.53e-1118
CD4-positive, alpha-beta T cell4.57e-116
lymphocyte of B lineage6.18e-0924
pro-B cell6.18e-0924
granulocyte8.00e-088
blood cell4.99e-0711
natural killer cell6.51e-073
pro-NK cell6.51e-073
Uber Anatomy
Ontology termp-valuen
bone marrow6.42e-4576
hematopoietic system1.62e-4498
blood island1.62e-4498
bone element1.90e-4082
immune system2.83e-4093
hemolymphoid system4.19e-40108
skeletal element2.01e-3590
skeletal system2.75e-30100
connective tissue1.90e-19371
lateral plate mesoderm3.43e-13203
musculoskeletal system3.52e-12167


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)
MA0003.10.162801
MA0004.10.861826
MA0006.10.552945
MA0007.10.305951
MA0009.10.756202
MA0014.10.169227
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.11.73404
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.10.155795
MA0050.10.837296
MA0051.10.410316
MA0052.10.682867
MA0055.10.107116
MA0056.10
MA0057.10.3421
MA0058.10.676094
MA0059.10.673606
MA0060.10.688558
MA0061.11.01669
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.226673
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.0900879
MA0074.10.40963
MA0076.10.706813
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.11.8015
MA0084.11.25286
MA0087.10.724294
MA0088.10.0806254
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.11.4437
MA0093.10.558691
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.11.07376
MA0103.10.535462
MA0105.10.563165
MA0106.10.452066
MA0107.10.427483
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.11.17934
MA0114.10.134281
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.11.20117
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.11.07857
MA0139.10.567946
MA0140.10.376643
MA0141.10.670251
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.441471
MA0146.10.246584
MA0147.10.865676
MA0148.10.344198
MA0149.10.367947
MA0062.21.47776
MA0035.20.376007
MA0039.21.49604
MA0138.20.503176
MA0002.20.652621
MA0137.20.20663
MA0104.21.13554
MA0047.20.440861
MA0112.20.681028
MA0065.20.733267
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.5526
MA0155.11.33153
MA0156.12.50267
MA0157.10.544523
MA0158.10
MA0159.10.867657
MA0160.10.940794
MA0161.10
MA0162.11.52545
MA0163.10.309131
MA0164.10.478818
MA0080.21.677
MA0018.22.00546
MA0099.20.382887
MA0079.22.08428
MA0102.21.28978
MA0258.10.375
MA0259.10.891845
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
CCNT2#90563.168100788481320.006015621942674210.0269653435800228
E2F1#186972.862643708679610.004360763229147680.0206724048335961
E2F4#187444.222686771761480.01146510237446740.0419391204121398
E2F6#187672.926674176823480.003823084322472550.0188713065296678
EBF1#187964.45323342328450.001011881476986250.00717934032438631
EGR1#195872.909771138639250.003957340760479120.0189962178463795
ELF1#199782.838731972538360.001804270346094040.0109149786072588
ETS1#211364.864380461101170.0006281377526434450.00516958855384782
GTF2B#295937.985957483581060.005455491186982880.02471655579027
GTF2F1#296244.246553625585880.01124277021557680.0412761865414498
HEY1#2346272.356731441811660.01346982061264720.0475776039963561
HMGN3#932453.407728218062750.01028040559075030.0381941332393856
IRF1#365974.455012189578940.0002850277586319370.00303105733466662
MAX#414963.226277754503560.00548348112691290.0248325941121176
MYC#460973.046331091772150.003007674913179810.0159816107991649
NFKB1#479083.658708949462560.0002973737521670860.0031041896354401
PAX5#507963.334782765588910.004629821511058920.021860569139359
POLR2A#5430111.968498745178230.00153515886455670.00975958465153622
POU2F2#545275.311905700349819.21465586752959e-050.00134202962508565
SIN3A#2594273.155182757308830.002433775882281460.0137069197244173
SP1#666773.324055803915520.001772697031948130.0108879502069884
SPI1#668853.418468128551140.01014461279531980.0378958872498179
SRF#672244.59905942072260.008506629938930720.0324668880350821
WRNIP1#56897218.30332739156270.005147580523620290.0239287916636124



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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