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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:26, 17 September 2013


Full id: C593_Dendritic_CD8_Natural_CD4_CD19_Basophils_Peripheral



Phase1 CAGE Peaks

Hg19::chr12:49076002..49076043,-p1@KANSL2
Hg19::chr15:52975108..52975140,-p@chr15:52975108..52975140
-
Hg19::chr17:43298790..43298799,+p20@FMNL1
Hg19::chr18:29671893..29671966,+p3@RNF138
Hg19::chr18:29671969..29671976,+p8@RNF138
Hg19::chr19:16738998..16739024,-p1@CALR3
p1@MED26
Hg19::chr19:39892910..39892923,+p@chr19:39892910..39892923
+
Hg19::chr21:43654778..43654795,-p@chr21:43654778..43654795
-
Hg19::chr2:220144814..220144821,+p@chr2:220144814..220144821
+
Hg19::chr2:235405385..235405401,+p@chr2:235405385..235405401
+
Hg19::chr3:185304128..185304151,+p3@SENP2
Hg19::chr4:140375103..140375117,-p4@AK097885
Hg19::chr7:127032296..127032317,-p4@ZNF800
Hg19::chr7:127032330..127032356,-p3@ZNF800
Hg19::chr7:127032363..127032382,-p6@ZNF800


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:0016929SUMO-specific protease activity0.0169257035205463



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
leukocyte9.55e-40136
hematopoietic stem cell3.58e-38168
angioblastic mesenchymal cell3.58e-38168
hematopoietic cell3.99e-36177
hematopoietic oligopotent progenitor cell2.20e-32161
hematopoietic multipotent progenitor cell2.20e-32161
hematopoietic lineage restricted progenitor cell2.23e-31120
nongranular leukocyte6.89e-31115
lymphoid lineage restricted progenitor cell1.33e-2752
lymphocyte7.36e-2753
common lymphoid progenitor7.36e-2753
nucleate cell1.87e-2555
T cell1.37e-1825
pro-T cell1.37e-1825
mature alpha-beta T cell5.68e-1818
alpha-beta T cell5.68e-1818
immature T cell5.68e-1818
mature T cell5.68e-1818
immature alpha-beta T cell5.68e-1818
CD4-positive, alpha-beta T cell6.17e-116
myeloid cell3.28e-10108
common myeloid progenitor3.28e-10108
myeloid leukocyte5.23e-1072
intermediate monocyte7.51e-109
CD14-positive, CD16-positive monocyte7.51e-109
classical monocyte2.06e-0942
CD14-positive, CD16-negative classical monocyte2.06e-0942
granulocyte monocyte progenitor cell2.93e-0967
CD8-positive, alpha-beta T cell1.74e-0811
lymphocyte of B lineage1.38e-0724
pro-B cell1.38e-0724
defensive cell1.45e-0748
phagocyte1.45e-0748
mesenchymal cell1.78e-07354
macrophage dendritic cell progenitor4.43e-0761
connective tissue cell5.68e-07361
myeloid lineage restricted progenitor cell7.30e-0766
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.09e-1298
blood island2.09e-1298
hemolymphoid system8.63e-12108
immune system8.91e-1193
bone marrow8.33e-0976
bone element1.28e-0782


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)
MA0003.11.62438
MA0004.10.256222
MA0006.10.426713
MA0007.13.58818
MA0009.10.669377
MA0014.11.81539
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.11.60692
MA0046.10.659066
MA0048.12.91484
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.12.57075
MA0056.10
MA0057.10.219783
MA0058.10.182945
MA0059.10.536577
MA0060.10.877206
MA0061.10.767139
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.0373092
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.146257
MA0074.10.894848
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.10.662469
MA0089.10
MA0090.10.205547
MA0091.10.258318
MA0092.10.228476
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.14.46706
MA0101.10.141917
MA0103.11.32375
MA0105.12.65495
MA0106.10.37688
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.320986
MA0117.11.6806
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.11.12143
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.917713
MA0139.10.71772
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.284854
MA0145.11.3964
MA0146.10.62917
MA0147.10.326612
MA0148.10.276339
MA0149.10.298252
MA0062.22.13276
MA0035.20.305721
MA0039.21.07256
MA0138.20.425279
MA0002.20.220677
MA0137.20.153033
MA0104.20.236755
MA0047.20.959769
MA0112.20.448515
MA0065.20.0514203
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.0156321
MA0155.10.240806
MA0156.10.469333
MA0157.10.46471
MA0158.10
MA0159.10.0995776
MA0160.10.288813
MA0161.10
MA0162.11.01404
MA0163.10.0365728
MA0164.10.402162
MA0080.20.432036
MA0018.20.98566
MA0099.20.312108
MA0079.21.38311
MA0102.21.1957
MA0258.10.964206
MA0259.10.693919
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
BRCA1#67256.728076881074590.0005889572751880370.00493304265485311
CCNT2#90572.956894069249230.00483592247754510.0226738005671081
CHD2#110674.82721065592120.0002511849755939860.00270615923932951
CTCFL#14069056.582158119658120.0006510422195080220.00533246007083353
E2F1#1869123.925911371903461.24796592318433e-065.02453018702575e-05
E2F6#1876124.013724585357919.71551435172565e-074.12470976983689e-05
EGR1#195892.992907456886080.0007989923066083970.00617112538898642
ELF1#199792.554858775284520.002645589518049610.0146145521884895
GABPB1#255373.298252456885010.002560140289154440.0141642470550935
GATA1#262354.520102714600150.003491678030095980.0177350141905065
GTF2F1#296254.246553625585880.004577350602586930.0216343358638537
HEY1#23462102.693407362070470.0007295052267864420.00581549472409352
IRF1#365963.054865501425560.008746772827476030.0332267925409657
NFKB1#479093.29283805451630.0003804048935776930.00376614908335962
NRF1#489954.070093149236970.005493687985816360.0248745027118128
PAX5#5079104.446377020785228.29479623652792e-060.000229240599139121
PBX3#509057.304837562248040.0004036629940786130.00388339714798971
POLR2A#5430142.00428963145420.0001911089001665770.00230689117250314
POU2F2#545274.249524560279840.0005548606876288750.00473595091167637
RFX5#599354.01597027573170.00581754997942610.0261504305027667
SIN3A#2594293.245330836089080.0004262424152144410.00398285153463192
TBP#6908102.471180458064260.001514967647045190.0096671171314079
YY1#7528103.27411383323590.0001326837928134460.00174306448272245
ZEB1#693555.629477339181290.001321625039835720.00884519048608799



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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