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{{Coexpression_clusters
{
|full_id=C451_CD14_CD4_Eosinophils_Neutrophils_adult_Natural_CD8

Latest revision as of 11:23, 17 September 2013


Full id: C451_CD14_CD4_Eosinophils_Neutrophils_adult_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr12:48592134..48592150,+p1@DKFZP779L1853
Hg19::chr12:66696322..66696383,+p2@HELB
Hg19::chr16:50715196..50715235,-p1@SNX20
Hg19::chr16:57023445..57023514,+p1@NLRC5
Hg19::chr16:57025612..57025617,+p@chr16:57025612..57025617
+
Hg19::chr16:89787973..89788001,+p3@ZNF276
Hg19::chr16:89788512..89788554,-p@chr16:89788512..89788554
-
Hg19::chr17:33701610..33701646,-p@chr17:33701610..33701646
-
Hg19::chr17:78237438..78237452,+p1@CU691854
Hg19::chr19:1133589..1133603,-p@chr19:1133589..1133603
-
Hg19::chr1:89664595..89664636,-p1@GBP4
Hg19::chr1:89738560..89738575,-p2@GBP5
Hg19::chr22:36556793..36556811,-p1@APOL3
Hg19::chr2:240189135..240189153,-p@chr2:240189135..240189153
-
Hg19::chr2:240189159..240189181,-p@chr2:240189159..240189181
-
Hg19::chr2:240189199..240189221,-p@chr2:240189199..240189221
-
Hg19::chr3:142166796..142166841,-p3@XRN1
Hg19::chr3:156893074..156893141,+p1@ENST00000488040
Hg19::chr5:42992974..42992986,-p6@uc003jnb.1
Hg19::chr6:106545946..106545979,+p@chr6:106545946..106545979
+
Hg19::chr6:18265050..18265072,-p5@DEK
Hg19::chr6:32811888..32811906,+p1@ENST00000413039
p1@ENST00000429600
p1@ENST00000458296


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
leukocyte9.28e-71136
hematopoietic stem cell8.93e-69168
angioblastic mesenchymal cell8.93e-69168
hematopoietic cell5.05e-66177
hematopoietic oligopotent progenitor cell4.18e-64161
hematopoietic multipotent progenitor cell4.18e-64161
nongranular leukocyte2.36e-63115
hematopoietic lineage restricted progenitor cell1.27e-59120
myeloid leukocyte6.95e-3772
myeloid cell2.30e-32108
common myeloid progenitor2.30e-32108
myeloid lineage restricted progenitor cell3.91e-3066
monopoietic cell9.80e-3059
monocyte9.80e-3059
monoblast9.80e-3059
promonocyte9.80e-3059
classical monocyte1.04e-2942
CD14-positive, CD16-negative classical monocyte1.04e-2942
granulocyte monocyte progenitor cell1.16e-2967
defensive cell2.71e-2948
phagocyte2.71e-2948
lymphocyte2.96e-2953
common lymphoid progenitor2.96e-2953
lymphoid lineage restricted progenitor cell3.18e-2952
nucleate cell1.60e-2855
macrophage dendritic cell progenitor4.63e-2861
T cell5.98e-1725
pro-T cell5.98e-1725
mature alpha-beta T cell2.78e-1518
alpha-beta T cell2.78e-1518
immature T cell2.78e-1518
mature T cell2.78e-1518
immature alpha-beta T cell2.78e-1518
mesenchymal cell6.96e-12354
lymphocyte of B lineage3.50e-1124
pro-B cell3.50e-1124
connective tissue cell3.56e-10361
CD8-positive, alpha-beta T cell3.77e-1011
B cell2.82e-0814
stuff accumulating cell6.39e-0887
motile cell8.28e-08386
granulocyte1.56e-078
intermediate monocyte1.73e-079
CD14-positive, CD16-positive monocyte1.73e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.69e-3998
blood island7.69e-3998
hemolymphoid system1.79e-37108
immune system4.15e-2893
bone marrow1.83e-2576
bone element5.97e-2282
skeletal element1.53e-1690
adult organism3.48e-16114
skeletal system2.07e-14100
blood1.11e-1015
haemolymphatic fluid1.11e-1015
organism substance1.11e-1015
lateral plate mesoderm3.50e-10203
connective tissue2.99e-09371


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)
MA0003.11.2709
MA0004.10.478761
MA0006.10.244486
MA0007.10.449227
MA0009.10.526253
MA0014.10.0851404
MA0017.10.619077
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.95287
MA0029.10.450974
MA0030.10.441064
MA0031.11.00334
MA0038.13.48385
MA0040.10.456051
MA0041.10.508527
MA0042.10.149889
MA0043.10.526535
MA0046.10.516541
MA0048.10.186532
MA0050.16.14918
MA0051.15.30854
MA0052.10.459414
MA0055.10.198233
MA0056.10
MA0057.10.0785329
MA0058.10.682118
MA0059.10.331581
MA0060.15.7216
MA0061.10.675348
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.149869
MA0069.10.51311
MA0070.10.503171
MA0071.10.583044
MA0072.11.24772
MA0073.10.0067226
MA0074.10.639966
MA0076.11.18848
MA0077.10.49237
MA0078.10.30111
MA0081.10.101139
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.42447
MA0089.10
MA0090.10.118716
MA0091.10.482932
MA0092.10.837387
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.917893
MA0103.10.0653004
MA0105.10.666274
MA0106.10.259598
MA0107.10.660828
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.272101
MA0114.10.643657
MA0115.10.747865
MA0116.10.672581
MA0117.10.560027
MA0119.11.5753
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.846727
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.11.23017
MA0139.10.928155
MA0140.10.199454
MA0141.10.329072
MA0142.10.359701
MA0143.10.272236
MA0144.15.52797
MA0145.10.0933513
MA0146.10.358703
MA0147.10.0444528
MA0148.10.99741
MA0149.10.192747
MA0062.21.33951
MA0035.20.198962
MA0039.21.25633
MA0138.20.302079
MA0002.21.49131
MA0137.23.99442
MA0104.20.108753
MA0047.20.698519
MA0112.20.45088
MA0065.20.192051
MA0150.10.115337
MA0151.10
MA0152.10.589582
MA0153.10.615584
MA0154.10.26587
MA0155.10.26573
MA0156.10.58361
MA0157.11.60668
MA0158.10
MA0159.10.386598
MA0160.10.18494
MA0161.10
MA0162.10.00890769
MA0163.10.472083
MA0164.10.28168
MA0080.20.9064
MA0018.20.260646
MA0099.20.204301
MA0079.20.00567359
MA0102.21.03595
MA0258.10.892318
MA0259.10.403807
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
BCL11A#5333556.447603432637970.0008654585595952050.00645902719062195
EBF1#1879104.048394021167735.69071288955694e-050.000949564408807217
ELF1#1997152.903248608277871.09648915323577e-050.000284088887806476
GATA1#262374.314643500300140.0007492385419969230.00589896148417766
IRF4#366254.980571065169120.002710389575557860.0148890372860134
MEF2A#420554.259825206737280.005297580344031970.0243400639457285
NFKB1#4790112.744031712096920.000705788843196090.00567319949161521
PAX5#5079103.031620695989920.0006486935838301440.0053148904998538
POLR2A#5430212.04984166853271.30673372631837e-065.18518098947434e-05
PRDM1#639317.97694851510830.0006021829833485840.00503090861514621
SMC3#912653.419302919302920.01314679266670590.0466163468227777
SPI1#668872.610466570893590.01288045219699750.0463326288834546
STAT1#677287.52966818079975.11850336669685e-060.000157273131248736
STAT2#6773514.83267526964561.78325817125753e-050.000406907800192191
STAT3#677494.303417498835839.9173625749362e-050.00139609034905481



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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