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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:29, 17 September 2013


Full id: C741_immature_CD14_Basophils_Peripheral_Mallassezderived_Astrocyte_renal



Phase1 CAGE Peaks

Hg19::chr11:62321495..62321531,-p@chr11:62321495..62321531
-
Hg19::chr11:62321782..62321794,+p@chr11:62321782..62321794
+
Hg19::chr14:65673392..65673400,+p@chr14:65673392..65673400
+
Hg19::chr16:85858477..85858488,+p@chr16:85858477..85858488
+
Hg19::chr16:85858491..85858507,+p@chr16:85858491..85858507
+
Hg19::chr17:29923862..29923868,-p@chr17:29923862..29923868
-
Hg19::chr20:47893707..47893719,-p@chr20:47893707..47893719
-
Hg19::chr2:27851106..27851120,+p2@GPN1
Hg19::chr3:71113123..71113139,+p@chr3:71113123..71113139
+
Hg19::chr3:71113153..71113163,+p@chr3:71113153..71113163
+
Hg19::chr6:32572606..32572629,+p@chr6:32572606..32572629
+


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
classical monocyte1.97e-9842
CD14-positive, CD16-negative classical monocyte1.97e-9842
defensive cell3.28e-8548
phagocyte3.28e-8548
granulocyte monocyte progenitor cell7.61e-7567
macrophage dendritic cell progenitor1.10e-7361
myeloid leukocyte2.38e-7372
myeloid lineage restricted progenitor cell7.29e-6766
monopoietic cell1.08e-6659
monocyte1.08e-6659
monoblast1.08e-6659
promonocyte1.08e-6659
leukocyte1.39e-55136
myeloid cell1.58e-55108
common myeloid progenitor1.58e-55108
stuff accumulating cell9.27e-4787
hematopoietic lineage restricted progenitor cell3.38e-46120
hematopoietic stem cell2.06e-43168
angioblastic mesenchymal cell2.06e-43168
nongranular leukocyte4.61e-43115
hematopoietic oligopotent progenitor cell5.51e-41161
hematopoietic multipotent progenitor cell5.51e-41161
hematopoietic cell8.91e-41177
intermediate monocyte2.84e-179
CD14-positive, CD16-positive monocyte2.84e-179
mesenchymal cell4.23e-17354
connective tissue cell1.36e-16361
motile cell8.21e-15386
basophil2.42e-143
natural killer cell3.16e-133
pro-NK cell3.16e-133
stem cell7.40e-13441
multi fate stem cell1.25e-12427
somatic stem cell2.50e-12433
CD1a-positive Langerhans cell1.76e-102
immature CD1a-positive Langerhans cell1.76e-102
Langerhans cell1.31e-085
single nucleate cell8.76e-073
mononuclear cell8.76e-073
Uber Anatomy
Ontology termp-valuen
bone marrow3.60e-6576
bone element6.96e-6082
hematopoietic system3.09e-5598
blood island3.09e-5598
skeletal element6.41e-5490
immune system6.05e-5293
hemolymphoid system2.04e-49108
skeletal system8.61e-48100
musculoskeletal system1.54e-25167
lateral plate mesoderm1.48e-22203
connective tissue6.64e-16371
mesoderm1.27e-11315
mesoderm-derived structure1.27e-11315
presumptive mesoderm1.27e-11315


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)
MA0003.10.0370565
MA0004.10.349539
MA0006.10.210781
MA0007.10.332734
MA0009.10.79061
MA0014.10.0144431
MA0017.10.24363
MA0019.10.486183
MA0024.10.688373
MA0025.10.921763
MA0027.12.39404
MA0028.10.637069
MA0029.10.707146
MA0030.10.696006
MA0031.10.633489
MA0038.10.443833
MA0040.10.712837
MA0041.10.366339
MA0042.10.337481
MA0043.10.790919
MA0046.10.779945
MA0048.10.185335
MA0050.10.897608
MA0051.10.439895
MA0052.10.716602
MA0055.10.00989454
MA0056.10
MA0057.10.0465155
MA0058.10.265212
MA0059.10.729981
MA0060.10.763267
MA0061.12.24862
MA0063.10
MA0066.10.444231
MA0067.11.1037
MA0068.10.262497
MA0069.10.776171
MA0070.10.765217
MA0071.10.40788
MA0072.10.760818
MA0073.10.00428338
MA0074.10.439193
MA0076.10.278993
MA0077.10.753278
MA0078.10.533387
MA0081.10.730303
MA0083.10.79797
MA0084.11.28962
MA0087.10.758426
MA0088.10.10094
MA0089.10
MA0090.10.792817
MA0091.10.351901
MA0092.10.318032
MA0093.10.213288
MA0095.10
MA0098.10
MA0100.11.15683
MA0101.12.55605
MA0103.10.203171
MA0105.11.43099
MA0106.10.482519
MA0107.11.47931
MA0108.21.52518
MA0109.10
MA0111.10.303543
MA0113.10.498009
MA0114.10.465415
MA0115.11.02805
MA0116.10.935607
MA0117.10.827487
MA0119.10.250314
MA0122.10.852927
MA0124.10.98702
MA0125.10.904129
MA0130.10
MA0131.10.550695
MA0132.10
MA0133.10
MA0135.10.820382
MA0136.11.14308
MA0139.11.06363
MA0140.10.405425
MA0141.10.2626
MA0142.11.46715
MA0143.10.498176
MA0144.10.142196
MA0145.10.515404
MA0146.10.0381286
MA0147.10.162359
MA0148.10.372124
MA0149.10.396509
MA0062.20.0969238
MA0035.20.404774
MA0039.20.0468759
MA0138.21.323
MA0002.20.111226
MA0137.20.649788
MA0104.20.118985
MA0047.20.47109
MA0112.21.55811
MA0065.20.11899
MA0150.10.781086
MA0151.10
MA0152.11.05873
MA0153.10.887528
MA0154.10.634487
MA0155.11.95377
MA0156.10.231442
MA0157.10.576556
MA0158.10
MA0159.10.489747
MA0160.10.386031
MA0161.10
MA0162.10.00470038
MA0163.10.585549
MA0164.10.509774
MA0080.22.53736
MA0018.20.483823
MA0099.22.78803
MA0079.20.000235118
MA0102.21.32663
MA0258.10.135061
MA0259.10.504687
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
EBF1#187954.048394021167730.004592383252421630.0217034216253976
FOS#235375.725971560205534.5912826243232e-050.000806982440258651
JUN#372566.825179559456188.44439089932034e-050.00126694977896009
NFKB1#479062.993489140469360.007285564963029570.0301405077906059
SMARCC2#6601217.11915898670870.005818446476053550.0261533346895871
STAT3#677454.781574998706470.002192062661377620.0126358777067898
TBP#690872.358854073606790.0117973486056640.0429783483684576



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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