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Coexpression cluster:C364: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:21, 17 September 2013


Full id: C364_CD14_immature_CD14CD16_Aortic_CD4_Reticulocytes_Basophils



Phase1 CAGE Peaks

Hg19::chr10:107445974..107445984,+p1@YWHAZP5
Hg19::chr10:86998558..86998561,+p@chr10:86998558..86998561
+
Hg19::chr11:59844699..59844715,+p1@ENST00000528891
Hg19::chr12:69004707..69004718,+p2@RAP1B
Hg19::chr14:35898950..35898961,+p@chr14:35898950..35898961
+
Hg19::chr15:37110690..37110722,-p1@CSNK1A1P1
Hg19::chr15:45344875..45344879,+p@chr15:45344875..45344879
+
Hg19::chr15:50086217..50086255,+p1@ENST00000558657
Hg19::chr16:22448582..22448637,+p1@ENST00000309865
Hg19::chr16:52689141..52689186,+p1@ENST00000540332
Hg19::chr16:86469492..86469500,-p@chr16:86469492..86469500
-
Hg19::chr17:74533416..74533417,+p@chr17:74533416..74533417
+
Hg19::chr19:42011981..42012002,+p@chr19:42011981..42012002
+
Hg19::chr19:54705025..54705034,+p7@RPS9
Hg19::chr1:24286287..24286326,+p1@PNRC2
Hg19::chr1:247289721..247289729,+p@chr1:247289721..247289729
+
Hg19::chr20:32990563..32990582,-p1@CDC42P1
Hg19::chr2:171608209..171608242,+p1@EIF2S2P4
Hg19::chr2:240497949..240497953,+p@chr2:240497949..240497953
+
Hg19::chr2:87754989..87755007,+p1@LINC00152
Hg19::chr2:87755107..87755119,+p4@LINC00152
Hg19::chr3:72978005..72978023,+p2@FTH1P23
Hg19::chr4:28829856..28829859,+p@chr4:28829856..28829859
+
Hg19::chr6:127676824..127676831,+p1@YWHAZP4
Hg19::chr7:156971838..156971846,+p@chr7:156971838..156971846
+
Hg19::chr7:5938351..5938379,+p2@CCZ1B
p2@CCZ1
Hg19::chr7:72395617..72395665,+p3@POM121
Hg19::chrX:109590174..109590203,-p1@GNG5P2
Hg19::chrX:43887933..43887952,+p@chrX:43887933..43887952
+
Hg19::chrX:63833271..63833273,-p1@YWHAZP7


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 monocyte8.12e-4742
CD14-positive, CD16-negative classical monocyte8.12e-4742
defensive cell3.83e-4648
phagocyte3.83e-4648
myeloid lineage restricted progenitor cell1.55e-3866
granulocyte monocyte progenitor cell3.58e-3867
macrophage dendritic cell progenitor9.63e-3661
myeloid leukocyte2.06e-3572
stuff accumulating cell5.85e-3487
monopoietic cell1.37e-3359
monocyte1.37e-3359
monoblast1.37e-3359
promonocyte1.37e-3359
myeloid cell1.83e-30108
common myeloid progenitor1.83e-30108
leukocyte1.47e-24136
hematopoietic lineage restricted progenitor cell7.18e-24120
hematopoietic oligopotent progenitor cell6.09e-21161
hematopoietic multipotent progenitor cell6.09e-21161
hematopoietic stem cell1.27e-20168
angioblastic mesenchymal cell1.27e-20168
hematopoietic cell1.83e-18177
nongranular leukocyte2.84e-17115
mesenchymal cell1.50e-07354
stem cell2.30e-07441
multi fate stem cell2.34e-07427
Langerhans cell2.35e-075
connective tissue cell5.47e-07361
somatic stem cell6.47e-07433
Uber Anatomy
Ontology termp-valuen
bone marrow3.93e-3376
bone element2.04e-2982
skeletal element4.16e-2890
immune system4.33e-2793
skeletal system1.62e-23100
hematopoietic system8.99e-2398
blood island8.99e-2398
hemolymphoid system7.16e-21108
musculoskeletal system9.05e-14167
larynx2.15e-109
lateral plate mesoderm4.26e-08203


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)
MA0003.10.12739
MA0004.10.0961566
MA0006.10.134363
MA0007.10.293913
MA0009.10.417521
MA0014.10.115452
MA0017.10.0455998
MA0019.11.02157
MA0024.10.332558
MA0025.11.31752
MA0027.11.95983
MA0028.10.346327
MA0029.10.347825
MA0030.10.338746
MA0031.10.288912
MA0038.10.15256
MA0040.10.352485
MA0041.10.105506
MA0042.10.300789
MA0043.10.417784
MA0046.10.408463
MA0048.10.246211
MA0050.10.301942
MA0051.10.150026
MA0052.10.355576
MA0055.11.20924
MA0056.10
MA0057.10.227938
MA0058.10.0546193
MA0059.10.0541371
MA0060.10.128077
MA0061.10.0324002
MA0063.10
MA0066.10.152817
MA0067.10.697961
MA0068.10.876891
MA0069.10.405267
MA0070.11.02498
MA0071.10.407159
MA0072.10.392323
MA0073.12.4642e-05
MA0074.10.149576
MA0076.10.477402
MA0077.10.386
MA0078.10.612611
MA0081.10.441387
MA0083.10.423797
MA0084.10.873335
MA0087.10.390315
MA0088.10.384887
MA0089.10
MA0090.10.236197
MA0091.10.0974512
MA0092.10.9717
MA0093.10.0341631
MA0095.10
MA0098.10
MA0100.10.161006
MA0101.10.140397
MA0103.10.125753
MA0105.10.0479994
MA0106.10.178189
MA0107.10.0779652
MA0108.20.286605
MA0109.10
MA0111.10.252572
MA0113.10.188804
MA0114.10.191937
MA0115.10.62811
MA0116.10.396969
MA0117.10.449155
MA0119.10.18197
MA0122.10.471243
MA0124.10.590699
MA0125.10.516292
MA0130.10
MA0131.10.642161
MA0132.10
MA0133.10
MA0135.11.97074
MA0136.10.156833
MA0139.10.18088
MA0140.10.128473
MA0141.10.197657
MA0142.10.732627
MA0143.11.05457
MA0144.12.02091
MA0145.10.453463
MA0146.10.450088
MA0147.10.0831159
MA0148.10.352161
MA0149.10.123091
MA0062.20.349972
MA0035.20.128078
MA0039.20.000790471
MA0138.20.214585
MA0002.20.238419
MA0137.21.00246
MA0104.20.127098
MA0047.20.508505
MA0112.20.00150724
MA0065.20.00887985
MA0150.10.495826
MA0151.10
MA0152.10.412817
MA0153.10.501603
MA0154.10.00419164
MA0155.10.0434015
MA0156.10.363341
MA0157.10.245386
MA0158.10
MA0159.10.669283
MA0160.10.116872
MA0161.10
MA0162.10.161648
MA0163.10.12889
MA0164.10.572716
MA0080.20.321686
MA0018.20.529473
MA0099.20.413335
MA0079.24.50322e-05
MA0102.20.908736
MA0258.10.0584056
MA0259.10.0895432
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

No analysis results for this cluster

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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