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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:04, 17 September 2013


Full id: C244_CD14_Monocytederived_Hepatocyte_heart_Neutrophils_acute_Macrophage



Phase1 CAGE Peaks

Hg19::chr10:81025241..81025245,+p@chr10:81025241..81025245
+
Hg19::chr10:81111074..81111077,+p@chr10:81111074..81111077
+
Hg19::chr11:104815548..104815551,-p@chr11:104815548..104815551
-
Hg19::chr12:56046384..56046387,+p@chr12:56046384..56046387
+
Hg19::chr12:89431933..89431936,-p@chr12:89431933..89431936
-
Hg19::chr14:100828867..100828870,-p@chr14:100828867..100828870
-
Hg19::chr14:55603238..55603250,+p15@LGALS3
Hg19::chr16:21623958..21623973,+p@chr16:21623958..21623973
+
Hg19::chr16:31360617..31360620,-p@chr16:31360617..31360620
-
Hg19::chr16:31381019..31381027,+p@chr16:31381019..31381027
+
Hg19::chr16:31926633..31926654,+p@chr16:31926633..31926654
+
Hg19::chr16:50706590..50706610,-p@chr16:50706590..50706610
-
Hg19::chr17:54976102..54976122,-p@chr17:54976102..54976122
-
Hg19::chr17:75352671..75352704,+p@chr17:75352671..75352704
+
Hg19::chr19:40972117..40972122,-p4@BLVRB
Hg19::chr19:4569647..4569651,+p@chr19:4569647..4569651
+
Hg19::chr19:6663476..6663487,-p8@AK026704
Hg19::chr19:6663488..6663497,-p5@AK026704
Hg19::chr19:6663518..6663558,-p2@AK026704
Hg19::chr19:6663572..6663662,-p1@AK026704
Hg19::chr19:6663833..6663841,-p6@AK026704
Hg19::chr19:6663876..6663885,-p7@AK026704
Hg19::chr1:145038845..145038849,-p@chr1:145038845..145038849
-
Hg19::chr1:154435643..154435648,+p@chr1:154435643..154435648
+
Hg19::chr1:159787777..159787780,-p@chr1:159787777..159787780
-
Hg19::chr1:25362175..25362187,+p@chr1:25362175..25362187
+
Hg19::chr1:25362249..25362302,+p@chr1:25362249..25362302
+
Hg19::chr1:25362605..25362625,+p@chr1:25362605..25362625
+
Hg19::chr20:39690091..39690102,+p@chr20:39690091..39690102
+
Hg19::chr20:48809000..48809053,+p12@CEBPB
Hg19::chr21:30613305..30613309,+p@chr21:30613305..30613309
+
Hg19::chr22:36632299..36632310,-p@chr22:36632299..36632310
-
Hg19::chr2:240202309..240202321,+p@chr2:240202309..240202321
+
Hg19::chr2:240202391..240202405,+p@chr2:240202391..240202405
+
Hg19::chr2:240202435..240202445,+p@chr2:240202435..240202445
+
Hg19::chr2:240202757..240202766,+p@chr2:240202757..240202766
+
Hg19::chr2:87781799..87781811,+p@chr2:87781799..87781811
+
Hg19::chr2:87781831..87781841,+p@chr2:87781831..87781841
+
Hg19::chr3:122399875..122399886,+p7@PARP14
Hg19::chr3:122444648..122444658,+p@chr3:122444648..122444658
+
Hg19::chr3:15483499..15483511,+p@chr3:15483499..15483511
+
Hg19::chr3:196044455..196044479,-p@chr3:196044455..196044479
-
Hg19::chr5:55160032..55160047,+p@chr5:55160032..55160047
+
Hg19::chr5:55160483..55160494,+p@chr5:55160483..55160494
+
Hg19::chr6:74410846..74410849,+p@chr6:74410846..74410849
+
Hg19::chr6:74492716..74492719,+p@chr6:74492716..74492719
+
Hg19::chr6:74512050..74512056,+p@chr6:74512050..74512056
+
Hg19::chr7:130575788..130575792,-p@chr7:130575788..130575792
-
Hg19::chr7:47513678..47513702,+p@chr7:47513678..47513702
+
Hg19::chr7:47514268..47514279,+p@chr7:47514268..47514279
+
Hg19::chr8:20094845..20094867,+p@chr8:20094845..20094867
+
Hg19::chr8:24250424..24250429,+p@chr8:24250424..24250429
+
Hg19::chr8:62606823..62606835,-p@chr8:62606823..62606835
-
Hg19::chr9:90343853..90343856,+p@chr9:90343853..90343856
+
Hg19::chrX:118129290..118129323,+p@chrX:118129290..118129323
+


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:0042602flavin reductase activity0.0151883084852404
GO:0004074biliverdin reductase activity0.0151883084852404
GO:0001892embryonic placenta development0.0189828707762266
GO:0019863IgE binding0.0189828707762266
GO:0045408regulation of interleukin-6 biosynthetic process0.0220784317266505
GO:0042226interleukin-6 biosynthetic process0.0220784317266505
GO:0032635interleukin-6 production0.0220784317266505
GO:0001890placenta development0.0220784317266505
GO:0045444fat cell differentiation0.0220784317266505
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.0220784317266505
GO:0019865immunoglobulin binding0.0220784317266505
GO:0005737cytoplasm0.0252768643803778
GO:0006953acute-phase response0.0368338048269068
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.0368338048269068
GO:0003950NAD+ ADP-ribosyltransferase activity0.0384159270903756
GO:0001701in utero embryonic development0.0463558843129863
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0463558843129863



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 monocyte2.30e-13542
CD14-positive, CD16-negative classical monocyte2.30e-13542
defensive cell9.49e-11848
phagocyte9.49e-11848
monopoietic cell4.45e-9359
monocyte4.45e-9359
monoblast4.45e-9359
promonocyte4.45e-9359
macrophage dendritic cell progenitor6.81e-9061
myeloid lineage restricted progenitor cell9.19e-8366
granulocyte monocyte progenitor cell1.84e-8167
myeloid leukocyte1.71e-7572
stuff accumulating cell1.99e-6287
nongranular leukocyte5.98e-55115
hematopoietic lineage restricted progenitor cell2.76e-49120
myeloid cell1.15e-48108
common myeloid progenitor1.15e-48108
leukocyte1.25e-45136
hematopoietic stem cell7.17e-36168
angioblastic mesenchymal cell7.17e-36168
hematopoietic oligopotent progenitor cell2.54e-35161
hematopoietic multipotent progenitor cell2.54e-35161
hematopoietic cell9.33e-34177
mesenchymal cell6.99e-14354
connective tissue cell1.71e-13361
motile cell4.04e-12386
multi fate stem cell1.94e-10427
somatic stem cell3.31e-10433
stem cell6.61e-10441
Uber Anatomy
Ontology termp-valuen
bone marrow2.81e-7176
bone element1.03e-6582
skeletal element1.97e-5990
hematopoietic system8.96e-5898
blood island8.96e-5898
immune system2.37e-5793
skeletal system5.61e-53100
hemolymphoid system6.09e-52108
musculoskeletal system1.61e-29167
lateral plate mesoderm5.33e-25203
mesoderm5.59e-14315
mesoderm-derived structure5.59e-14315
presumptive mesoderm5.59e-14315
connective tissue5.82e-13371


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)
MA0003.11.93026e-09
MA0004.11.09542
MA0006.10.284086
MA0007.10.218714
MA0009.11.89774
MA0014.13.90292e-06
MA0017.10.100529
MA0019.10.49919
MA0024.10.166016
MA0025.10.326531
MA0027.11.69857
MA0028.10.0803158
MA0029.10.177433
MA0030.10.170622
MA0031.10.134441
MA0038.10.0493765
MA0040.10.180954
MA0041.10.112944
MA0042.11.03598
MA0043.10.231848
MA0046.10.224416
MA0048.10.00191219
MA0050.11.03988
MA0051.10.406356
MA0052.10.183297
MA0055.16.84479e-05
MA0056.10
MA0057.10.0127133
MA0058.10.259805
MA0059.10.124055
MA0060.10.000350333
MA0061.10.00658749
MA0063.10
MA0066.10.18562
MA0067.10.473069
MA0068.10.672849
MA0069.10.221881
MA0070.10.61459
MA0071.10.623423
MA0072.10.211675
MA0073.14.38676
MA0074.10.180446
MA0076.10.0521825
MA0077.10.206727
MA0078.11.49866
MA0081.10.0442917
MA0083.10.236667
MA0084.10.635217
MA0087.10.603971
MA0088.10.00146476
MA0089.10
MA0090.10.318978
MA0091.11.10714
MA0092.10.0764316
MA0093.10.970565
MA0095.10
MA0098.10
MA0100.10.439549
MA0101.10.00403286
MA0103.10.262976
MA0105.10.0190813
MA0106.10.0633877
MA0107.10.0728099
MA0108.20.132819
MA0109.10
MA0111.10.175655
MA0113.10.244544
MA0114.10.140124
MA0115.10.410377
MA0116.10.00832495
MA0117.10.257218
MA0119.10.0374928
MA0122.10.275391
MA0124.10.377376
MA0125.10.841458
MA0130.10
MA0131.10.0923922
MA0132.10
MA0133.10
MA0135.10.252217
MA0136.10.0516336
MA0139.10.00486906
MA0140.10.147406
MA0141.10.122253
MA0142.10.756679
MA0143.10.244737
MA0144.10.509186
MA0145.10.000216889
MA0146.10.000266726
MA0147.10.160617
MA0148.10.117777
MA0149.10.139176
MA0062.20.0182116
MA0035.20.146798
MA0039.27.10127e-06
MA0138.20.085046
MA0002.20.212375
MA0137.21.08271
MA0104.20.144377
MA0047.23.52821
MA0112.20.0228832
MA0065.20.0315229
MA0150.10.792279
MA0151.10
MA0152.10.352609
MA0153.10.813475
MA0154.10.00758814
MA0155.10.00374263
MA0156.10.0876463
MA0157.10.696111
MA0158.10
MA0159.10.0802588
MA0160.10.306739
MA0161.10
MA0162.11.5748e-05
MA0163.10.00039778
MA0164.10.0743389
MA0080.20.157839
MA0018.20.228368
MA0099.20.634771
MA0079.20
MA0102.20.668584
MA0258.10.190476
MA0259.10.175745
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
FOSL1#806153.610325428761180.01239412647262730.0448722631356719
STAT2#677344.746456086286590.01009488904461830.03780479478381



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

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