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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:35, 17 September 2013


Full id: C997_testis_Neutrophils_Reticulocytes_embryonic_Basophils_CD14_tridermal



Phase1 CAGE Peaks

Hg19::chr11:64619747..64619758,+p@chr11:64619747..64619758
+
Hg19::chr17:4269248..4269257,-p@chr17:4269248..4269257
-
Hg19::chr17:74732889..74732898,+p19@MFSD11
Hg19::chr19:7621690..7621698,+p@chr19:7621690..7621698
+
Hg19::chr1:179335101..179335112,+p6@AXDND1
Hg19::chr22:40440578..40440589,-p5@BC038752
Hg19::chr3:38181238..38181245,+p10@MYD88
Hg19::chr5:176433664..176433675,-p10@UIMC1


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:0008063Toll signaling pathway0.00581292669125172
GO:0002755MyD88-dependent toll-like receptor signaling pathway0.00581292669125172
GO:0002238response to molecule of fungal origin0.00581292669125172
GO:0005121Toll binding0.00581292669125172
GO:0032760positive regulation of tumor necrosis factor production0.00581292669125172
GO:0002221pattern recognition receptor signaling pathway0.00581292669125172
GO:0002224toll-like receptor signaling pathway0.00581292669125172
GO:0032496response to lipopolysaccharide0.00581292669125172
GO:0032680regulation of tumor necrosis factor production0.00581292669125172
GO:0031663lipopolysaccharide-mediated signaling pathway0.00581292669125172
GO:0002218activation of innate immune response0.00581292669125172
GO:0002758innate immune response-activating signal transduction0.00581292669125172
GO:0045080positive regulation of chemokine biosynthetic process0.00606476986366401
GO:0005123death receptor binding0.00606476986366401
GO:0032606interferon type I production0.00606476986366401
GO:0048661positive regulation of smooth muscle cell proliferation0.00606476986366401
GO:0045351interferon type I biosynthetic process0.00606476986366401
GO:0045073regulation of chemokine biosynthetic process0.00606476986366401
GO:0032602chemokine production0.00606476986366401
GO:0002237response to molecule of bacterial origin0.00606476986366401
GO:0050755chemokine metabolic process0.00606476986366401
GO:0045089positive regulation of innate immune response0.00606476986366401
GO:0042033chemokine biosynthetic process0.00606476986366401
GO:0045088regulation of innate immune response0.00639309001654277
GO:0048660regulation of smooth muscle cell proliferation0.00669511170903356
GO:0046330positive regulation of JNK cascade0.00671557792129226
GO:0032640tumor necrosis factor production0.00671557792129226
GO:0048659smooth muscle cell proliferation0.00697366406672733
GO:0046328regulation of JNK cascade0.00883200757828019
GO:0009620response to fungus0.00883200757828019
GO:0033002muscle cell proliferation0.00899668680374902
GO:0051092activation of NF-kappaB transcription factor0.00971828956965259
GO:0001819positive regulation of cytokine production0.00971828956965259
GO:0051091positive regulation of transcription factor activity0.0123006698922749
GO:0002757immune response-activating signal transduction0.0127450863918242
GO:0002764immune response-regulating signal transduction0.0127779004540503
GO:0042108positive regulation of cytokine biosynthetic process0.0150364740853321
GO:0001817regulation of cytokine production0.0150364740853321
GO:0019221cytokine and chemokine mediated signaling pathway0.0153646976845699
GO:0016064immunoglobulin mediated immune response0.0171711618613322
GO:0051090regulation of transcription factor activity0.0171711618613322
GO:0019724B cell mediated immunity0.0171711618613322
GO:0045727positive regulation of translation0.0171711618613322
GO:0042035regulation of cytokine biosynthetic process0.018571264058464
GO:0031328positive regulation of cellular biosynthetic process0.018571264058464
GO:0007254JNK cascade0.0192787277651109
GO:0042089cytokine biosynthetic process0.0192787277651109
GO:0042107cytokine metabolic process0.0192787277651109
GO:0031098stress-activated protein kinase signaling pathway0.0192787277651109
GO:0009891positive regulation of biosynthetic process0.0192787277651109
GO:0002253activation of immune response0.0192787277651109
GO:0002449lymphocyte mediated immunity0.0192787277651109
GO:0002250adaptive immune response0.01959376415031
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.01959376415031
GO:0002443leukocyte mediated immunity0.0197426010253207
GO:0050778positive regulation of immune response0.0206367145530951
GO:0051247positive regulation of protein metabolic process0.0206367145530951
GO:0002684positive regulation of immune system process0.0206367145530951
GO:0050776regulation of immune response0.0224387813527228
GO:0009615response to virus0.0224387813527228
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0224387813527228
GO:0002682regulation of immune system process0.0224387813527228
GO:0051240positive regulation of multicellular organismal process0.0230377501732489
GO:0009617response to bacterium0.0230377501732489
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0231099484407606
GO:0002252immune effector process0.0231799092542062
GO:0001816cytokine production0.0233135133751135
GO:0045087innate immune response0.0233135133751135
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0275936114911375
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0275936114911375
GO:0000165MAPKKK cascade0.02934836211627
GO:0009967positive regulation of signal transduction0.0295169502447868
GO:0006417regulation of translation0.0349792540799756
GO:0031326regulation of cellular biosynthetic process0.0373030904630282
GO:0051707response to other organism0.0380925236663848
GO:0009889regulation of biosynthetic process0.0395857622340122
GO:0045893positive regulation of transcription, DNA-dependent0.0401448774887949
GO:0008284positive regulation of cell proliferation0.0413951240740178
GO:0051239regulation of multicellular organismal process0.0479245649695406
GO:0045941positive regulation of transcription0.0479245649695406
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0479245649695406
GO:0009607response to biotic stimulus0.0479245649695406
GO:0006954inflammatory response0.0479245649695406
GO:0016481negative regulation of transcription0.0479245649695406



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><br>uberon_data<br>disease_data<br>

Disease
Ontology termp-valuen
lymphoma5.94e-0710


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)
MA0003.10.797136
MA0004.11.15451
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.11.38556
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.11.19384
MA0042.11.12605
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.632427
MA0058.11.69448
MA0059.10.948176
MA0060.11.67203
MA0061.10.497495
MA0063.10
MA0066.11.3723
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.11.05311
MA0074.10.552456
MA0076.10.985027
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.11.07975
MA0093.11.48478
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.586268
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.623945
MA0145.11.25866
MA0146.10.934908
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.942487
MA0035.20.515566
MA0039.22.57832
MA0138.20.653421
MA0002.21.01797
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.458158
MA0065.20.226158
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.974997
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.12.16395
MA0163.10.288263
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.22.50395
MA0102.21.46209
MA0258.10.209744
MA0259.10.699589
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
CHD2#110645.172011417058430.004437884607941780.0210055848886849



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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