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{{Coexpression_clusters
{
|full_id=C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils
|gostat_on_coexpression_clusters

Latest revision as of 11:22, 17 September 2013


Full id: C413_CD14_Smooth_gall_mesothelioma_meningioma_Fibroblast_Neutrophils



Phase1 CAGE Peaks

Hg19::chr11:4414880..4414953,-p1@TRIM21
Hg19::chr11:5711010..5711105,+p1@TRIM22
Hg19::chr11:615570..615721,-p2@IRF7
Hg19::chr12:113344755..113344805,+p1@OAS1
Hg19::chr12:113376261..113376324,+p1@OAS3
Hg19::chr12:113376330..113376350,+p3@OAS3
Hg19::chr12:113416191..113416202,+p6@OAS2
Hg19::chr12:113416240..113416251,+p5@OAS2
Hg19::chr12:113416265..113416287,+p3@OAS2
Hg19::chr12:113416311..113416336,+p2@OAS2
Hg19::chr12:113416340..113416363,+p4@OAS2
Hg19::chr12:113416367..113416393,+p1@OAS2
Hg19::chr14:24630902..24630948,+p2@IRF9
Hg19::chr17:4847640..4847689,+p@chr17:4847640..4847689
+
Hg19::chr17:6659354..6659398,+p1@XAF1
Hg19::chr19:17516624..17516640,+p3@FAM125A
Hg19::chr20:62205570..62205609,-p1@PRIC285
Hg19::chr21:42798158..42798174,+p1@MX1
Hg19::chr2:37384085..37384134,-p1@EIF2AK2
Hg19::chr2:7005785..7005864,-p1@CMPK2
Hg19::chr3:122283100..122283153,-p1@PARP9
Hg19::chr3:122399656..122399694,+p1@PARP14
Hg19::chr3:146262365..146262412,-p1@PLSCR1
Hg19::chr3:187086155..187086211,+p1@RTP4
Hg19::chr9:32526172..32526181,-p3@DDX58


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

p.valueFDRnGenesnPathwayName
1.37766611460316e-122.90687550181267e-107135Hepatitis C (KEGG):05160
8.02404527164351e-155.07922065695034e-128134Measles (KEGG):05162
7.38492015576474e-142.33732722929954e-118176Influenza A (KEGG):05164
4.05004898661881e-060.000512736201705942350Type II interferon signaling (IFNG) (Wikipathways):WP619
3.73290025145396e-105.90731464792589e-088511Signaling in Immune system (Reactome):REACT_6900



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:0009615response to virus1.85714517836697e-14
GO:0051707response to other organism4.03157118129478e-12
GO:0009607response to biotic stimulus4.11531196650602e-11
GO:0051704multi-organism process9.61507303276969e-11
GO:0003723RNA binding1.04948661341494e-05
GO:0005792microsome0.0024331112221386
GO:0042598vesicular fraction0.0024331112221386
GO:0003950NAD+ ADP-ribosyltransferase activity0.00417910917080701
GO:0005634nucleus0.00417910917080701
GO:0016779nucleotidyltransferase activity0.00417910917080701
GO:0006955immune response0.00449250958849504
GO:0003676nucleic acid binding0.00519863380303236
GO:0002376immune system process0.00772038312651502
GO:0016763transferase activity, transferring pentosyl groups0.0113341044691317
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0121968044765909
GO:0032553ribonucleotide binding0.0121968044765909
GO:0032555purine ribonucleotide binding0.0121968044765909
GO:0005737cytoplasm0.0133518821572491
GO:0017076purine nucleotide binding0.0136007388506822
GO:0005524ATP binding0.017442046567622
GO:0032559adenyl ribonucleotide binding0.017442046567622
GO:0017128phospholipid scramblase activity0.017442046567622
GO:0004694eukaryotic translation initiation factor 2alpha kinase activity0.017442046567622
GO:0017121phospholipid scrambling0.017442046567622
GO:0006926virus-infected cell apoptosis0.017442046567622
GO:0030554adenyl nucleotide binding0.0185944180558335
GO:0001580detection of chemical stimulus during sensory perception of bitter taste0.020182800670166
GO:0044424intracellular part0.0207146498389662
GO:0050913sensory perception of bitter taste0.0218595978581463
GO:0000166nucleotide binding0.0218595978581463
GO:0005622intracellular0.0221159790034413
GO:0050912detection of chemical stimulus during sensory perception of taste0.0231075963630502
GO:0050907detection of chemical stimulus during sensory perception0.0231075963630502
GO:0016740transferase activity0.0241057480557124
GO:0032606interferon type I production0.0241057480557124
GO:0045351interferon type I biosynthetic process0.0241057480557124
GO:0043231intracellular membrane-bound organelle0.0241057480557124
GO:0043227membrane-bound organelle0.0241057480557124
GO:0006355regulation of transcription, DNA-dependent0.0242975136235004
GO:0005624membrane fraction0.0242975136235004
GO:0006351transcription, DNA-dependent0.0258731915644999
GO:0032774RNA biosynthetic process0.0258731915644999
GO:0007009plasma membrane organization and biogenesis0.0321401529072117
GO:0030968unfolded protein response0.0321401529072117
GO:0045449regulation of transcription0.0323666252050385
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0342513187993206
GO:0006350transcription0.0375499264667628
GO:0004386helicase activity0.0375499264667628
GO:0010468regulation of gene expression0.0375499264667628
GO:0009593detection of chemical stimulus0.0391154881512025
GO:0031323regulation of cellular metabolic process0.0402711693658135
GO:0000267cell fraction0.0402711693658135
GO:0003712transcription cofactor activity0.0403451482669919
GO:0065007biological regulation0.0414568524609404
GO:0006984ER-nuclear signaling pathway0.0414568524609404
GO:0019222regulation of metabolic process0.0467566200919185
GO:0016070RNA metabolic process0.0467566200919185
GO:0030168platelet activation0.0467566200919185
GO:0017111nucleoside-triphosphatase activity0.0470607886633734



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
leukocyte3.67e-38136
nongranular leukocyte9.49e-37115
hematopoietic lineage restricted progenitor cell2.42e-33120
myeloid leukocyte1.64e-2972
hematopoietic stem cell4.42e-27168
angioblastic mesenchymal cell4.42e-27168
monopoietic cell2.54e-2659
monocyte2.54e-2659
monoblast2.54e-2659
promonocyte2.54e-2659
defensive cell2.75e-2648
phagocyte2.75e-2648
hematopoietic oligopotent progenitor cell1.12e-25161
hematopoietic multipotent progenitor cell1.12e-25161
macrophage dendritic cell progenitor6.45e-2561
myeloid lineage restricted progenitor cell2.15e-2466
classical monocyte3.58e-2442
CD14-positive, CD16-negative classical monocyte3.58e-2442
granulocyte monocyte progenitor cell3.96e-2467
hematopoietic cell1.69e-23177
myeloid cell4.30e-15108
common myeloid progenitor4.30e-15108
lymphoid lineage restricted progenitor cell1.81e-1052
lymphocyte2.42e-1053
common lymphoid progenitor2.42e-1053
nucleate cell1.26e-0955
stuff accumulating cell6.28e-0887
Uber Anatomy
Ontology termp-valuen
hemolymphoid system5.60e-29108
hematopoietic system7.64e-2998
blood island7.64e-2998
immune system3.17e-2493
bone marrow3.27e-2176
bone element9.36e-1782
skeletal element5.37e-1590
skeletal system8.14e-14100
lateral plate mesoderm6.82e-10203
adult organism4.57e-07114


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)
MA0003.10.980161
MA0004.10.130779
MA0006.10.194765
MA0007.10.120068
MA0009.10.480543
MA0014.10.123643
MA0017.11.33864
MA0019.10.227177
MA0024.11.79458
MA0025.10.599238
MA0027.12.03861
MA0028.10.467419
MA0029.10.407394
MA0030.10.397801
MA0031.10.344829
MA0038.10.195728
MA0040.10.412311
MA0041.10.141769
MA0042.10.389397
MA0043.10.480818
MA0046.10.47108
MA0048.10.852225
MA0050.131.373
MA0051.126.7492
MA0052.10.41557
MA0055.10.440389
MA0056.10
MA0057.10.378103
MA0058.10.0802423
MA0059.10.273146
MA0060.10.017391
MA0061.12.91115
MA0063.10
MA0066.11.70382
MA0067.10.769322
MA0068.10.618605
MA0069.10.467738
MA0070.10.458064
MA0071.10.170069
MA0072.10.454189
MA0073.10.00266812
MA0074.10.561594
MA0076.10.296049
MA0077.10.44756
MA0078.10.72884
MA0081.10.972974
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.11.10628
MA0089.10
MA0090.10.0951695
MA0091.10.132307
MA0092.10.110943
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.777596
MA0103.10.411939
MA0105.11.26663
MA0106.10.224407
MA0107.10.85764
MA0108.20.342362
MA0109.10
MA0111.10.102187
MA0113.10.236174
MA0114.10.524336
MA0115.10.697973
MA0116.10.299877
MA0117.10.513502
MA0119.10.0722294
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.11.10054
MA0139.10.285737
MA0140.10.168354
MA0141.10.571374
MA0142.10.319458
MA0143.10.665621
MA0144.11.13005
MA0145.10.120776
MA0146.10.850099
MA0147.10.561572
MA0148.10.446835
MA0149.10.162171
MA0062.20.78545
MA0035.20.50217
MA0039.22.20165
MA0138.21.34409
MA0002.20.0700986
MA0137.21.26125
MA0104.20.64251
MA0047.20.215827
MA0112.20.477898
MA0065.20.990205
MA0150.10.307678
MA0151.10
MA0152.10.172601
MA0153.10.567879
MA0154.10.0935732
MA0155.10.625371
MA0156.10.840015
MA0157.10.298026
MA0158.10
MA0159.10.130397
MA0160.10.154993
MA0161.10
MA0162.10.093934
MA0163.10.297942
MA0164.10.245213
MA0080.21.17211
MA0018.20.225392
MA0099.20.989801
MA0079.23.45595
MA0102.20.983247
MA0258.11.07678
MA0259.10.323342
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#1879134.631362760215886.26618592042133e-072.86279173815785e-05
EGR1#1958132.593853129301270.000377785726401510.00374696709208427
ELF1#1997132.214210938579920.001847705895137980.0109277170837712
HEY1#23462142.26246218413920.0008220701032371530.00625910764102829
IRF1#365992.7493789512830.003181199298650190.0166980586797873
IRF4#366265.259483044818590.0007529204584399410.0059266098702901
NFKB1#4790224.829495813290576.96316904821618e-141.10688951632671e-11
POLR2A#5430252.147453176558075.02456472262233e-094.04283909912137e-07
POU2F2#5452145.099429472335815.03322093134357e-083.21901139527613e-06
SPI1#668892.953556463068180.001926757153081220.0113246997754882
STAT1#67722319.05006049742331.42509837352088e-285.29664943174902e-26
STAT2#67732360.04266949152544.88212981441461e-402.8326930871536e-37
STAT3#6774104.20778599886175.1112914742446e-050.000870544961315446
SUZ12#2351236.013893709327550.01315455203308180.0466391098816253
TAF1#6872212.808158880026053.24290519342898e-082.18084852219272e-06
TBP#6908202.965416549677115.02099441389296e-083.2131595318172e-06
YY1#7528163.143149279906472.64335913146096e-069.267196519995e-05
ZBTB33#1000945.066356004796980.007391990141568670.0305469100777624



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C413&oldid=3067530"