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

Latest revision as of 11:22, 17 September 2013


Full id: C411_vagina_Mast_breast_heart_CD14_aorta_liver



Phase1 CAGE Peaks

Hg19::chr11:133904003..133904027,-p@chr11:133904003..133904027
-
Hg19::chr11:133907166..133907180,+p2@ENST00000531938
Hg19::chr11:133907234..133907249,+p3@ENST00000531938
Hg19::chr11:133907376..133907387,+p5@ENST00000531938
Hg19::chr11:65374430..65374474,-p5@MAP3K11
Hg19::chr12:2903742..2903763,-p3@CBX3P4
Hg19::chr12:2903775..2903794,-p2@CBX3P4
Hg19::chr12:57082286..57082368,+p@chr12:57082286..57082368
+
Hg19::chr13:31736027..31736053,-p1@HSPH1
Hg19::chr14:70195360..70195363,-p@chr14:70195360..70195363
-
Hg19::chr14:77924458..77924475,+p2@AHSA1
Hg19::chr16:87378830..87378846,-p@chr16:87378830..87378846
-
Hg19::chr16:89930250..89930272,-p1@AK098674
Hg19::chr16:89930279..89930301,-p2@AK098674
Hg19::chr18:19284854..19284899,+p2@MIB1
Hg19::chr19:14629195..14629216,-p1@DNAJB1
Hg19::chr1:245026181..245026208,-p19@HNRNPU
Hg19::chr22:43041411..43041417,+p@chr22:43041411..43041417
+
Hg19::chr4:88343933..88343946,+p6@NUDT9
Hg19::chr6:31783311..31783328,+p1@HSPA1A
p1@HSPA1B
Hg19::chr6:31789738..31789757,-p@chr6:31789738..31789757
-
Hg19::chr6:31795506..31795525,+p2@HSPA1A
p2@HSPA1B
Hg19::chr7:75923952..75923971,-p@chr7:75923952..75923971
-
Hg19::chr7:75924283..75924306,+p@chr7:75924283..75924306
+
Hg19::chr7:75931755..75931775,-p@chr7:75931755..75931775
-


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
2.54761513593594e-050.0161264038104745232{HSPA8,34} (Static Module):NA



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:0051789response to protein stimulus5.16481965377491e-05
GO:0006986response to unfolded protein5.16481965377491e-05
GO:0009607response to biotic stimulus0.00408991908245404
GO:0006950response to stress0.0113033427993079
GO:0030189chaperone activator activity0.0131932179441893
GO:0042221response to chemical stimulus0.0167213722932249
GO:0019144ADP-sugar diphosphatase activity0.0183373558696005
GO:0005737cytoplasm0.0183373558696005
GO:0047631ADP-ribose diphosphatase activity0.0197851668314843
GO:0004706JUN kinase kinase kinase activity0.0197851668314843
GO:0051082unfolded protein binding0.0273491196999661
GO:0001671ATPase activator activity0.0274729278152382
GO:0005739mitochondrion0.0320692916310955
GO:0001947heart looping0.0320692916310955
GO:0044424intracellular part0.0320692916310955
GO:0045665negative regulation of neuron differentiation0.0320692916310955
GO:0051085chaperone cofactor-dependent protein folding0.0320692916310955
GO:0016071mRNA metabolic process0.0320692916310955
GO:0044444cytoplasmic part0.0320692916310955
GO:0006457protein folding0.0320692916310955
GO:0005524ATP binding0.0320692916310955
GO:0032559adenyl ribonucleotide binding0.0320692916310955
GO:0003007heart morphogenesis0.0320692916310955
GO:0051084'de novo' posttranslational protein folding0.0320692916310955
GO:0001839neural plate morphogenesis0.0320692916310955
GO:0051087chaperone binding0.0320692916310955
GO:0001841neural tube formation0.0320692916310955
GO:0006458'de novo' protein folding0.0320692916310955
GO:0001840neural plate development0.0320692916310955
GO:0000080G1 phase of mitotic cell cycle0.0320692916310955
GO:0001838embryonic epithelial tube formation0.0320692916310955
GO:0045807positive regulation of endocytosis0.0320692916310955
GO:0030530heterogeneous nuclear ribonucleoprotein complex0.0320692916310955
GO:0004709MAP kinase kinase kinase activity0.0320692916310955
GO:0001756somitogenesis0.0320692916310955
GO:0030554adenyl nucleotide binding0.0320692916310955
GO:0046328regulation of JNK cascade0.0320692916310955
GO:0051318G1 phase0.0320692916310955
GO:0021915neural tube development0.0320692916310955
GO:0007257activation of JNK activity0.0343930784770196
GO:0016331morphogenesis of embryonic epithelium0.0343930784770196
GO:0043229intracellular organelle0.0343930784770196
GO:0043226organelle0.0343930784770196
GO:0043507positive regulation of JNK activity0.0343930784770196
GO:0043506regulation of JNK activity0.0365444265241635
GO:0045664regulation of neuron differentiation0.0371756059842438
GO:0035282segmentation0.037779597917854
GO:0006402mRNA catabolic process0.0397233584196399
GO:0005227calcium activated cation channel activity0.0446830244551175
GO:0030100regulation of endocytosis0.0446830244551175
GO:0032553ribonucleotide binding0.0447701239990005
GO:0032555purine ribonucleotide binding0.0447701239990005
GO:0051050positive regulation of transport0.047090896044346
GO:0017076purine nucleotide binding0.0491008753794253



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 monocyte7.51e-0742
CD14-positive, CD16-negative classical monocyte7.51e-0742
Uber Anatomy
Ontology termp-valuen
adult organism1.99e-41114
neural tube2.64e-2656
neural rod2.64e-2656
future spinal cord2.64e-2656
neural keel2.64e-2656
regional part of nervous system7.07e-2453
regional part of brain7.07e-2453
neurectoderm3.22e-2086
neural plate5.62e-2082
presumptive neural plate5.62e-2082
brain1.05e-1668
future brain1.05e-1668
regional part of forebrain1.49e-1641
forebrain1.49e-1641
anterior neural tube1.49e-1641
future forebrain1.49e-1641
central nervous system1.53e-1581
nervous system2.03e-1489
brainstem4.30e-146
ecto-epithelium5.60e-14104
brain grey matter7.78e-1334
gray matter7.78e-1334
telencephalon1.09e-1234
posterior neural tube2.17e-1115
chordal neural plate2.17e-1115
structure with developmental contribution from neural crest5.12e-11132
pre-chordal neural plate1.14e-1061
regional part of telencephalon2.53e-1032
cerebral hemisphere4.45e-1032
neural nucleus5.51e-099
nucleus of brain5.51e-099
segmental subdivision of hindbrain6.56e-0912
hindbrain6.56e-0912
presumptive hindbrain6.56e-0912
medulla oblongata2.15e-083
myelencephalon2.15e-083
future myelencephalon2.15e-083
segmental subdivision of nervous system3.89e-0813
regional part of cerebral cortex6.99e-0822
organ system subdivision9.09e-08223
pons2.18e-073
organ3.45e-07503
ectoderm-derived structure3.71e-07171
ectoderm3.71e-07171
presumptive ectoderm3.71e-07171
neocortex5.08e-0720
tube7.55e-07192
cerebral cortex9.50e-0725
pallium9.50e-0725


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)
MA0003.11.32414
MA0004.10.812914
MA0006.10.194765
MA0007.10.120068
MA0009.10.480543
MA0014.12.54242
MA0017.10.242343
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.11.23143
MA0029.10.407394
MA0030.10.397801
MA0031.10.344829
MA0038.11.7022
MA0040.10.412311
MA0041.10.141769
MA0042.10.123063
MA0043.10.480818
MA0046.10.47108
MA0048.10.128228
MA0050.10.390696
MA0051.10.562815
MA0052.10.41557
MA0055.10.601885
MA0056.10
MA0057.11.0874
MA0058.10.274844
MA0059.10.273146
MA0060.11.7471
MA0061.11.52142
MA0063.10
MA0066.10.570377
MA0067.10.769322
MA0068.12.41944
MA0069.10.467738
MA0070.10.458064
MA0071.10.170069
MA0072.10.454189
MA0073.13.45441
MA0074.10.561594
MA0076.11.03285
MA0077.11.1369
MA0078.10.263604
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.13.66743
MA0089.10
MA0090.10.0951695
MA0091.10.132307
MA0092.10.357807
MA0093.10.766566
MA0095.10
MA0098.10
MA0100.10.592379
MA0101.11.18678
MA0103.10.049017
MA0105.12.34733
MA0106.11.19314
MA0107.10.539977
MA0108.21.62457
MA0109.10
MA0111.10.102187
MA0113.10.665323
MA0114.10.118114
MA0115.10.697973
MA0116.10.550701
MA0117.10.513502
MA0119.10.916487
MA0122.10.53644
MA0124.10.659634
MA0125.10.583056
MA0130.10
MA0131.12.1352
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.581198
MA0139.10.748833
MA0140.10.168354
MA0141.10.270862
MA0142.10.319458
MA0143.10.236302
MA0144.13.65785
MA0145.12.24107
MA0146.11.46595
MA0147.10.306717
MA0148.10.145617
MA0149.10.94608
MA0062.20.78545
MA0035.20.167901
MA0039.27.97659
MA0138.20.264522
MA0002.20.359117
MA0137.23.5878
MA0104.20.200815
MA0047.20.215827
MA0112.20.10763
MA0065.20.535761
MA0150.10.307678
MA0151.10
MA0152.10.172601
MA0153.10.567879
MA0154.10.488003
MA0155.10.625371
MA0156.10.487034
MA0157.10.298026
MA0158.10
MA0159.10.563553
MA0160.10.154993
MA0161.10
MA0162.12.01892
MA0163.10.870896
MA0164.10.245213
MA0080.20.438824
MA0018.20.640077
MA0099.20.172833
MA0079.210.7306
MA0102.20.983247
MA0258.10.0222068
MA0259.11.78654
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
BRCA1#67254.036846128644750.006892546890970770.0291874753576652
CCNT2#905143.548272883099084.62126213135399e-060.00014368561945117
EBF1#1879103.56258673862760.0002092504843153790.00243687682107648
EGR1#1958132.593853129301270.000377785726401510.00374661128854309
EP300#203392.438619021440350.007171248819054740.0297784603162204
GATA3#262566.536763925729440.0002368283656653750.00257942618434937
GTF2B#295967.666519184237829.94934489292016e-050.00140040381573004
GTF2F1#296273.567105045492140.002484878598094690.0139555945314267
HMGN3#9324123.925702907208281.23148160281096e-050.000304197509735037
HSF1#32971172.28789333333331.66913017282451e-183.78961491564389e-16
IRF1#3659123.665838601710672.49394930213504e-050.000539936921985244
MXI1#460193.586165786353350.0004703238892508280.00431825553138173
NFKB1#4790122.634270443613040.0006484616231784390.00531340683062396
POLR2A#5430211.803860668308780.0001299031054458090.00171062292644747
PPARGC1A#108918112.0163636363644.35959567622917e-157.71714936999488e-13
PRDM1#639315.81971469329530.0008842492462514420.0065926689769599
RDBP#7936424.5821446384042.02574085028561e-050.000449471741370254
SIN3A#25942102.163553890726050.01004308775449890.0376540078256789
SRF#672263.311322782920270.00771352676699060.0317512621006515
STAT1#677254.141317499439840.006195451371514410.027376634050755
STAT2#6773410.44220338983050.0005379670924503480.00464797693319176
STAT3#6774104.20778599886175.1112914742446e-050.000870403016922602
TAF1#6872162.139549622876990.0004368871040772260.00407247878103547
TAF7#687983.658582209575650.000947062513460020.00685258846080443
TBP#6908131.927520757290120.006834711734069660.0289825189327419
TCF12#693872.97765017261220.006801290727968670.0288419685860939
TFAP2C#702283.458953155155270.001368070086251090.0090014409209335
ZBTB33#1000945.066356004796980.007391990141568670.0305457014479422



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:C411&oldid=3067528"