Personal tools

Coexpression cluster:C4333: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C4333_CD14_Mesenchymal_Eosinophils_CD14CD16_Smooth_xeroderma_Monocytederived
|

Latest revision as of 12:43, 17 September 2013


Full id: C4333_CD14_Mesenchymal_Eosinophils_CD14CD16_Smooth_xeroderma_Monocytederived



Phase1 CAGE Peaks

Hg19::chr3:48507621..48507689,+p1@TREX1
Hg19::chr6:37401042..37401063,+p2@FTSJD2
Hg19::chr6:37401066..37401079,+p4@FTSJD2


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:00082963'-5'-exodeoxyribonuclease activity0.00191754554170662
GO:0008853exodeoxyribonuclease III activity0.00191754554170662
GO:0032405MutLalpha complex binding0.00191754554170662
GO:0032407MutSalpha complex binding0.00191754554170662
GO:0016895exodeoxyribonuclease activity, producing 5'-phosphomonoesters0.00191754554170662
GO:0032404mismatch repair complex binding0.00191754554170662
GO:0004529exodeoxyribonuclease activity0.00191754554170662
GO:0016796exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters0.00461409395973154
GO:00084083'-5' exonuclease activity0.00503355704697986
GO:0004536deoxyribonuclease activity0.00838926174496644
GO:0003697single-stranded DNA binding0.00922818791946309
GO:0004527exonuclease activity0.00922818791946309
GO:0006298mismatch repair0.00922818791946309
GO:0045005maintenance of fidelity during DNA-dependent DNA replication0.00922818791946309
GO:0032403protein complex binding0.0112975391498881
GO:0042803protein homodimerization activity0.0153803131991051
GO:0043566structure-specific DNA binding0.0153803131991051
GO:0006261DNA-dependent DNA replication0.0153803131991051
GO:0005635nuclear envelope0.0165268456375839
GO:0006310DNA recombination0.0165268456375839
GO:0004518nuclease activity0.0196548418024928
GO:0006260DNA replication0.0255872483221476
GO:0042802identical protein binding0.0255872483221476
GO:0046983protein dimerization activity0.0255872483221476
GO:0006281DNA repair0.0263087248322147
GO:0000287magnesium ion binding0.0278399204573701
GO:0006974response to DNA damage stimulus0.0278399204573701
GO:0009719response to endogenous stimulus0.0316994247363375
GO:0031967organelle envelope0.0348993288590604
GO:0031975envelope0.0348993288590604



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
leukocyte1.48e-56136
nongranular leukocyte2.74e-51115
hematopoietic lineage restricted progenitor cell6.17e-48120
hematopoietic stem cell2.24e-45168
angioblastic mesenchymal cell2.24e-45168
hematopoietic cell8.26e-44177
hematopoietic oligopotent progenitor cell9.80e-42161
hematopoietic multipotent progenitor cell9.80e-42161
myeloid leukocyte4.19e-3172
macrophage dendritic cell progenitor2.08e-3061
monopoietic cell4.42e-3059
monocyte4.42e-3059
monoblast4.42e-3059
promonocyte4.42e-3059
granulocyte monocyte progenitor cell3.79e-2967
myeloid lineage restricted progenitor cell5.70e-2866
defensive cell1.35e-2648
phagocyte1.35e-2648
classical monocyte3.16e-2642
CD14-positive, CD16-negative classical monocyte3.16e-2642
myeloid cell6.49e-22108
common myeloid progenitor6.49e-22108
lymphocyte1.03e-1853
common lymphoid progenitor1.03e-1853
nucleate cell1.98e-1855
lymphoid lineage restricted progenitor cell2.24e-1852
lymphocyte of B lineage2.62e-1124
pro-B cell2.62e-1124
stuff accumulating cell9.70e-1187
mesenchymal cell4.17e-10354
connective tissue cell4.92e-09361
motile cell1.62e-08386
B cell1.41e-0714
T cell1.99e-0725
pro-T cell1.99e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.02e-3598
blood island4.02e-3598
hemolymphoid system5.83e-34108
immune system3.11e-2993
bone marrow3.23e-2876
bone element9.10e-2582
skeletal element1.15e-2090
skeletal system8.68e-18100
lateral plate mesoderm8.83e-13203
adult organism2.45e-09114
connective tissue2.19e-08371
musculoskeletal system2.80e-07167


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.12.94978
MA0046.11.31611
MA0048.11.62115
MA0050.13.16043
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.11.70328
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.12.1667
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.22.26143
MA0099.20.902716
MA0079.20.69213
MA0102.21.88331
MA0258.12.22591
MA0259.10.575594
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
ATF3#467322.46317452600878.81932387510763e-050.00129931071546391
BRCA1#672213.45615376214920.007119807716084560.029637912952296
E2F6#187635.017155731697390.00791769806886330.0323507088382307
EGR1#195834.988179094810140.008056488137383440.0321726595258743
ELF1#199734.258097958807540.01295179875054610.0463959152703921
FOSL2#2355211.28680040304110.0100534586973120.0376888320789893
HNF4A#3172215.42152690863580.005444210486686610.0246857942525534
IRF4#3662321.91451268674419.49854535978121e-050.00137132786678213
MAX#414936.452555509007120.003721913834265510.0187124131775312
MEF2A#4205212.4954872730960.008235029478029740.0324954941495427
MEF2C#4208227.54090299508270.001729119938369690.0106509912853667
MYC#460935.22228187160940.007020843755740150.0295474653854669
NFKB1#479035.488063424193840.006049381815655430.0270331345447451
NR3C1#290829.982015554115360.01278474365547170.0460613302964609
PAX5#507936.669565531177830.003370290999677260.0173411085681
POU2F2#545239.106124057742520.001324165192682130.0088417932714359
SIX5#147912211.3911435703060.009873820081429030.0370859489133412
SP1#666735.69838137814090.005403962701712170.024737429787601
SPI1#668838.204323508522730.001810593189410520.0109285408373603
STAT1#6772213.80439166479950.006770931708444080.0287599372335363
STAT2#6773243.50918079096040.0006968990898868230.00560994635799984
TCF12#6938310.63446490218640.0008313523990202070.00630679256201579
USF1#739136.361499277207960.00388404057290560.0190882929459173
YY1#752834.911170749853860.008441455341808260.0330490761149765
ZEB1#6935211.25895467836260.01010222676646330.0378227804718644



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:C4333&oldid=3071450"