Personal tools

Coexpression cluster:C1685: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Coexpression_clusters
{
|full_id=C1685_immature_CD14_Eosinophils_CD34_migratory_lymphoma_Neutrophils
 

Latest revision as of 11:50, 17 September 2013


Full id: C1685_immature_CD14_Eosinophils_CD34_migratory_lymphoma_Neutrophils



Phase1 CAGE Peaks

Hg19::chr12:72148728..72148739,+p3@RAB21
Hg19::chr2:61108695..61108753,+p1@REL
Hg19::chr2:61108771..61108789,+p4@REL
Hg19::chr2:61108808..61108821,+p3@REL
Hg19::chr2:61118914..61118929,+p1@AB464350


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
2.08996656875732e-050.01322948838023382131IL-5 up reg. targets (Netpath):NetPath_17



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

No GOStat results

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-49136
hematopoietic stem cell1.71e-42168
angioblastic mesenchymal cell1.71e-42168
hematopoietic oligopotent progenitor cell3.31e-40161
hematopoietic multipotent progenitor cell3.31e-40161
hematopoietic cell1.91e-39177
hematopoietic lineage restricted progenitor cell1.96e-38120
nongranular leukocyte3.59e-37115
myeloid leukocyte1.68e-3372
granulocyte monocyte progenitor cell4.96e-3067
myeloid cell4.31e-28108
common myeloid progenitor4.31e-28108
defensive cell3.44e-2748
phagocyte3.44e-2748
myeloid lineage restricted progenitor cell5.40e-2766
macrophage dendritic cell progenitor9.33e-2761
monopoietic cell2.03e-2559
monocyte2.03e-2559
monoblast2.03e-2559
promonocyte2.03e-2559
classical monocyte3.58e-2542
CD14-positive, CD16-negative classical monocyte3.58e-2542
lymphocyte6.84e-1153
common lymphoid progenitor6.84e-1153
lymphoid lineage restricted progenitor cell1.08e-1052
nucleate cell3.14e-1055
stuff accumulating cell1.32e-0887
dendritic cell9.64e-0810
lymphocyte of B lineage7.54e-0724
pro-B cell7.54e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.61e-2998
blood island1.61e-2998
hemolymphoid system1.08e-28108
immune system1.40e-2493
bone marrow2.53e-2376
bone element3.52e-2282
skeletal element3.89e-1990
skeletal system4.16e-14100


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)
MA0003.14.3611
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.45664
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.554727
MA0058.11.29981
MA0059.10.522232
MA0060.10.321781
MA0061.14.98588
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.49156
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.11.15584
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.15.23994
MA0103.10.442769
MA0105.15.61073
MA0106.10.779931
MA0107.15.76816
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.11.39016
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.82062
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.8814
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.22.6393
MA0065.21.41695
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.77901
MA0160.10.669748
MA0161.10
MA0162.14.22787
MA0163.16.71536
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.24.80311
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CCNT2#90545.068961261570110.002709998091280770.0148923699371361
CTCF#1066444.288205098460020.005152015588243280.0239259796354013
E2F1#186943.925911371903460.007214984547106360.0298709970314454
E2F4#187437.600836189170660.004354147360375710.0206476024414402
E2F6#187644.013724585357910.006632118233933880.0282899769740982
EGR1#195854.988179094810140.0003237398000590710.00330541215938697
ETS1#211335.83725655332140.009253279045631430.03496899733126
MEF2A#4205311.24593854578640.001399366787411950.00910128707874682
MYC#460944.177825497287520.005691969036823440.0256732262680546
NFKB1#479055.488063424193840.0002008162847462320.00238873029186921
POU2F2#545235.463674434645510.01115650094469780.0410070318210491
REST#597835.790017229676810.009468788694433940.0356917321419853
RFX5#599337.228746496317060.00502918278958660.0234640527746989
SMARCB1#6598414.60217262492594.30486693344344e-050.00076814624579173
TAF7#687936.859841642954350.005843286407019040.0262412705995296
TCF12#693836.380678941311850.007185168653258840.0298267748709289
TFAP2A#702039.911180623826970.002021546977511280.0117450125046896
TFAP2C#702236.485537165916130.006858951517940.0290569925600185
YY1#752843.928936599883080.007193866269917620.0298356047718182



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:C1685&oldid=3068802"