Personal tools

Coexpression cluster:C1739

From FANTOM5_SSTAR

Revision as of 11:38, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1739_CD14_Mast_Natural_Eosinophils_immature_Melanocyte_CD14CD16



Phase1 CAGE Peaks

Hg19::chr15:45879287..45879319,-p@chr15:45879287..45879319
-
Hg19::chr17:66243950..66243978,-p1@BC056237
Hg19::chr17:66244002..66244037,-p2@BC056237
Hg19::chr19:10514593..10514606,+p@chr19:10514593..10514606
+
Hg19::chr1:115053955..115053993,+p@chr1:115053955..115053993
+


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


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
leukocyte2.33e-45136
hematopoietic cell8.55e-38177
hematopoietic stem cell1.15e-36168
angioblastic mesenchymal cell1.15e-36168
hematopoietic oligopotent progenitor cell1.03e-32161
hematopoietic multipotent progenitor cell1.03e-32161
hematopoietic lineage restricted progenitor cell1.92e-32120
nongranular leukocyte2.27e-32115
myeloid leukocyte2.91e-2272
classical monocyte1.03e-2142
CD14-positive, CD16-negative classical monocyte1.03e-2142
defensive cell6.04e-2048
phagocyte6.04e-2048
granulocyte monocyte progenitor cell6.01e-1967
myeloid cell4.55e-17108
common myeloid progenitor4.55e-17108
macrophage dendritic cell progenitor2.58e-1661
myeloid lineage restricted progenitor cell7.52e-1666
lymphocyte2.94e-1553
common lymphoid progenitor2.94e-1553
lymphoid lineage restricted progenitor cell4.93e-1552
monopoietic cell5.15e-1559
monocyte5.15e-1559
monoblast5.15e-1559
promonocyte5.15e-1559
nucleate cell4.41e-1455
intermediate monocyte5.47e-099
CD14-positive, CD16-positive monocyte5.47e-099
stuff accumulating cell6.89e-0987
mature alpha-beta T cell1.41e-0818
alpha-beta T cell1.41e-0818
immature T cell1.41e-0818
mature T cell1.41e-0818
immature alpha-beta T cell1.41e-0818
granulocyte1.26e-078
T cell1.81e-0725
pro-T cell1.81e-0725
lymphocyte of B lineage7.11e-0724
pro-B cell7.11e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.92e-2198
blood island1.92e-2198
hemolymphoid system1.91e-17108
bone marrow7.21e-1776
bone element5.86e-1682
immune system4.29e-1493
skeletal element1.27e-1290
skeletal system7.21e-10100


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)

{{{tfbs_overrepresentation_jaspar}}}



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#90556.336201576962639.78880505817628e-050.00138998370016434
CEBPB#105146.376918100659850.001113944176677320.00765288882173412
CHD2#110648.275218267293490.0004028373567101730.00387723995000034
E2F6#187655.017155731697390.0003144978599297790.00322682404884627
EGR1#195843.990543275848110.0067800983001440.0287626096254413
HMGN3#932446.542838178680470.00100801277768350.00722007039904583
IRF1#365946.109731002851120.001315525264767990.00880831793352381
MAX#414945.16204440720570.002526309009485180.013997092129529
MXI1#460147.969257303007440.0004668546380070170.00429433076790689
MYC#460955.22228187160940.0002573944848850610.00276393405376423
NANOG#79923211.69791139240510.01091164951956080.0402188729194781
NFKB1#479055.488063424193840.0002008162847462320.00238954676570715
NRF1#489937.326167668626540.004839689817117540.0226884085110844
PAX5#507956.669565531177837.57493746384605e-050.00116977509062046
POU2F2#545247.284899246194020.0006631223288743860.00542502216084224
SIN3A#2594255.408884726815140.0002159522671657270.00247953373246717
SP1#666744.558705102512720.00407573565781680.0194821619463924
SREBF1#6720328.2035096642939.31681575395428e-050.00135483002022728
TBP#690853.706770687096390.001428755106721120.009184891948224
USF1#739145.089199421766370.00266867775360040.0147171842807198
ZBTB33#10009212.66589001199250.009357016059651590.0353392905020776
ZBTB7A#5134145.881527446300720.001524947561042230.00971358857817088
ZNF143#770238.100525931336740.003624870512090980.018329517353165



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.