Personal tools

Coexpression cluster:C443

From FANTOM5_SSTAR

Revision as of 20:01, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C443_CD4_CD8_Natural_Eosinophils_Neutrophils_Peripheral_blood



Phase1 CAGE Peaks

Hg19::chr11:117103208..117103288,-p2@PCSK7
Hg19::chr12:46123273..46123329,+p3@ARID2
Hg19::chr14:91884150..91884234,-p1@CCDC88C
Hg19::chr15:34394292..34394326,+p1@PGBD4
Hg19::chr17:38297024..38297041,-p@chr17:38297024..38297041
-
Hg19::chr1:100818009..100818072,+p1@CDC14A
Hg19::chr1:155533011..155533044,+p1@LOC645676
Hg19::chr1:226926972..226927038,-p1@ITPKB
Hg19::chr1:231473640..231473651,-p3@EXOC8
Hg19::chr2:234160287..234160335,+p1@ATG16L1
Hg19::chr4:54930662..54930701,-p3@CHIC2
Hg19::chr4:78741344..78741385,-p@chr4:78741344..78741385
-
Hg19::chr4:83351124..83351222,-p4@HNRPDL
Hg19::chr6:12009042..12009092,+p6@HIVEP1
Hg19::chr6:38607628..38607651,-p3@BTBD9
Hg19::chr7:130791091..130791104,+p@chr7:130791091..130791104
+
Hg19::chr7:35734730..35734777,-p1@HERPUD2
Hg19::chr7:39989788..39989876,+p1@CDK13
Hg19::chr8:29940544..29940555,-p3@TMEM66
Hg19::chr8:29940569..29940596,-p1@TMEM66
Hg19::chr8:41909898..41909910,-p4@KAT6A
Hg19::chr8:41909982..41910009,-p2@KAT6A


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
hematopoietic stem cell1.83e-47172
angioblastic mesenchymal cell1.83e-47172
leukocyte5.40e-46140
hematopoietic cell7.52e-44182
hematopoietic oligopotent progenitor cell2.78e-43165
hematopoietic multipotent progenitor cell2.78e-43165
hematopoietic lineage restricted progenitor cell5.38e-37124
nongranular leukocyte4.98e-36119
myeloid cell9.08e-23112
common myeloid progenitor9.08e-23112
myeloid leukocyte5.34e-2176
lymphoid lineage restricted progenitor cell2.64e-1952
lymphocyte2.77e-1953
common lymphoid progenitor2.77e-1953
CD14-positive, CD16-negative classical monocyte1.19e-1842
granulocyte monocyte progenitor cell5.35e-1871
myeloid lineage restricted progenitor cell1.26e-1670
classical monocyte2.57e-1645
macrophage dendritic cell progenitor1.13e-1565
monopoietic cell6.64e-1563
monocyte6.64e-1563
monoblast6.64e-1563
promonocyte6.64e-1563
mature alpha-beta T cell2.19e-1218
alpha-beta T cell2.19e-1218
immature T cell2.19e-1218
mature T cell2.19e-1218
immature alpha-beta T cell2.19e-1218
T cell6.66e-1225
pro-T cell6.66e-1225
CD8-positive, alpha-beta T cell2.93e-0811
B cell3.31e-0714
lymphocyte of B lineage3.88e-0724
pro-B cell3.88e-0724
Uber Anatomy
Ontology termp-valuen
adult organism2.10e-26115
hematopoietic system5.60e-22102
blood island5.60e-22102
hemolymphoid system2.64e-21112
bone marrow3.18e-1380
bone element8.11e-1386
neural tube2.83e-1157
neural rod2.83e-1157
future spinal cord2.83e-1157
neural keel2.83e-1157
immune system3.08e-11115
anterior neural tube9.54e-1042
regional part of forebrain1.39e-0941
forebrain1.39e-0941
future forebrain1.39e-0941
regional part of brain1.83e-0859
blood2.78e-0815
haemolymphatic fluid2.78e-0815
organism substance2.78e-0815
gray matter3.19e-0834
brain grey matter3.19e-0834
telencephalon3.48e-0834
regional part of telencephalon5.45e-0833
skeletal element8.53e-08101
skeletal system8.53e-08101
cerebral hemisphere1.15e-0732
central nervous system1.29e-0782
brain1.85e-0769
future brain1.85e-0769


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


No analysis results for this cluster

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.