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Coexpression cluster:C777: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C777_Neutrophils_Eosinophils_CD19_CD4_CD8_Whole_Natural
|full_id=C777_Neutrophils_Eosinophils_CD19_CD4_CD8_Whole_Natural
|id=C777
|id=C777

Revision as of 18:29, 12 September 2012


Full id: C777_Neutrophils_Eosinophils_CD19_CD4_CD8_Whole_Natural



Phase1 CAGE Peaks

Hg19::chr10:104404775..104404890,+p2@TRIM8
Hg19::chr11:114271463..114271474,+p7@RBM7
Hg19::chr12:12849622..12849654,+p@chr12:12849622..12849654
+
Hg19::chr12:32112340..32112358,+p2@C12orf35
Hg19::chr12:32112527..32112546,+p4@C12orf35
Hg19::chr15:55611128..55611179,+p2@PIGB
Hg19::chr1:176176198..176176259,-p2@RFWD2
Hg19::chr22:40440804..40440859,+p1@TNRC6B
Hg19::chr3:141205852..141205929,+p1@RASA2
Hg19::chr6:159466042..159466066,-p2@TAGAP


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 cell3.87e-53172
angioblastic mesenchymal cell3.87e-53172
leukocyte1.00e-52140
hematopoietic oligopotent progenitor cell5.18e-49165
hematopoietic multipotent progenitor cell5.18e-49165
hematopoietic cell1.37e-47182
hematopoietic lineage restricted progenitor cell4.83e-43124
nongranular leukocyte1.34e-41119
myeloid cell1.82e-24112
common myeloid progenitor1.82e-24112
lymphocyte2.70e-2353
common lymphoid progenitor2.70e-2353
lymphoid lineage restricted progenitor cell4.29e-2352
myeloid leukocyte6.17e-2376
granulocyte monocyte progenitor cell1.72e-1971
myeloid lineage restricted progenitor cell1.25e-1870
CD14-positive, CD16-negative classical monocyte1.64e-1842
macrophage dendritic cell progenitor2.80e-1765
classical monocyte1.59e-1645
monopoietic cell1.92e-1663
monocyte1.92e-1663
monoblast1.92e-1663
promonocyte1.92e-1663
mature alpha-beta T cell4.81e-1218
alpha-beta T cell4.81e-1218
immature T cell4.81e-1218
mature T cell4.81e-1218
immature alpha-beta T cell4.81e-1218
T cell6.07e-1225
pro-T cell6.07e-1225
lymphocyte of B lineage1.57e-1024
pro-B cell1.57e-1024
B cell1.56e-0814
CD8-positive, alpha-beta T cell5.19e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.08e-26102
blood island7.08e-26102
hemolymphoid system2.61e-23112
adult organism1.15e-18115
bone marrow4.82e-1680
bone element2.48e-1486
immune system9.56e-12115
skeletal element3.78e-10101
skeletal system3.78e-10101
blood6.40e-0915
haemolymphatic fluid6.40e-0915
organism substance6.40e-0915


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
CTBP2#1488212.54340006786560.01050432187371690.0388945923622321
E2F1#186973.435172450415530.0009731854789143080.00699556185782445
E2F6#187694.515440158527654.07099158370721e-060.000129506637225342
EGR1#195862.992907456886080.006446587185075730.0280076175806866
ELF1#199793.832288162926781.71269377095518e-050.00039191942319191
GATA1#262345.424123257520180.004321563399478210.0205163761933772
HEY1#2346283.232088834484570.0003859230867685430.00377745278903653
MYC#460973.655597310126580.000654500840128410.00535952746135887
NFKB1#479073.841644396935680.0004759144006094030.00433641808456163
PAX5#507964.00173931870670.001379489661762990.008985438492258
POLR2A#5430102.147453176558070.0004793377491637920.00436342327071536
POU2F2#545265.463674434645510.0002482209573289410.00267781722574912
REST#597865.790017229676810.0001793585011357230.00217510711798814
SIN3A#2594294.867996254133622.10202316614545e-067.66526527405952e-05
TAF1#6872103.343046285745295.73229241267096e-060.00017233013450977
TBP#6908103.706770687096392.04059382584877e-067.45166358663707e-05
TCF7L2#693444.308070625254940.009860462317564680.0370504343941046
YY1#752883.928936599883088.91962924709433e-050.00130616539391094
ZBTB7A#5134153.675954653937950.00645854601955880.0280490721780066



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.