Personal tools

Coexpression cluster:C623: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|gostat_on_coexpression_clusters=GO:0035300!inositol trisphosphate 5/6-kinase activity!0.0113730683144134!3705$GO:0043647!inositol phosphate metabolic process!0.0113730683144134!3705$GO:0051765!inositol tetrakisphosphate kinase activity!0.0113730683144134!3705$GO:0032957!inositol trisphosphate metabolic process!0.0113730683144134!3705$GO:0047325!inositol tetrakisphosphate 1-kinase activity!0.0113730683144134!3705$GO:0022610!biological adhesion!0.0142547691685994!3684;50856;397$GO:0007155!cell adhesion!0.0142547691685994!3684;50856;397$GO:0001948!glycoprotein binding!0.0213169715519573!3684$GO:0048268!clathrin cage assembly!0.0227340873511213!8301$GO:0006901!vesicle coating!0.0227340873511213!8301$GO:0006900!membrane budding!0.02324871800575!8301$GO:0030276!clathrin binding!0.0260425749057417!8301$GO:0006020!inositol metabolic process!0.0266215290817958!3705$GO:0051766!inositol trisphosphate kinase activity!0.0266215290817958!3705$GO:0031410!cytoplasmic vesicle!0.0266215290817958!8301;397$GO:0031982!vesicle!0.0266215290817958!8301;397$GO:0016050!vesicle organization and biogenesis!0.0266215290817958!8301$GO:0000287!magnesium ion binding!0.0266215290817958!3705;3684$GO:0005545!phosphatidylinositol binding!0.0269705183200261!8301$GO:0005094!Rho GDP-dissociation inhibitor activity!0.0269705183200261!397$GO:0007162!negative regulation of cell adhesion!0.0351278293777307!397$GO:0005092!GDP-dissociation inhibitor activity!0.036104050016986!397$GO:0006898!receptor-mediated endocytosis!0.0487274734501486!8301$GO:0044459!plasma membrane part!0.0487274734501486!8301;3684;50856$GO:0005905!coated pit!0.0487274734501486!8301
|gostat_on_coexpression_clusters=GO:0035300!inositol trisphosphate 5/6-kinase activity!0.0113730683144134!3705$GO:0043647!inositol phosphate metabolic process!0.0113730683144134!3705$GO:0051765!inositol tetrakisphosphate kinase activity!0.0113730683144134!3705$GO:0032957!inositol trisphosphate metabolic process!0.0113730683144134!3705$GO:0047325!inositol tetrakisphosphate 1-kinase activity!0.0113730683144134!3705$GO:0022610!biological adhesion!0.0142547691685994!3684;50856;397$GO:0007155!cell adhesion!0.0142547691685994!3684;50856;397$GO:0001948!glycoprotein binding!0.0213169715519573!3684$GO:0048268!clathrin cage assembly!0.0227340873511213!8301$GO:0006901!vesicle coating!0.0227340873511213!8301$GO:0006900!membrane budding!0.02324871800575!8301$GO:0030276!clathrin binding!0.0260425749057417!8301$GO:0006020!inositol metabolic process!0.0266215290817958!3705$GO:0051766!inositol trisphosphate kinase activity!0.0266215290817958!3705$GO:0031410!cytoplasmic vesicle!0.0266215290817958!8301;397$GO:0031982!vesicle!0.0266215290817958!8301;397$GO:0016050!vesicle organization and biogenesis!0.0266215290817958!8301$GO:0000287!magnesium ion binding!0.0266215290817958!3705;3684$GO:0005545!phosphatidylinositol binding!0.0269705183200261!8301$GO:0005094!Rho GDP-dissociation inhibitor activity!0.0269705183200261!397$GO:0007162!negative regulation of cell adhesion!0.0351278293777307!397$GO:0005092!GDP-dissociation inhibitor activity!0.036104050016986!397$GO:0006898!receptor-mediated endocytosis!0.0487274734501486!8301$GO:0044459!plasma membrane part!0.0487274734501486!8301;3684;50856$GO:0005905!coated pit!0.0487274734501486!8301
|id=C623
|id=C623
|ontology_enrichment_celltype=CL:0000763!7.94e-45!112;CL:0000049!7.94e-45!112;CL:0000766!6.53e-41!76;CL:0000557!5.07e-37!71;CL:0000839!1.88e-35!70;CL:0002009!3.24e-34!65;CL:0000037!5.38e-34!172;CL:0000566!5.38e-34!172;CL:0002194!3.48e-33!63;CL:0000576!3.48e-33!63;CL:0000040!3.48e-33!63;CL:0000559!3.48e-33!63;CL:0002032!4.28e-32!165;CL:0000837!4.28e-32!165;CL:0000988!7.08e-30!182;CL:0000738!2.22e-28!140;CL:0002057!1.49e-25!42;CL:0000860!3.06e-25!45;CL:0002031!4.36e-22!124;CL:0002087!1.78e-20!119;CL:0000134!7.87e-08!358;CL:0002393!9.66e-07!9;CL:0002397!9.66e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.15e-34!102;UBERON:0003061!1.15e-34!102;UBERON:0002193!1.43e-33!112;UBERON:0007023!1.08e-30!115;UBERON:0002371!1.49e-29!80;UBERON:0001474!1.91e-26!86;UBERON:0003081!1.14e-25!216;UBERON:0002405!1.52e-21!115;UBERON:0004765!7.85e-19!101;UBERON:0001434!7.85e-19!101;UBERON:0002204!1.36e-13!167;UBERON:0000479!3.38e-09!787;UBERON:0001049!6.13e-09!57;UBERON:0005068!6.13e-09!57;UBERON:0006241!6.13e-09!57;UBERON:0007135!6.13e-09!57;UBERON:0003080!1.20e-07!42;UBERON:0002780!1.87e-07!41;UBERON:0001890!1.87e-07!41;UBERON:0006240!1.87e-07!41;UBERON:0002616!3.10e-07!59;UBERON:0001893!7.63e-07!34;UBERON:0002020!8.81e-07!34;UBERON:0003528!8.81e-07!34
}}
}}

Revision as of 14:55, 21 May 2012


Full id: C623_Dendritic_Neutrophils_Eosinophils_Whole_Macrophage_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr11:85779986..85780014,-p3@PICALM
Hg19::chr11:85780015..85780042,-p2@PICALM
Hg19::chr12:15114191..15114233,-p5@ARHGDIB
Hg19::chr12:8276205..8276219,+p2@CLEC4A
Hg19::chr12:8276224..8276237,+p3@CLEC4A
Hg19::chr14:93581500..93581509,-p12@ITPK1
Hg19::chr16:28192360..28192372,-p3@AB384470
Hg19::chr16:31271322..31271339,+p2@ITGAM
Hg19::chr16:8738211..8738249,+p@chr16:8738211..8738249
+
Hg19::chr16:8738462..8738501,+p@chr16:8738462..8738501
+
Hg19::chr16:90023641..90023698,+p@chr16:90023641..90023698
+
Hg19::chr3:149531627..149531651,+p7@RNF13
Hg19::chr5:142193841..142193874,+p@chr5:142193841..142193874
+
Hg19::chr8:38662960..38663003,+p9@TACC1


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:0035300inositol trisphosphate 5/6-kinase activity0.0113730683144134
GO:0043647inositol phosphate metabolic process0.0113730683144134
GO:0051765inositol tetrakisphosphate kinase activity0.0113730683144134
GO:0032957inositol trisphosphate metabolic process0.0113730683144134
GO:0047325inositol tetrakisphosphate 1-kinase activity0.0113730683144134
GO:0022610biological adhesion0.0142547691685994
GO:0007155cell adhesion0.0142547691685994
GO:0001948glycoprotein binding0.0213169715519573
GO:0048268clathrin cage assembly0.0227340873511213
GO:0006901vesicle coating0.0227340873511213
GO:0006900membrane budding0.02324871800575
GO:0030276clathrin binding0.0260425749057417
GO:0006020inositol metabolic process0.0266215290817958
GO:0051766inositol trisphosphate kinase activity0.0266215290817958
GO:0031410cytoplasmic vesicle0.0266215290817958
GO:0031982vesicle0.0266215290817958
GO:0016050vesicle organization and biogenesis0.0266215290817958
GO:0000287magnesium ion binding0.0266215290817958
GO:0005545phosphatidylinositol binding0.0269705183200261
GO:0005094Rho GDP-dissociation inhibitor activity0.0269705183200261
GO:0007162negative regulation of cell adhesion0.0351278293777307
GO:0005092GDP-dissociation inhibitor activity0.036104050016986
GO:0006898receptor-mediated endocytosis0.0487274734501486
GO:0044459plasma membrane part0.0487274734501486
GO:0005905coated pit0.0487274734501486



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
myeloid cell7.94e-45112
common myeloid progenitor7.94e-45112
myeloid leukocyte6.53e-4176
granulocyte monocyte progenitor cell5.07e-3771
myeloid lineage restricted progenitor cell1.88e-3570
macrophage dendritic cell progenitor3.24e-3465
hematopoietic stem cell5.38e-34172
angioblastic mesenchymal cell5.38e-34172
monopoietic cell3.48e-3363
monocyte3.48e-3363
monoblast3.48e-3363
promonocyte3.48e-3363
hematopoietic oligopotent progenitor cell4.28e-32165
hematopoietic multipotent progenitor cell4.28e-32165
hematopoietic cell7.08e-30182
leukocyte2.22e-28140
CD14-positive, CD16-negative classical monocyte1.49e-2542
classical monocyte3.06e-2545
hematopoietic lineage restricted progenitor cell4.36e-22124
nongranular leukocyte1.78e-20119
mesenchymal cell7.87e-08358
intermediate monocyte9.66e-079
CD14-positive, CD16-positive monocyte9.66e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.15e-34102
blood island1.15e-34102
hemolymphoid system1.43e-33112
adult organism1.08e-30115
bone marrow1.49e-2980
bone element1.91e-2686
lateral plate mesoderm1.14e-25216
immune system1.52e-21115
skeletal element7.85e-19101
skeletal system7.85e-19101
musculoskeletal system1.36e-13167
tissue3.38e-09787
neural tube6.13e-0957
neural rod6.13e-0957
future spinal cord6.13e-0957
neural keel6.13e-0957
anterior neural tube1.20e-0742
regional part of forebrain1.87e-0741
forebrain1.87e-0741
future forebrain1.87e-0741
regional part of brain3.10e-0759
telencephalon7.63e-0734
gray matter8.81e-0734
brain grey matter8.81e-0734


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.