Coexpression cluster:C1115
From FANTOM5_SSTAR
Full id: C1115_CD4_CD34_CD8_CD19_Basophils_Peripheral_Dendritic
Phase1 CAGE Peaks
Hg19::chr10:32667648..32667659,- | p5@EPC1 |
Hg19::chr10:32667660..32667735,- | p2@EPC1 |
Hg19::chr13:103249302..103249321,+ | p2@TPP2 |
Hg19::chr16:10479876..10479887,+ | p2@ATF7IP2 |
Hg19::chr2:242823508..242823531,+ | p1@ENST00000415434 p1@ENST00000430555 p1@ENST00000457686 |
Hg19::chr4:89205879..89205911,- | p3@PPM1K |
Hg19::chr9:100396030..100396055,+ | p3@NCBP1 |
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 ID | GO name | FDR corrected p-value |
---|---|---|
GO:0031442 | positive regulation of mRNA 3'-end processing | 0.00520005491694157 |
GO:0050685 | positive regulation of mRNA processing | 0.00520005491694157 |
GO:0004294 | tripeptidyl-peptidase II activity | 0.00520005491694157 |
GO:0008717 | D-alanyl-D-alanine endopeptidase activity | 0.00520005491694157 |
GO:0031974 | membrane-enclosed lumen | 0.00520005491694157 |
GO:0043233 | organelle lumen | 0.00520005491694157 |
GO:0051254 | positive regulation of RNA metabolic process | 0.00520005491694157 |
GO:0008240 | tripeptidyl-peptidase activity | 0.00520005491694157 |
GO:0031440 | regulation of mRNA 3'-end processing | 0.00520005491694157 |
GO:0045935 | positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0112746726374699 |
GO:0000339 | RNA cap binding | 0.0133668470752712 |
GO:0031325 | positive regulation of cellular metabolic process | 0.0133668470752712 |
GO:0006379 | mRNA cleavage | 0.0133668470752712 |
GO:0050684 | regulation of mRNA processing | 0.0133668470752712 |
GO:0009893 | positive regulation of metabolic process | 0.0136880817127755 |
GO:0031124 | mRNA 3'-end processing | 0.0204607554870117 |
GO:0005654 | nucleoplasm | 0.0211322557389912 |
GO:0031123 | RNA 3'-end processing | 0.0233768379318203 |
GO:0051252 | regulation of RNA metabolic process | 0.0233768379318203 |
GO:0006406 | mRNA export from nucleus | 0.025709980262606 |
GO:0043170 | macromolecule metabolic process | 0.0273417798653032 |
GO:0045814 | negative regulation of gene expression, epigenetic | 0.0273417798653032 |
GO:0031981 | nuclear lumen | 0.0273417798653032 |
GO:0006405 | RNA export from nucleus | 0.0292021291118577 |
GO:0004289 | subtilase activity | 0.0323355491475181 |
GO:0015071 | protein phosphatase type 2C activity | 0.0323355491475181 |
GO:0051168 | nuclear export | 0.0380395566131108 |
GO:0044237 | cellular metabolic process | 0.0396635721962796 |
GO:0048522 | positive regulation of cellular process | 0.0396635721962796 |
GO:0044238 | primary metabolic process | 0.0396635721962796 |
GO:0044424 | intracellular part | 0.0413916159462054 |
GO:0008287 | protein serine/threonine phosphatase complex | 0.0415469369327996 |
GO:0048518 | positive regulation of biological process | 0.0432967094918313 |
GO:0040029 | regulation of gene expression, epigenetic | 0.0432967094918313 |
GO:0004722 | protein serine/threonine phosphatase activity | 0.0432967094918313 |
GO:0044428 | nuclear part | 0.043958325953636 |
GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0472815342760447 |
GO:0051028 | mRNA transport | 0.0475876790435889 |
GO:0043283 | biopolymer metabolic process | 0.0475876790435889 |
GO:0004177 | aminopeptidase activity | 0.0475876790435889 |
GO:0031323 | regulation of cellular metabolic process | 0.0475876790435889 |
GO:0050658 | RNA transport | 0.0475876790435889 |
GO:0051236 | establishment of RNA localization | 0.0475876790435889 |
GO:0050657 | nucleic acid transport | 0.0475876790435889 |
GO:0006403 | RNA localization | 0.0475876790435889 |
GO:0044446 | intracellular organelle part | 0.0483810973952469 |
GO:0044422 | organelle part | 0.0483810973952469 |
GO:0019222 | regulation of metabolic process | 0.0483810973952469 |
GO:0016070 | RNA metabolic process | 0.0483810973952469 |
GO:0015931 | nucleobase, nucleoside, nucleotide and nucleic acid transport | 0.0483810973952469 |
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>disease_data<br>
Ontology term | p-value | n |
---|---|---|
hematopoietic stem cell | 8.80e-24 | 172 |
angioblastic mesenchymal cell | 8.80e-24 | 172 |
lymphocyte | 1.24e-23 | 53 |
common lymphoid progenitor | 1.24e-23 | 53 |
lymphoid lineage restricted progenitor cell | 2.43e-23 | 52 |
hematopoietic cell | 3.84e-22 | 182 |
hematopoietic oligopotent progenitor cell | 1.58e-20 | 165 |
hematopoietic multipotent progenitor cell | 1.58e-20 | 165 |
leukocyte | 3.71e-19 | 140 |
hematopoietic lineage restricted progenitor cell | 1.36e-14 | 124 |
nongranular leukocyte | 2.43e-14 | 119 |
T cell | 3.35e-12 | 25 |
pro-T cell | 3.35e-12 | 25 |
mature alpha-beta T cell | 9.14e-12 | 18 |
alpha-beta T cell | 9.14e-12 | 18 |
immature T cell | 9.14e-12 | 18 |
mature T cell | 9.14e-12 | 18 |
immature alpha-beta T cell | 9.14e-12 | 18 |
lymphocyte of B lineage | 1.25e-10 | 24 |
pro-B cell | 1.25e-10 | 24 |
B cell | 4.31e-09 | 14 |
CD8-positive, alpha-beta T cell | 2.77e-08 | 11 |
Ontology term | p-value | n |
---|---|---|
adult organism | 1.30e-25 | 115 |
neural tube | 1.80e-15 | 57 |
neural rod | 1.80e-15 | 57 |
future spinal cord | 1.80e-15 | 57 |
neural keel | 1.80e-15 | 57 |
central nervous system | 2.89e-15 | 82 |
regional part of nervous system | 2.47e-14 | 94 |
nervous system | 2.47e-14 | 94 |
regional part of brain | 5.50e-14 | 59 |
anterior neural tube | 1.00e-13 | 42 |
regional part of forebrain | 1.19e-13 | 41 |
forebrain | 1.19e-13 | 41 |
future forebrain | 1.19e-13 | 41 |
brain | 2.48e-13 | 69 |
future brain | 2.48e-13 | 69 |
telencephalon | 2.94e-11 | 34 |
gray matter | 3.12e-11 | 34 |
brain grey matter | 3.12e-11 | 34 |
cerebral hemisphere | 4.28e-11 | 32 |
regional part of telencephalon | 4.91e-11 | 33 |
neurectoderm | 9.34e-09 | 90 |
regional part of cerebral cortex | 1.11e-08 | 22 |
cerebral cortex | 1.27e-08 | 25 |
pallium | 1.27e-08 | 25 |
neocortex | 4.38e-08 | 20 |
neural plate | 7.21e-08 | 86 |
presumptive neural plate | 7.21e-08 | 86 |
blood | 8.89e-08 | 15 |
haemolymphatic fluid | 8.89e-08 | 15 |
organism substance | 8.89e-08 | 15 |
pre-chordal neural plate | 6.59e-07 | 61 |
Ontology term | p-value | n |
---|---|---|
hematologic cancer | 8.37e-07 | 51 |
immune system cancer | 8.37e-07 | 51 |
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 | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
CHD2#1106 | 5 | 7.3885877386549 | 0.000149868960082067 | 0.00193141218188685 |
E2F1#1869 | 5 | 3.50527801062809 | 0.00509055358791505 | 0.0236837280010807 |
E2F4#1874 | 3 | 5.42916870655047 | 0.0135067508217614 | 0.0477032075030923 |
EGR1#1958 | 5 | 3.56298506772153 | 0.00472235121105893 | 0.0222552068106937 |
ELF1#1997 | 5 | 3.04149854200538 | 0.00971956226937075 | 0.0365565169926106 |
EP300#2033 | 4 | 3.87082384355611 | 0.0114256758668448 | 0.041859408631473 |
FOS#2353 | 4 | 5.14168874793966 | 0.00404209586567825 | 0.0193479284163147 |
GTF2B#2959 | 4 | 18.2536171053281 | 3.11241110089347e-05 | 0.0006292239701243 |
GTF2F1#2962 | 3 | 5.45985466146756 | 0.013298821684157 | 0.0470213161985129 |
HEY1#23462 | 6 | 3.46295232266204 | 0.00126789009587212 | 0.00850354313657776 |
IRF1#3659 | 4 | 4.36409357346509 | 0.0073934558242782 | 0.0305493405931236 |
NANOG#79923 | 3 | 12.5334764918626 | 0.00126105218950347 | 0.00846747007969353 |
NFKB1#4790 | 5 | 3.9200453029956 | 0.00303658142448461 | 0.0161155306363 |
NFYA#4800 | 6 | 15.793354885569 | 1.7032585757508e-07 | 9.38220582240704e-06 |
NFYB#4801 | 6 | 14.3655370744598 | 2.99325254948281e-07 | 1.50947514734638e-05 |
PAX5#5079 | 4 | 3.81118030353019 | 0.0120826168155519 | 0.0438204124596112 |
POLR2A#5430 | 7 | 2.14745317655807 | 0.00474763644761028 | 0.0223219917594188 |
REST#5978 | 5 | 6.89287765437716 | 0.000209438858484651 | 0.00243825492601477 |
RFX5#5993 | 6 | 10.3267807090244 | 2.12421369818918e-06 | 7.73538195345816e-05 |
SP1#6667 | 6 | 4.88432689554934 | 0.000173636112229091 | 0.00211282557673238 |
SP2#6668 | 4 | 14.9448745679112 | 6.81071539656055e-05 | 0.00108762126192873 |
TAF1#6872 | 6 | 2.86546824492454 | 0.00372833020747146 | 0.0185818696510671 |
TBP#6908 | 6 | 3.17723201751119 | 0.00207411205185266 | 0.0120149863322114 |
TCF7L2#6934 | 4 | 6.15438660750705 | 0.00206467614813804 | 0.0119689560521419 |
TRIM28#10155 | 3 | 7.96736787654108 | 0.00462234126315646 | 0.0218311716719937 |
YY1#7528 | 5 | 3.50797910703847 | 0.00507257067280898 | 0.0236095284325281 |
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.