Coexpression cluster:C560
From FANTOM5_SSTAR
Full id: C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic
Phase1 CAGE Peaks
Hg19::chr11:3862154..3862165,- | p3@RHOG |
Hg19::chr15:40600066..40600089,- | p3@PLCB2 |
Hg19::chr16:3137080..3137121,- | p@chr16:3137080..3137121 - |
Hg19::chr19:2282186..2282208,- | p1@C19orf35 |
Hg19::chr19:48753064..48753095,- | p1@CARD8 |
Hg19::chr1:161039493..161039519,- | p3@ARHGAP30 |
Hg19::chr1:161039535..161039544,- | p11@ARHGAP30 |
Hg19::chr20:62708698..62708701,+ | p@chr20:62708698..62708701 + |
Hg19::chr20:62710832..62710879,- | p1@RGS19 |
Hg19::chr20:62710880..62710898,- | p3@RGS19 |
Hg19::chr20:62711425..62711470,+ | p2@OPRL1 |
Hg19::chr22:40859415..40859478,- | p2@MKL1 |
Hg19::chr2:220042536..220042549,- | p5@CNPPD1 |
Hg19::chr6:31554456..31554512,+ | p6@LST1 |
Hg19::chrX:109245878..109245916,+ | p2@TMEM164 |
Hg19::chrX:77583054..77583100,- | p1@CYSLTR1 |
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
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
1.43919346767955e-05 | 0.00911009465041154 | 5 | 932 | Signaling by GPCR (Reactome):REACT_14797 |
0.000123219497261582 | 0.0389989708832906 | 4 | 733 | {ARRB2,743} (Static Module):NA |
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:0065007 | biological regulation | 0.00768606826536886 |
GO:0007242 | intracellular signaling cascade | 0.00768606826536886 |
GO:0007165 | signal transduction | 0.00768606826536886 |
GO:0051480 | cytosolic calcium ion homeostasis | 0.00768606826536886 |
GO:0007204 | elevation of cytosolic calcium ion concentration | 0.00768606826536886 |
GO:0051345 | positive regulation of hydrolase activity | 0.00768606826536886 |
GO:0007154 | cell communication | 0.00768606826536886 |
GO:0008047 | enzyme activator activity | 0.00768606826536886 |
GO:0032089 | NACHT domain binding | 0.00768606826536886 |
GO:0009968 | negative regulation of signal transduction | 0.00963686219868977 |
GO:0006874 | cellular calcium ion homeostasis | 0.00963686219868977 |
GO:0055074 | calcium ion homeostasis | 0.00963686219868977 |
GO:0006875 | cellular metal ion homeostasis | 0.00963686219868977 |
GO:0055065 | metal ion homeostasis | 0.00963686219868977 |
GO:0007186 | G-protein coupled receptor protein signaling pathway | 0.0153133997986742 |
GO:0015051 | X-opioid receptor activity | 0.0164799494906198 |
GO:0030005 | cellular di-, tri-valent inorganic cation homeostasis | 0.0164799494906198 |
GO:0055066 | di-, tri-valent inorganic cation homeostasis | 0.0164799494906198 |
GO:0004974 | leukotriene receptor activity | 0.0173368271137648 |
GO:0030003 | cellular cation homeostasis | 0.0173368271137648 |
GO:0055080 | cation homeostasis | 0.0173368271137648 |
GO:0043124 | negative regulation of I-kappaB kinase/NF-kappaB cascade | 0.0188533124660523 |
GO:0055082 | cellular chemical homeostasis | 0.0202857552107383 |
GO:0006873 | cellular ion homeostasis | 0.0202857552107383 |
GO:0050718 | positive regulation of interleukin-1 beta secretion | 0.0202857552107383 |
GO:0050706 | regulation of interleukin-1 beta secretion | 0.0202857552107383 |
GO:0043085 | positive regulation of catalytic activity | 0.0202857552107383 |
GO:0050716 | positive regulation of interleukin-1 secretion | 0.0202857552107383 |
GO:0050704 | regulation of interleukin-1 secretion | 0.0202857552107383 |
GO:0050801 | ion homeostasis | 0.0202857552107383 |
GO:0019932 | second-messenger-mediated signaling | 0.0202857552107383 |
GO:0050702 | interleukin-1 beta secretion | 0.0215913114519548 |
GO:0050672 | negative regulation of lymphocyte proliferation | 0.0217118145535234 |
GO:0032945 | negative regulation of mononuclear cell proliferation | 0.0217118145535234 |
GO:0050701 | interleukin-1 secretion | 0.0217118145535234 |
GO:0048878 | chemical homeostasis | 0.021812809706439 |
GO:0051336 | regulation of hydrolase activity | 0.021812809706439 |
GO:0016358 | dendrite development | 0.021812809706439 |
GO:0048523 | negative regulation of cellular process | 0.0222381094285401 |
GO:0050715 | positive regulation of cytokine secretion | 0.0222381094285401 |
GO:0007166 | cell surface receptor linked signal transduction | 0.0222381094285401 |
GO:0004985 | opioid receptor activity | 0.0224114206445887 |
GO:0008656 | caspase activator activity | 0.0224114206445887 |
GO:0048519 | negative regulation of biological process | 0.0224114206445887 |
GO:0005096 | GTPase activator activity | 0.0225427971115012 |
GO:0050707 | regulation of cytokine secretion | 0.0225427971115012 |
GO:0007202 | phospholipase C activation | 0.0225427971115012 |
GO:0050714 | positive regulation of protein secretion | 0.0225427971115012 |
GO:0016505 | apoptotic protease activator activity | 0.0225427971115012 |
GO:0019725 | cellular homeostasis | 0.0238912041264944 |
GO:0016504 | protease activator activity | 0.0238912041264944 |
GO:0007193 | G-protein signaling, adenylate cyclase inhibiting pathway | 0.0238912041264944 |
GO:0051250 | negative regulation of lymphocyte activation | 0.024739396424922 |
GO:0050663 | cytokine secretion | 0.0255558362491887 |
GO:0043028 | caspase regulator activity | 0.0258718582086354 |
GO:0051047 | positive regulation of secretion | 0.0258718582086354 |
GO:0006914 | autophagy | 0.0309068112179078 |
GO:0050708 | regulation of protein secretion | 0.0309068112179078 |
GO:0042127 | regulation of cell proliferation | 0.031677914247718 |
GO:0042592 | homeostatic process | 0.0325735113717887 |
GO:0007585 | respiratory gaseous exchange | 0.032764573503621 |
GO:0005834 | heterotrimeric G-protein complex | 0.0410853019415701 |
GO:0022603 | regulation of anatomical structure morphogenesis | 0.0431284191752502 |
GO:0022604 | regulation of cell morphogenesis | 0.0431284191752502 |
GO:0050670 | regulation of lymphocyte proliferation | 0.0431284191752502 |
GO:0032944 | regulation of mononuclear cell proliferation | 0.0431284191752502 |
GO:0008360 | regulation of cell shape | 0.0431284191752502 |
GO:0050790 | regulation of catalytic activity | 0.0442110780729895 |
GO:0004435 | phosphoinositide phospholipase C activity | 0.0442110780729895 |
GO:0004434 | inositol or phosphatidylinositol phosphodiesterase activity | 0.0442110780729895 |
GO:0019897 | extrinsic to plasma membrane | 0.0477272926776687 |
GO:0043280 | positive regulation of caspase activity | 0.0477272926776687 |
GO:0032943 | mononuclear cell proliferation | 0.048449248386039 |
GO:0046651 | lymphocyte proliferation | 0.048449248386039 |
GO:0065009 | regulation of a molecular function | 0.048449248386039 |
GO:0050794 | regulation of cellular process | 0.048449248386039 |
GO:0005624 | membrane fraction | 0.048449248386039 |
GO:0004629 | phospholipase C activity | 0.048449248386039 |
GO:0009306 | protein secretion | 0.048449248386039 |
GO:0005794 | Golgi apparatus | 0.048449248386039 |
GO:0030695 | GTPase regulator activity | 0.048449248386039 |
GO:0051046 | regulation of secretion | 0.048449248386039 |
GO:0004871 | signal transducer activity | 0.048449248386039 |
GO:0060089 | molecular transducer activity | 0.048449248386039 |
GO:0043281 | regulation of caspase activity | 0.048449248386039 |
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 system | 5.85e-53 | 98 |
blood island | 5.85e-53 | 98 |
hemolymphoid system | 3.59e-49 | 108 |
bone marrow | 5.23e-41 | 76 |
immune system | 1.00e-40 | 93 |
bone element | 8.88e-36 | 82 |
skeletal element | 5.74e-30 | 90 |
skeletal system | 7.99e-25 | 100 |
adult organism | 1.67e-20 | 114 |
lateral plate mesoderm | 5.10e-15 | 203 |
connective tissue | 9.79e-11 | 371 |
blood | 8.70e-09 | 15 |
haemolymphatic fluid | 8.70e-09 | 15 |
organism substance | 8.70e-09 | 15 |
musculoskeletal system | 3.19e-07 | 167 |
Ontology term | p-value | n |
---|---|---|
myeloid leukemia | 7.34e-11 | 31 |
leukemia | 7.25e-09 | 39 |
hematologic cancer | 6.93e-08 | 51 |
immune system cancer | 6.93e-08 | 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 |
---|---|---|---|---|
EGR1#1958 | 8 | 2.49408954740507 | 0.007106561314776 | 0.0296288286288978 |
ELF1#1997 | 12 | 3.19357346910565 | 1.93117413800973e-05 | 0.000435803577786514 |
MAX#4149 | 7 | 2.82299303519062 | 0.0067149521973491 | 0.0285442180202264 |
POLR2A#5430 | 15 | 2.01323735302319 | 9.45926752373161e-05 | 0.00137115397766968 |
SPI1#6688 | 13 | 6.66601285067472 | 5.10515875363416e-10 | 4.93226341416094e-08 |
ZEB1#6935 | 4 | 4.22210800438596 | 0.0125811231488872 | 0.0454956518315372 |
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.