Coexpression cluster:C47
From FANTOM5_SSTAR
Full id: C47_CD19_Burkitt_acute_xeroderma_tonsil_lymphoma_appendix
Phase1 CAGE Peaks
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 |
|---|---|---|---|---|
| 3.61851816327161e-06 | 0.000572630499337732 | 6 | 88 | Hematopoietic cell lineage (KEGG):04640 |
| 2.33011253571778e-09 | 7.37480617554678e-07 | 8 | 75 | B cell receptor signaling pathway (KEGG):04662 |
| 2.7166582023335e-10 | 1.71964464207711e-07 | 11 | 161 | B Cell Receptor Signaling Pathway (Wikipathways):WP23 |
| 1.2724155829856e-07 | 2.68479688009961e-05 | 14 | 511 | Signaling in Immune system (Reactome):REACT_6900 |
| 7.47507525897941e-05 | 0.00788620439822327 | 4 | 48 | {FCGR2B,50} (Static Module):NA |
| 6.40970841609321e-05 | 0.00788620439822327 | 3 | 17 | {HCLS1,17} (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:0044459 | plasma membrane part | 8.69684340157993e-10 |
| GO:0002376 | immune system process | 2.61187697123425e-09 |
| GO:0006955 | immune response | 1.07273223209228e-06 |
| GO:0005887 | integral to plasma membrane | 1.07273223209228e-06 |
| GO:0031226 | intrinsic to plasma membrane | 1.07273223209228e-06 |
| GO:0019814 | immunoglobulin complex | 3.62679970799788e-06 |
| GO:0019815 | B cell receptor complex | 3.62679970799788e-06 |
| GO:0046649 | lymphocyte activation | 3.62679970799788e-06 |
| GO:0042113 | B cell activation | 3.85021397573723e-06 |
| GO:0045321 | leukocyte activation | 9.23683158082192e-06 |
| GO:0005886 | plasma membrane | 2.41354283046012e-05 |
| GO:0001775 | cell activation | 2.41354283046012e-05 |
| GO:0002521 | leukocyte differentiation | 2.778117368804e-05 |
| GO:0044425 | membrane part | 4.40320254142735e-05 |
| GO:0030098 | lymphocyte differentiation | 0.000105905021606921 |
| GO:0006959 | humoral immune response | 0.000218718152574894 |
| GO:0050853 | B cell receptor signaling pathway | 0.000252420369364762 |
| GO:0016021 | integral to membrane | 0.000272367815823108 |
| GO:0031224 | intrinsic to membrane | 0.000300970046953354 |
| GO:0030097 | hemopoiesis | 0.000533940840611148 |
| GO:0048534 | hemopoietic or lymphoid organ development | 0.000758483053711932 |
| GO:0001772 | immunological synapse | 0.000758483053711932 |
| GO:0050731 | positive regulation of peptidyl-tyrosine phosphorylation | 0.000758483053711932 |
| GO:0002520 | immune system development | 0.000890481036423185 |
| GO:0042327 | positive regulation of phosphorylation | 0.00179276517811719 |
| GO:0004871 | signal transducer activity | 0.00185694193701626 |
| GO:0060089 | molecular transducer activity | 0.00185694193701626 |
| GO:0045937 | positive regulation of phosphate metabolic process | 0.00206939013156447 |
| GO:0001934 | positive regulation of protein amino acid phosphorylation | 0.00229232763956547 |
| GO:0050851 | antigen receptor-mediated signaling pathway | 0.00229232763956547 |
| GO:0033240 | positive regulation of amine metabolic process | 0.00229232763956547 |
| GO:0045764 | positive regulation of amino acid metabolic process | 0.00229232763956547 |
| GO:0050730 | regulation of peptidyl-tyrosine phosphorylation | 0.00248396264683151 |
| GO:0016020 | membrane | 0.00260633384870108 |
| GO:0030183 | B cell differentiation | 0.00260633384870108 |
| GO:0002429 | immune response-activating cell surface receptor signaling pathway | 0.00280910288616024 |
| GO:0002768 | immune response-regulating cell surface receptor signaling pathway | 0.00295687741871095 |
| GO:0005515 | protein binding | 0.00295687741871095 |
| GO:0002757 | immune response-activating signal transduction | 0.00315348454123003 |
| GO:0006661 | phosphatidylinositol biosynthetic process | 0.00321766955635076 |
| GO:0002764 | immune response-regulating signal transduction | 0.00329214608495478 |
| GO:0044464 | cell part | 0.0033552672498784 |
| GO:0004872 | receptor activity | 0.00490011872974427 |
| GO:0005057 | receptor signaling protein activity | 0.00490011872974427 |
| GO:0030217 | T cell differentiation | 0.00575516284705213 |
| GO:0007275 | multicellular organismal development | 0.00579735245880817 |
| GO:0032502 | developmental process | 0.00579735245880817 |
| GO:0018108 | peptidyl-tyrosine phosphorylation | 0.00579735245880817 |
| GO:0018212 | peptidyl-tyrosine modification | 0.00652206006996487 |
| GO:0032501 | multicellular organismal process | 0.00656820216743222 |
| GO:0001932 | regulation of protein amino acid phosphorylation | 0.00669869866920849 |
| GO:0033238 | regulation of amine metabolic process | 0.00688003703562435 |
| GO:0006521 | regulation of amino acid metabolic process | 0.00688003703562435 |
| GO:0008283 | cell proliferation | 0.00919648698864331 |
| GO:0048731 | system development | 0.00965496260403426 |
| GO:0032943 | mononuclear cell proliferation | 0.00971713845269114 |
| GO:0046651 | lymphocyte proliferation | 0.00971713845269114 |
| GO:0048869 | cellular developmental process | 0.0101981191409447 |
| GO:0030154 | cell differentiation | 0.0101981191409447 |
| GO:0000187 | activation of MAPK activity | 0.0114264093519731 |
| GO:0048513 | organ development | 0.0130248394829955 |
| GO:0042325 | regulation of phosphorylation | 0.0154983822395476 |
| GO:0046632 | alpha-beta T cell differentiation | 0.0160138393456127 |
| GO:0043406 | positive regulation of MAP kinase activity | 0.0164157822660956 |
| GO:0051174 | regulation of phosphorus metabolic process | 0.0181030532310509 |
| GO:0019220 | regulation of phosphate metabolic process | 0.0181030532310509 |
| GO:0050871 | positive regulation of B cell activation | 0.0188043845351736 |
| GO:0042100 | B cell proliferation | 0.0188043845351736 |
| GO:0002253 | activation of immune response | 0.0188043845351736 |
| GO:0006968 | cellular defense response | 0.0192980607195311 |
| GO:0046631 | alpha-beta T cell activation | 0.0201251896329609 |
| GO:0016044 | membrane organization and biogenesis | 0.0250298625119534 |
| GO:0006486 | protein amino acid glycosylation | 0.0270368996375643 |
| GO:0030595 | leukocyte chemotaxis | 0.0272679408203429 |
| GO:0000118 | histone deacetylase complex | 0.0272679408203429 |
| GO:0003823 | antigen binding | 0.0272679408203429 |
| GO:0043413 | biopolymer glycosylation | 0.0272679408203429 |
| GO:0051247 | positive regulation of protein metabolic process | 0.0275008024621621 |
| GO:0050778 | positive regulation of immune response | 0.0275008024621621 |
| GO:0002684 | positive regulation of immune system process | 0.0280753251900952 |
| GO:0009101 | glycoprotein biosynthetic process | 0.0283173514595235 |
| GO:0050864 | regulation of B cell activation | 0.0283173514595235 |
| GO:0046488 | phosphatidylinositol metabolic process | 0.0283173514595235 |
| GO:0048856 | anatomical structure development | 0.0283173514595235 |
| GO:0030674 | protein binding, bridging | 0.0283173514595235 |
| GO:0043126 | regulation of 1-phosphatidylinositol 4-kinase activity | 0.0283173514595235 |
| GO:0046638 | positive regulation of alpha-beta T cell differentiation | 0.0283173514595235 |
| GO:0043128 | positive regulation of 1-phosphatidylinositol 4-kinase activity | 0.0283173514595235 |
| GO:0045588 | positive regulation of gamma-delta T cell differentiation | 0.0283173514595235 |
| GO:0046643 | regulation of gamma-delta T cell activation | 0.0283173514595235 |
| GO:0042492 | gamma-delta T cell differentiation | 0.0283173514595235 |
| GO:0046645 | positive regulation of gamma-delta T cell activation | 0.0283173514595235 |
| GO:0042571 | immunoglobulin complex, circulating | 0.0283173514595235 |
| GO:0043366 | beta selection | 0.0283173514595235 |
| GO:0045586 | regulation of gamma-delta T cell differentiation | 0.0283173514595235 |
| GO:0046629 | gamma-delta T cell activation | 0.0283173514595235 |
| GO:0004502 | kynurenine 3-monooxygenase activity | 0.0283173514595235 |
| GO:0046813 | virion attachment, binding of host cell surface receptor | 0.0283173514595235 |
| GO:0043405 | regulation of MAP kinase activity | 0.0283173514595235 |
| GO:0007154 | cell communication | 0.0301890713169142 |
| GO:0010324 | membrane invagination | 0.030230777816049 |
| GO:0006897 | endocytosis | 0.030230777816049 |
| GO:0042110 | T cell activation | 0.0312412174493656 |
| GO:0050776 | regulation of immune response | 0.0312412174493656 |
| GO:0002682 | regulation of immune system process | 0.032750037631295 |
| GO:0032403 | protein complex binding | 0.0329122703697938 |
| GO:0050671 | positive regulation of lymphocyte proliferation | 0.0329122703697938 |
| GO:0032946 | positive regulation of mononuclear cell proliferation | 0.0329122703697938 |
| GO:0009100 | glycoprotein metabolic process | 0.0343096599299752 |
| GO:0050900 | leukocyte migration | 0.0344723708533048 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.0355138752750945 |
| GO:0043235 | receptor complex | 0.0400692173493072 |
| GO:0046489 | phosphoinositide biosynthetic process | 0.0425917706931027 |
| GO:0009887 | organ morphogenesis | 0.0434769008379179 |
| GO:0008284 | positive regulation of cell proliferation | 0.0434769008379179 |
| GO:0032632 | interleukin-3 production | 0.0434769008379179 |
| GO:0005232 | serotonin-activated cation-selective channel activity | 0.0434769008379179 |
| GO:0046637 | regulation of alpha-beta T cell differentiation | 0.0434769008379179 |
| GO:0042223 | interleukin-3 biosynthetic process | 0.0434769008379179 |
| GO:0001865 | NK T cell differentiation | 0.0434769008379179 |
| GO:0045401 | positive regulation of interleukin-3 biosynthetic process | 0.0434769008379179 |
| GO:0051138 | positive regulation of NK T cell differentiation | 0.0434769008379179 |
| GO:0048007 | antigen processing and presentation, exogenous lipid antigen via MHC class Ib | 0.0434769008379179 |
| GO:0004949 | cannabinoid receptor activity | 0.0434769008379179 |
| GO:0001820 | serotonin secretion | 0.0434769008379179 |
| GO:0051136 | regulation of NK T cell differentiation | 0.0434769008379179 |
| GO:0030144 | alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity | 0.0434769008379179 |
| GO:0045399 | regulation of interleukin-3 biosynthetic process | 0.0434769008379179 |
| GO:0051050 | positive regulation of transport | 0.0434769008379179 |
| GO:0008373 | sialyltransferase activity | 0.0434769008379179 |
| GO:0018193 | peptidyl-amino acid modification | 0.0445979381121493 |
| GO:0007243 | protein kinase cascade | 0.0447639609071618 |
| GO:0004715 | non-membrane spanning protein tyrosine kinase activity | 0.0469602334005007 |
| GO:0005178 | integrin binding | 0.0489009162029623 |
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 | 1.79e-25 | 102 |
| blood island | 1.79e-25 | 102 |
| adult organism | 7.02e-25 | 115 |
| hemolymphoid system | 2.84e-22 | 112 |
| bone marrow | 1.60e-15 | 80 |
| immune system | 1.93e-13 | 115 |
| bone element | 1.06e-12 | 86 |
| skeletal element | 4.84e-10 | 101 |
| skeletal system | 4.84e-10 | 101 |
| blood | 2.14e-08 | 15 |
| haemolymphatic fluid | 2.14e-08 | 15 |
| organism substance | 2.14e-08 | 15 |
| Ontology term | p-value | n |
|---|---|---|
| hematologic cancer | 1.80e-08 | 51 |
| immune system cancer | 1.80e-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 |
|---|---|---|---|---|
| BATF#10538 | 50 | 3.11480841333806 | 1.88201254971634e-12 | 2.56935305463823e-10 |
| BCL11A#53335 | 78 | 5.65937979048939 | 1.90937378925643e-35 | 9.4958613893406e-33 |
| BCL3#602 | 26 | 2.29724980280613 | 9.45122834304396e-05 | 0.00137017884080951 |
| BRF2#55290 | 3 | 8.24482543270089 | 0.00601277090289085 | 0.0269537205050656 |
| EBF1#1879 | 116 | 2.64232776010743 | 3.92488792169293e-23 | 1.16122201035039e-20 |
| IRF4#3662 | 66 | 3.69912490364479 | 6.18276274702846e-20 | 1.55971390950943e-17 |
| MEF2A#4205 | 94 | 4.50604528262542 | 3.73920679942783e-35 | 1.83342262406311e-32 |
| MEF2C#4208 | 47 | 4.96581499016197 | 3.69611987148275e-19 | 8.8333881752354e-17 |
| NFKB1#4790 | 175 | 2.45629437144225 | 1.44756699683587e-33 | 6.71921998144627e-31 |
| PAX5#5079 | 131 | 2.23456031862991 | 5.65802214481225e-20 | 1.43079461206307e-17 |
| POLR2A#5430 | 279 | 1.53232592393786 | 2.52749475939695e-23 | 7.54197214790451e-21 |
| POU2F2#5452 | 122 | 2.84129702057439 | 2.97030653114101e-27 | 1.05515593131237e-24 |
| SPI1#6688 | 142 | 2.97957528954022 | 1.14078653949464e-34 | 5.54151653015261e-32 |
| TAF1#6872 | 143 | 1.22264864158971 | 0.00272667277550075 | 0.0149745479308263 |
| TBP#6908 | 147 | 1.39359409463726 | 2.94930946171222e-06 | 0.000101024247580112 |
| TCF12#6938 | 90 | 2.44783079589969 | 1.3162764663363e-15 | 2.44609604746792e-13 |
| ZEB1#6935 | 50 | 2.15964603804909 | 3.17975967025818e-07 | 1.59505725361236e-05 |
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
