Coexpression cluster:C57
From FANTOM5_SSTAR
Full id: C57_Neutrophils_Eosinophils_Whole_CD4_CD8_CD19_Natural
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 |
|---|---|---|---|---|
| 1.66393622232006e-06 | 0.000150467375532657 | 9 | 189 | Chemokine signaling pathway (KEGG):04062 |
| 2.6083048043839e-05 | 0.00150096085561364 | 8 | 204 | Endocytosis (KEGG):04144 |
| 0.00108340414988846 | 0.0403408721693763 | 3 | 35 | Primary immunodeficiency (KEGG):05340 |
| 0.000522019915664187 | 0.0206524129134644 | 4 | 64 | IL-4 signaling Pathway (Wikipathways):WP395 |
| 8.36232923303133e-05 | 0.00441112867042403 | 4 | 40 | G13 Signaling Pathway (Wikipathways):WP524 |
| 3.53351911337367e-10 | 1.11835879938277e-07 | 11 | 133 | T Cell Receptor Signaling Pathway (Wikipathways):WP69 |
| 6.41276890061639e-07 | 8.11856542818034e-05 | 7 | 85 | Integrin cell surface interactions (Reactome):REACT_13552 |
| 1.55851378778502e-10 | 9.86539227667916e-08 | 19 | 511 | Signaling in Immune system (Reactome):REACT_6900 |
| 3.47160198084761e-06 | 0.000274690506734567 | 13 | 466 | Hemostasis (Reactome):REACT_604 |
| 5.43343015399396e-07 | 8.11856542818034e-05 | 8 | 121 | Signaling by Rho GTPases (Reactome):REACT_11044 |
| 1.28207912517131e-06 | 0.000135259347705573 | 11 | 295 | IL-2 down reg. targets (Netpath):NetPath_14 |
| 4.65649974928251e-06 | 0.00032750714903287 | 12 | 406 | {GRB2,414} (Static Module):NA |
| 3.55175527931001e-08 | 7.49420363934413e-06 | 5 | 17 | {HCLS1,17} (Static Module):NA |
| 0.000217637458112359 | 0.00984032221322309 | 4 | 51 | {HLA-A,53} (Static Module):NA |
| 1.22010885576084e-05 | 0.000772328905696613 | 7 | 132 | {RAC1,133} (Static Module):NA |
| 0.000269357017808511 | 0.0113668661515192 | 3 | 22 | {RAP1A,22} (Static Module):NA |
| 0.000201094783456266 | 0.00979176907137047 | 3 | 20 | {SEPT2,21} (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:0030695 | GTPase regulator activity | 6.69754590003444e-11 |
| GO:0005515 | protein binding | 2.96276810717286e-08 |
| GO:0007165 | signal transduction | 2.96276810717286e-08 |
| GO:0005096 | GTPase activator activity | 3.44757962320888e-07 |
| GO:0007154 | cell communication | 6.34812840990484e-07 |
| GO:0008047 | enzyme activator activity | 6.34812840990484e-07 |
| GO:0007242 | intracellular signaling cascade | 1.00556473591337e-06 |
| GO:0044464 | cell part | 1.37047040346379e-05 |
| GO:0009966 | regulation of signal transduction | 7.39182975357727e-05 |
| GO:0005737 | cytoplasm | 0.000224555448856817 |
| GO:0048523 | negative regulation of cellular process | 0.000224555448856817 |
| GO:0005622 | intracellular | 0.000224555448856817 |
| GO:0006793 | phosphorus metabolic process | 0.000224555448856817 |
| GO:0006796 | phosphate metabolic process | 0.000224555448856817 |
| GO:0005085 | guanyl-nucleotide exchange factor activity | 0.000249065636103417 |
| GO:0048519 | negative regulation of biological process | 0.000271166935493937 |
| GO:0005083 | small GTPase regulator activity | 0.00105457326875663 |
| GO:0043687 | post-translational protein modification | 0.00279701940806723 |
| GO:0016310 | phosphorylation | 0.00475609600344279 |
| GO:0016773 | phosphotransferase activity, alcohol group as acceptor | 0.00480933041583784 |
| GO:0051056 | regulation of small GTPase mediated signal transduction | 0.00501149392782198 |
| GO:0007264 | small GTPase mediated signal transduction | 0.00788346418871303 |
| GO:0006468 | protein amino acid phosphorylation | 0.00888485381338819 |
| GO:0044424 | intracellular part | 0.00888485381338819 |
| GO:0045786 | negative regulation of progression through cell cycle | 0.0098002953816129 |
| GO:0050794 | regulation of cellular process | 0.00985184691038585 |
| GO:0065007 | biological regulation | 0.0105433643864069 |
| GO:0007265 | Ras protein signal transduction | 0.0105433643864069 |
| GO:0050789 | regulation of biological process | 0.0105433643864069 |
| GO:0008277 | regulation of G-protein coupled receptor protein signaling pathway | 0.0109549788468241 |
| GO:0004691 | cAMP-dependent protein kinase activity | 0.0114286417244299 |
| GO:0043412 | biopolymer modification | 0.0117317148626051 |
| GO:0004674 | protein serine/threonine kinase activity | 0.0128423856255069 |
| GO:0002376 | immune system process | 0.0128423856255069 |
| GO:0004715 | non-membrane spanning protein tyrosine kinase activity | 0.0128423856255069 |
| GO:0051020 | GTPase binding | 0.0143246460336337 |
| GO:0043621 | protein self-association | 0.0149288019354728 |
| GO:0006464 | protein modification process | 0.0149288019354728 |
| GO:0007498 | mesoderm development | 0.0152699367873361 |
| GO:0005070 | SH3/SH2 adaptor activity | 0.020155545189995 |
| GO:0004690 | cyclic nucleotide-dependent protein kinase activity | 0.020155545189995 |
| GO:0035004 | phosphoinositide 3-kinase activity | 0.0300857148965339 |
| GO:0016303 | 1-phosphatidylinositol-3-kinase activity | 0.0300857148965339 |
| GO:0031410 | cytoplasmic vesicle | 0.0300857148965339 |
| GO:0022610 | biological adhesion | 0.0300857148965339 |
| GO:0007155 | cell adhesion | 0.0300857148965339 |
| GO:0060090 | molecular adaptor activity | 0.0308849183944295 |
| GO:0031982 | vesicle | 0.0308849183944295 |
| GO:0007254 | JNK cascade | 0.0377042552840043 |
| GO:0016301 | kinase activity | 0.0382960047285508 |
| GO:0004672 | protein kinase activity | 0.0388422829624299 |
| GO:0031098 | stress-activated protein kinase signaling pathway | 0.0404099427357716 |
| GO:0000074 | regulation of progression through cell cycle | 0.0466701585089559 |
| GO:0051726 | regulation of cell cycle | 0.0497445654238121 |
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 | 2.53e-43 | 98 |
| blood island | 2.53e-43 | 98 |
| hemolymphoid system | 6.82e-39 | 108 |
| immune system | 1.59e-28 | 93 |
| bone marrow | 8.59e-28 | 76 |
| bone element | 5.36e-24 | 82 |
| skeletal element | 8.36e-20 | 90 |
| skeletal system | 3.33e-16 | 100 |
| adult organism | 8.74e-15 | 114 |
| connective tissue | 1.07e-12 | 371 |
| blood | 5.92e-12 | 15 |
| haemolymphatic fluid | 5.92e-12 | 15 |
| organism substance | 5.92e-12 | 15 |
| lateral plate mesoderm | 4.91e-10 | 203 |
| Ontology term | p-value | n |
|---|---|---|
| hematologic cancer | 1.46e-13 | 51 |
| immune system cancer | 1.46e-13 | 51 |
| leukemia | 1.06e-10 | 39 |
| myeloid leukemia | 2.75e-07 | 31 |
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 | 25 | 1.95802265211444 | 0.00121747767719077 | 0.0081927932427917 |
| BCL11A#53335 | 25 | 2.28050282183337 | 0.000134597234438146 | 0.00176442833782924 |
| CCNT2#905 | 69 | 1.40578105726824 | 0.00185924649470735 | 0.0109680210495222 |
| CTCF#10664 | 75 | 1.29266632791198 | 0.00969999569835197 | 0.0364973826688829 |
| E2F6#1876 | 83 | 1.33898368402213 | 0.00237987888553504 | 0.0134796990577794 |
| EBF1#1879 | 124 | 3.55113147580243 | 1.13785549189177e-38 | 6.25455209040447e-36 |
| EGR1#1958 | 134 | 2.14924758425903 | 2.48862897078138e-20 | 6.43341388810486e-18 |
| ELF1#1997 | 228 | 3.12169239423832 | 7.0546765553469e-77 | 8.66803958545735e-74 |
| ETS1#2113 | 67 | 2.09590669385066 | 4.32096525468803e-09 | 3.52560382995596e-07 |
| GABPB1#2553 | 103 | 2.34074416439474 | 2.15175186185779e-17 | 4.52166625152044e-15 |
| GATA1#2623 | 39 | 1.70048880259877 | 0.000870702796802549 | 0.00649584465999439 |
| HEY1#23462 | 105 | 1.36402462870128 | 0.000226171336606992 | 0.0024958905562022 |
| IRF4#3662 | 36 | 2.53672815666492 | 3.83290559628327e-07 | 1.87320930074978e-05 |
| MAX#4149 | 101 | 2.09552445790907 | 7.37544821467009e-14 | 1.17064503965339e-11 |
| MEF2A#4205 | 35 | 2.10936682262875 | 3.00898357121811e-05 | 0.000619344176575577 |
| MYC#4609 | 85 | 1.42731176555241 | 0.000278936036645551 | 0.00296990526365835 |
| NFKB1#4790 | 171 | 3.01755255799725 | 8.2862295969632e-48 | 5.69345745313973e-45 |
| PAX5#5079 | 105 | 2.25178257483496 | 1.35710136898059e-16 | 2.72042821257129e-14 |
| POLR2A#5430 | 294 | 2.03006827623175 | 2.17317920283812e-75 | 2.60878922718632e-72 |
| POU2F2#5452 | 99 | 2.89873402481193 | 3.79835507507458e-23 | 1.12697842524351e-20 |
| SIN3A#25942 | 96 | 1.66962358126769 | 9.67342133891119e-08 | 5.70136823484506e-06 |
| SP1#6667 | 88 | 1.61240373400771 | 1.91433974329882e-06 | 7.04481072763866e-05 |
| SPI1#6688 | 153 | 4.03621060065588 | 2.58329055838661e-57 | 2.2297213440276e-54 |
| SRF#6722 | 42 | 1.86328452415128 | 8.00107997729139e-05 | 0.00122489708552966 |
| STAT1#6772 | 25 | 1.66451667983916 | 0.00949735604708451 | 0.0357774624225025 |
| STAT2#6773 | 15 | 3.14777031445855 | 0.000113948675852865 | 0.0015601318507338 |
| TAF1#6872 | 182 | 1.95638078458406 | 1.30182250441192e-25 | 4.24878251682113e-23 |
| TBP#6908 | 147 | 1.75207489068543 | 1.74196730624563e-14 | 2.95820038206484e-12 |
| TCF12#6938 | 54 | 1.846498728997 | 8.49569769508425e-06 | 0.000231424666556313 |
| USF1#7391 | 65 | 1.32957380391806 | 0.00917277709632075 | 0.0346961597610605 |
| USF2#7392 | 52 | 2.17232882322707 | 1.10462079781917e-07 | 6.41632322043585e-06 |
| YY1#7528 | 140 | 2.21081641472521 | 1.11974543483412e-22 | 3.2216279192463e-20 |
| ZBTB7A#51341 | 78 | 1.843887221911 | 4.6534295720924e-08 | 3.0393966921811e-06 |
| ZEB1#6935 | 37 | 2.00923467732837 | 4.87850741035938e-05 | 0.000846918941872545 |
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
