Coexpression cluster:C2383
From FANTOM5_SSTAR
Full id: C2383_Eosinophils_CD14_Monocytederived_Neutrophils_Alveolar_Mesenchymal_Melanocyte
Phase1 CAGE Peaks
| Hg19::chr16:67514983..67515130,- | p1@ATP6V0D1 |
| Hg19::chr19:48018203..48018358,- | p1@NAPA |
| Hg19::chr19:7587491..7587547,+ | p1@MCOLN1 |
| Hg19::chr1:44440575..44440646,+ | p1@ATP6V0B |
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 |
|---|---|---|---|---|
| 0.0001265553105429 | 0.0114442159390936 | 2 | 132 | Oxidative phosphorylation (KEGG):00190 |
| 2.96233908517502e-07 | 0.000187516064091579 | 3 | 121 | Lysosome (KEGG):04142 |
| 0.000176767794609482 | 0.0139867517484752 | 2 | 156 | Phagosome (KEGG):04145 |
| 2.10227775867002e-05 | 0.00443580607079374 | 2 | 54 | Vibrio cholerae infection (KEGG):05110 |
| 3.34441238781418e-05 | 0.00529253260371594 | 2 | 68 | Epithelial cell signaling in Helicobacter pylori infection (KEGG):05120 |
| 0.000240529056385976 | 0.016917210299147 | 2 | 182 | Tuberculosis (KEGG):05152 |
| 6.13871776917587e-05 | 0.00777161669577665 | 2 | 92 | Rheumatoid arthritis (KEGG):05323 |
| 8.46702301374934e-05 | 0.00893270927950556 | 2 | 108 | Signaling by Insulin receptor (Reactome):REACT_498 |
| 1.08913416837795e-05 | 0.00344710964291621 | 3 | 401 | Transmembrane transport of small molecules (Reactome):REACT_15518 |
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:0005774 | vacuolar membrane | 2.12690639495335e-06 |
| GO:0044437 | vacuolar part | 2.12690639495335e-06 |
| GO:0005773 | vacuole | 7.05626795813025e-05 |
| GO:0046933 | hydrogen ion transporting ATP synthase activity, rotational mechanism | 0.000654494485802874 |
| GO:0046961 | hydrogen ion transporting ATPase activity, rotational mechanism | 0.000654494485802874 |
| GO:0015985 | energy coupled proton transport, down electrochemical gradient | 0.000654494485802874 |
| GO:0015986 | ATP synthesis coupled proton transport | 0.000654494485802874 |
| GO:0006754 | ATP biosynthetic process | 0.000654494485802874 |
| GO:0006753 | nucleoside phosphate metabolic process | 0.000654494485802874 |
| GO:0046034 | ATP metabolic process | 0.000679327575874629 |
| GO:0019829 | cation-transporting ATPase activity | 0.000679327575874629 |
| GO:0016469 | proton-transporting two-sector ATPase complex | 0.000679327575874629 |
| GO:0006812 | cation transport | 0.000679327575874629 |
| GO:0008324 | cation transmembrane transporter activity | 0.000679327575874629 |
| GO:0009145 | purine nucleoside triphosphate biosynthetic process | 0.000679327575874629 |
| GO:0009206 | purine ribonucleoside triphosphate biosynthetic process | 0.000679327575874629 |
| GO:0009201 | ribonucleoside triphosphate biosynthetic process | 0.000679327575874629 |
| GO:0009142 | nucleoside triphosphate biosynthetic process | 0.000679327575874629 |
| GO:0009205 | purine ribonucleoside triphosphate metabolic process | 0.000679327575874629 |
| GO:0009144 | purine nucleoside triphosphate metabolic process | 0.000679327575874629 |
| GO:0009199 | ribonucleoside triphosphate metabolic process | 0.000679327575874629 |
| GO:0015992 | proton transport | 0.000679327575874629 |
| GO:0006818 | hydrogen transport | 0.000679327575874629 |
| GO:0006752 | group transfer coenzyme metabolic process | 0.000680308140524998 |
| GO:0009141 | nucleoside triphosphate metabolic process | 0.00071262377934093 |
| GO:0009152 | purine ribonucleotide biosynthetic process | 0.00071262377934093 |
| GO:0009150 | purine ribonucleotide metabolic process | 0.000722588983265508 |
| GO:0009260 | ribonucleotide biosynthetic process | 0.000722588983265508 |
| GO:0006119 | oxidative phosphorylation | 0.000722588983265508 |
| GO:0006164 | purine nucleotide biosynthetic process | 0.000722588983265508 |
| GO:0006163 | purine nucleotide metabolic process | 0.000765303057262317 |
| GO:0009259 | ribonucleotide metabolic process | 0.000765303057262317 |
| GO:0009108 | coenzyme biosynthetic process | 0.000976243098870716 |
| GO:0006810 | transport | 0.000976243098870716 |
| GO:0015078 | hydrogen ion transmembrane transporter activity | 0.000992598112457579 |
| GO:0051234 | establishment of localization | 0.000992598112457579 |
| GO:0042625 | ATPase activity, coupled to transmembrane movement of ions | 0.000992598112457579 |
| GO:0015075 | ion transmembrane transporter activity | 0.00100129924810985 |
| GO:0015077 | monovalent inorganic cation transmembrane transporter activity | 0.00102071509263668 |
| GO:0051188 | cofactor biosynthetic process | 0.00102071509263668 |
| GO:0006811 | ion transport | 0.00102071509263668 |
| GO:0051179 | localization | 0.0012022022451786 |
| GO:0009165 | nucleotide biosynthetic process | 0.00125724219440041 |
| GO:0044444 | cytoplasmic part | 0.00125724219440041 |
| GO:0031090 | organelle membrane | 0.00125724219440041 |
| GO:0022891 | substrate-specific transmembrane transporter activity | 0.00125724219440041 |
| GO:0022890 | inorganic cation transmembrane transporter activity | 0.00134974205414562 |
| GO:0042626 | ATPase activity, coupled to transmembrane movement of substances | 0.00134974205414562 |
| GO:0043492 | ATPase activity, coupled to movement of substances | 0.00134974205414562 |
| GO:0016820 | hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances | 0.00137805436761323 |
| GO:0006732 | coenzyme metabolic process | 0.00137805436761323 |
| GO:0022857 | transmembrane transporter activity | 0.00137805436761323 |
| GO:0015399 | primary active transmembrane transporter activity | 0.0014539511882513 |
| GO:0015405 | P-P-bond-hydrolysis-driven transmembrane transporter activity | 0.0014539511882513 |
| GO:0022892 | substrate-specific transporter activity | 0.0016371179135362 |
| GO:0009117 | nucleotide metabolic process | 0.00176300585492439 |
| GO:0051186 | cofactor metabolic process | 0.00176300585492439 |
| GO:0055086 | nucleobase, nucleoside and nucleotide metabolic process | 0.00198205606435121 |
| GO:0033176 | proton-transporting V-type ATPase complex | 0.00229343837091778 |
| GO:0016471 | vacuolar proton-transporting V-type ATPase complex | 0.00229343837091778 |
| GO:0045176 | apical protein localization | 0.00257799018318488 |
| GO:0008105 | asymmetric protein localization | 0.00317023212644919 |
| GO:0042623 | ATPase activity, coupled | 0.00369739411654434 |
| GO:0015672 | monovalent inorganic cation transport | 0.00369739411654434 |
| GO:0006891 | intra-Golgi vesicle-mediated transport | 0.00506942459940437 |
| GO:0016887 | ATPase activity | 0.00506942459940437 |
| GO:0008553 | hydrogen-exporting ATPase activity, phosphorylative mechanism | 0.00527870060479556 |
| GO:0019905 | syntaxin binding | 0.00547717104572753 |
| GO:0022804 | active transmembrane transporter activity | 0.00547717104572753 |
| GO:0005737 | cytoplasm | 0.00560961641398419 |
| GO:0000149 | SNARE binding | 0.00581075732840653 |
| GO:0031902 | late endosome membrane | 0.00791013438453246 |
| GO:0006944 | membrane fusion | 0.00993720419036831 |
| GO:0006091 | generation of precursor metabolites and energy | 0.00993720419036831 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0100104220092021 |
| GO:0043227 | membrane-bound organelle | 0.0100104220092021 |
| GO:0017111 | nucleoside-triphosphatase activity | 0.0108493781914646 |
| GO:0016462 | pyrophosphatase activity | 0.0115653026832529 |
| GO:0016818 | hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides | 0.0116131230087479 |
| GO:0016817 | hydrolase activity, acting on acid anhydrides | 0.0116181970340841 |
| GO:0005765 | lysosomal membrane | 0.0122026095197474 |
| GO:0005770 | late endosome | 0.0122026095197474 |
| GO:0044446 | intracellular organelle part | 0.012978169055937 |
| GO:0044422 | organelle part | 0.012978169055937 |
| GO:0016020 | membrane | 0.0133078004997655 |
| GO:0016310 | phosphorylation | 0.0185497400184379 |
| GO:0043229 | intracellular organelle | 0.0187225231232309 |
| GO:0044440 | endosomal part | 0.0187225231232309 |
| GO:0010008 | endosome membrane | 0.0187225231232309 |
| GO:0043226 | organelle | 0.0187225231232309 |
| GO:0048193 | Golgi vesicle transport | 0.0191564945824311 |
| GO:0006793 | phosphorus metabolic process | 0.0251155195204847 |
| GO:0006796 | phosphate metabolic process | 0.0251155195204847 |
| GO:0007420 | brain development | 0.0288998111940217 |
| GO:0015662 | ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism | 0.0298220377738366 |
| GO:0044249 | cellular biosynthetic process | 0.0314260659506957 |
| GO:0044424 | intracellular part | 0.0364240838290581 |
| GO:0006816 | calcium ion transport | 0.0364240838290581 |
| GO:0005768 | endosome | 0.0380096433782001 |
| GO:0005764 | lysosome | 0.0389788408700863 |
| GO:0000323 | lytic vacuole | 0.0389788408700863 |
| GO:0030182 | neuron differentiation | 0.040111091519398 |
| GO:0007417 | central nervous system development | 0.0442719283451152 |
| GO:0046872 | metal ion binding | 0.0442719283451152 |
| GO:0045045 | secretory pathway | 0.0442719283451152 |
| GO:0048699 | generation of neurons | 0.0442719283451152 |
| GO:0009058 | biosynthetic process | 0.0442719283451152 |
| GO:0015674 | di-, tri-valent inorganic cation transport | 0.0444844505046673 |
| GO:0043167 | ion binding | 0.0445540920969773 |
| GO:0022008 | neurogenesis | 0.0462972966958267 |
| GO:0016044 | membrane organization and biogenesis | 0.0496843878099752 |
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>
| Ontology term | p-value | n |
|---|---|---|
| myeloid leukocyte | 1.66e-31 | 72 |
| macrophage dendritic cell progenitor | 2.55e-30 | 61 |
| defensive cell | 1.23e-29 | 48 |
| phagocyte | 1.23e-29 | 48 |
| monopoietic cell | 1.73e-29 | 59 |
| monocyte | 1.73e-29 | 59 |
| monoblast | 1.73e-29 | 59 |
| promonocyte | 1.73e-29 | 59 |
| myeloid lineage restricted progenitor cell | 3.47e-28 | 66 |
| granulocyte monocyte progenitor cell | 5.85e-27 | 67 |
| classical monocyte | 1.09e-25 | 42 |
| CD14-positive, CD16-negative classical monocyte | 1.09e-25 | 42 |
| stuff accumulating cell | 1.96e-24 | 87 |
| myeloid cell | 2.00e-15 | 108 |
| common myeloid progenitor | 2.00e-15 | 108 |
| somatic cell | 8.62e-09 | 588 |
| somatic stem cell | 1.65e-08 | 433 |
| multi fate stem cell | 2.14e-08 | 427 |
| smooth muscle cell | 6.51e-08 | 43 |
| smooth muscle myoblast | 6.51e-08 | 43 |
| vascular associated smooth muscle cell | 1.08e-07 | 32 |
| stem cell | 1.94e-07 | 441 |
| mesodermal cell | 3.14e-07 | 121 |
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) |
|---|---|
| MA0003.1 | 0.720743 |
| MA0004.1 | 5.48953 |
| MA0006.1 | 0.532262 |
| MA0007.1 | 0.6918 |
| MA0009.1 | 1.20602 |
| MA0014.1 | 0.896009 |
| MA0017.1 | 0.577281 |
| MA0019.1 | 0.873355 |
| MA0024.1 | 1.09684 |
| MA0025.1 | 1.34373 |
| MA0027.1 | 2.83281 |
| MA0028.1 | 0.550763 |
| MA0029.1 | 1.11704 |
| MA0030.1 | 1.10506 |
| MA0031.1 | 1.03735 |
| MA0038.1 | 0.824639 |
| MA0040.1 | 1.12314 |
| MA0041.1 | 0.732902 |
| MA0042.1 | 0.697662 |
| MA0043.1 | 1.20635 |
| MA0046.1 | 1.19471 |
| MA0048.1 | 0.709734 |
| MA0050.1 | 0.69864 |
| MA0051.1 | 0.820063 |
| MA0052.1 | 1.12718 |
| MA0055.1 | 0.396851 |
| MA0056.1 | 0 |
| MA0057.1 | 0.248209 |
| MA0058.1 | 10.5809 |
| MA0059.1 | 2.50216 |
| MA0060.1 | 1.01899 |
| MA0061.1 | 0.360128 |
| MA0063.1 | 0 |
| MA0066.1 | 0.825101 |
| MA0067.1 | 1.53181 |
| MA0068.1 | 0.313194 |
| MA0069.1 | 1.19071 |
| MA0070.1 | 1.17908 |
| MA0071.1 | 0.782546 |
| MA0072.1 | 1.1744 |
| MA0073.1 | 0.380957 |
| MA0074.1 | 0.819248 |
| MA0076.1 | 0.623864 |
| MA0077.1 | 1.16637 |
| MA0078.1 | 0.926725 |
| MA0081.1 | 0.604638 |
| MA0083.1 | 1.21381 |
| MA0084.1 | 1.72172 |
| MA0087.1 | 1.17185 |
| MA0088.1 | 1.02755 |
| MA0089.1 | 0 |
| MA0090.1 | 0.640115 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 9.86257 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.83965 |
| MA0101.1 | 0.539569 |
| MA0103.1 | 0.521546 |
| MA0105.1 | 0.232357 |
| MA0106.1 | 0.869173 |
| MA0107.1 | 0.453492 |
| MA0108.2 | 1.03412 |
| MA0109.1 | 0 |
| MA0111.1 | 0.655276 |
| MA0113.1 | 0.886811 |
| MA0114.1 | 0.447443 |
| MA0115.1 | 1.45393 |
| MA0116.1 | 1.15856 |
| MA0117.1 | 1.24497 |
| MA0119.1 | 1.43218 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 0.94608 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 0.912459 |
| MA0140.1 | 0.779643 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 0.887001 |
| MA0144.1 | 1.09982 |
| MA0145.1 | 0.569905 |
| MA0146.1 | 0.481 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.931615 |
| MA0035.2 | 0.778873 |
| MA0039.2 | 0.483275 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 0.379056 |
| MA0137.2 | 0.558189 |
| MA0104.2 | 1.79838 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 0.187982 |
| MA0065.2 | 0.199162 |
| MA0150.1 | 0.633493 |
| MA0151.1 | 0 |
| MA0152.1 | 0.78681 |
| MA0153.1 | 1.30799 |
| MA0154.1 | 0.229241 |
| MA0155.1 | 0.180766 |
| MA0156.1 | 0.560797 |
| MA0157.1 | 0.97481 |
| MA0158.1 | 0 |
| MA0159.1 | 0.462502 |
| MA0160.1 | 0.756582 |
| MA0161.1 | 0 |
| MA0162.1 | 1.06783 |
| MA0163.1 | 0.539587 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 0.535868 |
| MA0018.2 | 0.870662 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 0.20937 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 1.07498 |
| MA0259.1 | 0.471671 |
| MA0442.1 | 0 |
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 |
|---|---|---|---|---|
| ATF3#467 | 4 | 22.4631745260087 | 3.92475754624726e-06 | 0.00012733698458295 |
| CCNT2#905 | 4 | 6.33620157696263 | 0.000620310058721564 | 0.00511807254090863 |
| E2F1#1869 | 4 | 4.90738921487932 | 0.00172402235736179 | 0.0106440748983511 |
| E2F4#1874 | 4 | 12.6680603152844 | 3.88145892637771e-05 | 0.000726219435349269 |
| E2F6#1876 | 4 | 5.01715573169739 | 0.0015780219347306 | 0.0099641495067309 |
| ELF1#1997 | 4 | 4.25809795880754 | 0.00304152556578124 | 0.0160780426463849 |
| EP300#2033 | 3 | 5.0804562946674 | 0.0114429840539824 | 0.0418860862054488 |
| ETS1#2113 | 4 | 9.72876092220234 | 0.000111595531741814 | 0.00154451706063918 |
| FOS#2353 | 4 | 8.9979553088944 | 0.000152514771116863 | 0.0019477244045823 |
| FOSL2#2355 | 3 | 12.6976504534213 | 0.00078756857297571 | 0.00616588262316418 |
| GABPB1#2553 | 3 | 5.30076287713663 | 0.0101267882423427 | 0.0378536734875459 |
| HEY1#23462 | 4 | 4.04011104310571 | 0.0037530463691798 | 0.0185862017995528 |
| HMGN3#9324 | 4 | 8.17854772335059 | 0.000223457028444047 | 0.00248008805458745 |
| IRF1#3659 | 4 | 7.6371637535639 | 0.000293885399618549 | 0.00307268968372826 |
| MAX#4149 | 4 | 6.45255550900712 | 0.000576761319564549 | 0.00485190297656077 |
| MXI1#4601 | 3 | 7.47117872156947 | 0.00374131473855096 | 0.018631469100683 |
| MYC#4609 | 4 | 5.2222818716094 | 0.00134430939527274 | 0.00887025075391012 |
| NANOG#79923 | 3 | 21.9335838607595 | 0.000155753581638277 | 0.00196482042670854 |
| NFE2#4778 | 4 | 77.204260651629 | 2.80776035215453e-08 | 1.9165992380305e-06 |
| NFKB1#4790 | 4 | 5.48806342419384 | 0.00110219956630198 | 0.00767570984230261 |
| NR3C1#2908 | 3 | 11.2297674983798 | 0.00113167206806385 | 0.00775427759588773 |
| NRF1#4899 | 4 | 12.2102794477109 | 4.49717228915276e-05 | 0.000793244682835375 |
| PAX5#5079 | 4 | 6.66956553117783 | 0.000505277416948326 | 0.00443600102123959 |
| POU2F2#5452 | 3 | 6.82959304330689 | 0.00486047377520374 | 0.0227552008520936 |
| RXRA#6256 | 2 | 10.0373085695666 | 0.0139170380592011 | 0.048876237065872 |
| SIN3A#25942 | 4 | 5.40888472681514 | 0.00116817238488516 | 0.00795635553052177 |
| SIX5#147912 | 3 | 12.8150365165942 | 0.000766447113693038 | 0.006014951165238 |
| SMARCB1#6598 | 3 | 13.6895368358681 | 0.000630578340937934 | 0.0051815083673656 |
| SMARCC2#6601 | 2 | 47.0776872134488 | 0.000666928296709587 | 0.00545018187637344 |
| SRF#6722 | 3 | 10.3478836966259 | 0.00143989377840126 | 0.00923659887736929 |
| STAT1#6772 | 2 | 10.3532937485996 | 0.0131077747617126 | 0.0464890443284037 |
| TAF1#6872 | 4 | 3.34304628574529 | 0.00800566489870165 | 0.0321887829203273 |
| TBP#6908 | 4 | 3.70677068709639 | 0.00529637781478435 | 0.0243935615892689 |
| THAP1#55145 | 4 | 31.3691446028513 | 1.03171810326891e-06 | 4.31697143378613e-05 |
| USF1#7391 | 4 | 6.36149927720796 | 0.000610501139914083 | 0.00507644335601011 |
| USF2#7392 | 4 | 12.9921973850696 | 3.50833029870167e-05 | 0.000681179602279426 |
| YY1#7528 | 4 | 4.91117074985386 | 0.0017187183805544 | 0.0106737960960172 |
| ZNF143#7702 | 3 | 10.1256574141709 | 0.00153486161068818 | 0.00976423291458021 |
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.
