Coexpression cluster:C2428
From FANTOM5_SSTAR
Full id: C2428_Mast_CD14_Eosinophils_immature_CD19_CD4_CD8
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Hg19::chr17:62502942..62502965,- | p6@DDX5 |
| Hg19::chr2:157189180..157189290,- | p1@NR4A2 |
| Hg19::chr2:157189298..157189305,- | p23@NR4A2 |
| Hg19::chr9:102584128..102584144,+ | p3@NR4A3 |
Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont
link to source dataset
data
No results for this coexpression
Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner
link to source dataset
data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0003707 | steroid hormone receptor activity | 0.00364664345425225 |
| GO:0004879 | ligand-dependent nuclear receptor activity | 0.00364664345425225 |
| GO:0042053 | regulation of dopamine metabolic process | 0.0106843266182394 |
| GO:0042069 | regulation of catecholamine metabolic process | 0.0106843266182394 |
| GO:0004887 | thyroid hormone receptor activity | 0.0195838960000424 |
| GO:0042417 | dopamine metabolic process | 0.0195838960000424 |
| GO:0016070 | RNA metabolic process | 0.0284680595302614 |
| GO:0043565 | sequence-specific DNA binding | 0.0284680595302614 |
| GO:0006584 | catecholamine metabolic process | 0.0284680595302614 |
| GO:0018958 | phenol metabolic process | 0.0284680595302614 |
| GO:0003724 | RNA helicase activity | 0.0284680595302614 |
| GO:0042133 | neurotransmitter metabolic process | 0.0284680595302614 |
| GO:0010467 | gene expression | 0.038496700016013 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0428660141712666 |
| GO:0003700 | transcription factor activity | 0.0428660141712666 |
| GO:0005634 | nucleus | 0.0428660141712666 |
| GO:0006576 | biogenic amine metabolic process | 0.0437664922796501 |
| GO:0003676 | nucleic acid binding | 0.0437664922796501 |
| GO:0001505 | regulation of neurotransmitter levels | 0.0437664922796501 |
| GO:0065007 | biological regulation | 0.0456741439377732 |
| GO:0006575 | amino acid derivative metabolic process | 0.0456741439377732 |
Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji
links to source dataset
cell_data
uberon_data
| Ontology term | p-value | n |
|---|---|---|
| myeloid leukocyte | 5.32e-25 | 72 |
| classical monocyte | 1.13e-24 | 42 |
| CD14-positive, CD16-negative classical monocyte | 1.13e-24 | 42 |
| leukocyte | 2.92e-24 | 136 |
| defensive cell | 1.55e-22 | 48 |
| phagocyte | 1.55e-22 | 48 |
| granulocyte monocyte progenitor cell | 6.83e-22 | 67 |
| macrophage dendritic cell progenitor | 1.46e-19 | 61 |
| myeloid lineage restricted progenitor cell | 8.04e-19 | 66 |
| hematopoietic stem cell | 2.36e-18 | 168 |
| angioblastic mesenchymal cell | 2.36e-18 | 168 |
| monopoietic cell | 2.41e-18 | 59 |
| monocyte | 2.41e-18 | 59 |
| monoblast | 2.41e-18 | 59 |
| promonocyte | 2.41e-18 | 59 |
| hematopoietic lineage restricted progenitor cell | 1.12e-17 | 120 |
| nongranular leukocyte | 9.99e-17 | 115 |
| myeloid cell | 1.86e-16 | 108 |
| common myeloid progenitor | 1.86e-16 | 108 |
| hematopoietic oligopotent progenitor cell | 3.47e-16 | 161 |
| hematopoietic multipotent progenitor cell | 3.47e-16 | 161 |
| hematopoietic cell | 8.28e-16 | 177 |
| stuff accumulating cell | 5.49e-08 | 87 |
| Ontology term | p-value | n |
|---|---|---|
| bone marrow | 1.54e-17 | 76 |
| bone element | 3.44e-17 | 82 |
| hematopoietic system | 1.14e-15 | 98 |
| blood island | 1.14e-15 | 98 |
| skeletal element | 9.33e-14 | 90 |
| skeletal system | 6.82e-13 | 100 |
| immune system | 1.55e-12 | 93 |
| hemolymphoid system | 1.10e-11 | 108 |
| adult organism | 8.80e-11 | 114 |
Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon
link to source data
Novel motifs
data
Jaspar motifs
data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 0.720743 |
| MA0004.1 | 0.71247 |
| MA0006.1 | 1.31813 |
| 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 | 2.49947 |
| 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 | 0.605914 |
| MA0059.1 | 0.604454 |
| MA0060.1 | 1.80156 |
| 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 | 0.866596 |
| MA0074.1 | 1.91637 |
| 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 | 0.182167 |
| MA0089.1 | 0 |
| MA0090.1 | 1.54523 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 0.535768 |
| 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 | 2.78257 |
| MA0119.1 | 0.586221 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 2.17614 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 0.344952 |
| MA0140.1 | 0.779643 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 0.887001 |
| MA0144.1 | 1.09982 |
| MA0145.1 | 1.08195 |
| MA0146.1 | 0.221129 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.931615 |
| MA0035.2 | 0.778873 |
| MA0039.2 | 0.0247757 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 0.379056 |
| MA0137.2 | 1.37305 |
| MA0104.2 | 0.392359 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 1.65877 |
| 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 | 0.640035 |
| MA0163.1 | 0.0725493 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 0.535868 |
| MA0018.2 | 3.34398 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 0.327251 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 0.418966 |
| MA0259.1 | 0.471671 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner
link to source dataset
data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| BRCA1#672 | 3 | 15.1381729824178 | 0.000468218442143119 | 0.00430119323414418 |
| CCNT2#905 | 4 | 6.33620157696263 | 0.000620310058721564 | 0.00512049970145601 |
| CTBP2#1488 | 2 | 31.3585001696641 | 0.00149267688204723 | 0.00954003309981829 |
| E2F1#1869 | 4 | 4.90738921487932 | 0.00172402235736179 | 0.010647851625104 |
| E2F4#1874 | 3 | 9.50104523646333 | 0.00185075103472827 | 0.0109271630570403 |
| E2F6#1876 | 4 | 5.01715573169739 | 0.0015780219347306 | 0.0099665597993063 |
| ELF1#1997 | 4 | 4.25809795880754 | 0.00304152556578124 | 0.0160845556010242 |
| ELK4#2005 | 3 | 12.176761243851 | 0.000891263257762061 | 0.00663738187231973 |
| ETS1#2113 | 3 | 7.29657069165175 | 0.0040085737751139 | 0.0192041943348221 |
| FOXA1#3169 | 4 | 11.0814197493855 | 6.62943068949433e-05 | 0.00107029078958123 |
| GABPB1#2553 | 3 | 5.30076287713663 | 0.0101267882423427 | 0.0378577383842944 |
| HEY1#23462 | 4 | 4.04011104310571 | 0.0037530463691798 | 0.0185959014019722 |
| IRF1#3659 | 4 | 7.6371637535639 | 0.000293885399618549 | 0.00307392060598514 |
| MAX#4149 | 3 | 4.83941663175534 | 0.0131573713783684 | 0.0466190361441652 |
| MYC#4609 | 4 | 5.2222818716094 | 0.00134430939527274 | 0.00887417539554322 |
| NFYA#4800 | 3 | 13.8191855248729 | 0.000613241180673451 | 0.00508707670121959 |
| NFYB#4801 | 3 | 12.5698449401523 | 0.00081145639769735 | 0.0061886734861336 |
| RFX5#5993 | 3 | 9.03593312039632 | 0.00214456119132407 | 0.0123846185380533 |
| SETDB1#9869 | 2 | 20.1600130890052 | 0.0035690868540764 | 0.0180842160854301 |
| SIN3A#25942 | 4 | 5.40888472681514 | 0.00116817238488516 | 0.00795946997031712 |
| SP1#6667 | 4 | 5.6983813781409 | 0.000948260606533398 | 0.00683851605342781 |
| TAF1#6872 | 4 | 3.34304628574529 | 0.00800566489870165 | 0.0322061413795887 |
| TBP#6908 | 4 | 3.70677068709639 | 0.00529637781478435 | 0.024408631303427 |
| TCF7L2#6934 | 4 | 10.7701765631373 | 7.42969445082454e-05 | 0.00115400038481509 |
| USF1#7391 | 4 | 6.36149927720796 | 0.000610501139914083 | 0.00507846503795197 |
| YY1#7528 | 4 | 4.91117074985386 | 0.0017187183805544 | 0.0106814179676716 |
Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA
link to data source
data
This analysis result is provided for C0 - C305 clusters.
