Coexpression cluster:C175
From FANTOM5_SSTAR
Full id: C175_Eosinophils_Neutrophils_CD4_Basophils_CD19_CD8_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 |
|---|---|---|---|---|
| 3.29309746147737e-05 | 0.0104226534655759 | 6 | 295 | IL-2 down reg. targets (Netpath):NetPath_14 |
| 3.22276158462554e-05 | 0.0104226534655759 | 4 | 87 | {SP1,88} (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:0043231 | intracellular membrane-bound organelle | 2.00929791310734e-05 |
| GO:0043227 | membrane-bound organelle | 2.00929791310734e-05 |
| GO:0044424 | intracellular part | 2.00929791310734e-05 |
| GO:0005634 | nucleus | 2.23850107378566e-05 |
| GO:0050789 | regulation of biological process | 2.36490426387637e-05 |
| GO:0050794 | regulation of cellular process | 2.36490426387637e-05 |
| GO:0005622 | intracellular | 4.0132310206678e-05 |
| GO:0005515 | protein binding | 6.14241783218931e-05 |
| GO:0043229 | intracellular organelle | 6.14241783218931e-05 |
| GO:0043226 | organelle | 6.14241783218931e-05 |
| GO:0065007 | biological regulation | 0.000114041797104917 |
| GO:0008219 | cell death | 0.000114041797104917 |
| GO:0016265 | death | 0.000114041797104917 |
| GO:0043283 | biopolymer metabolic process | 0.000200635873300654 |
| GO:0007243 | protein kinase cascade | 0.00039507661929914 |
| GO:0006915 | apoptosis | 0.000544550867032678 |
| GO:0012501 | programmed cell death | 0.000544550867032678 |
| GO:0048468 | cell development | 0.00100894717394533 |
| GO:0043170 | macromolecule metabolic process | 0.0016171534722155 |
| GO:0007165 | signal transduction | 0.00163563275083118 |
| GO:0006512 | ubiquitin cycle | 0.00233480609996001 |
| GO:0048869 | cellular developmental process | 0.0025960305645621 |
| GO:0030154 | cell differentiation | 0.0025960305645621 |
| GO:0044238 | primary metabolic process | 0.0025960305645621 |
| GO:0043687 | post-translational protein modification | 0.0029134465650679 |
| GO:0007242 | intracellular signaling cascade | 0.00462050747171611 |
| GO:0007154 | cell communication | 0.00505811137582919 |
| GO:0008134 | transcription factor binding | 0.00553116473850967 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.00593178786824636 |
| GO:0044237 | cellular metabolic process | 0.00593178786824636 |
| GO:0043065 | positive regulation of apoptosis | 0.00661195532487194 |
| GO:0006351 | transcription, DNA-dependent | 0.00661195532487194 |
| GO:0032774 | RNA biosynthetic process | 0.00661195532487194 |
| GO:0043068 | positive regulation of programmed cell death | 0.00661195532487194 |
| GO:0006350 | transcription | 0.00702630858840345 |
| GO:0010468 | regulation of gene expression | 0.00767206357890407 |
| GO:0046966 | thyroid hormone receptor binding | 0.00809067641426571 |
| GO:0018193 | peptidyl-amino acid modification | 0.00874997488750814 |
| GO:0006464 | protein modification process | 0.00970417535690027 |
| GO:0045449 | regulation of transcription | 0.00978470602682331 |
| GO:0031323 | regulation of cellular metabolic process | 0.00978470602682331 |
| GO:0016563 | transcription activator activity | 0.0105269427212639 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.01070744314417 |
| GO:0043412 | biopolymer modification | 0.0120346947535803 |
| GO:0032502 | developmental process | 0.0140057100823751 |
| GO:0001667 | ameboidal cell migration | 0.0145462930256289 |
| GO:0046048 | UDP metabolic process | 0.0145462930256289 |
| GO:0009195 | pyrimidine ribonucleoside diphosphate catabolic process | 0.0145462930256289 |
| GO:0009140 | pyrimidine nucleoside diphosphate catabolic process | 0.0145462930256289 |
| GO:0009222 | pyrimidine ribonucleotide catabolic process | 0.0145462930256289 |
| GO:0009193 | pyrimidine ribonucleoside diphosphate metabolic process | 0.0145462930256289 |
| GO:0006256 | UDP catabolic process | 0.0145462930256289 |
| GO:0045134 | uridine-diphosphatase activity | 0.0145462930256289 |
| GO:0032027 | myosin light chain binding | 0.0145462930256289 |
| GO:0019222 | regulation of metabolic process | 0.0153136016538708 |
| GO:0016070 | RNA metabolic process | 0.0153136016538708 |
| GO:0048522 | positive regulation of cellular process | 0.0160668303072055 |
| GO:0001666 | response to hypoxia | 0.0190343299892699 |
| GO:0003713 | transcription coactivator activity | 0.0197477665414595 |
| GO:0035257 | nuclear hormone receptor binding | 0.0241535730739225 |
| GO:0044464 | cell part | 0.0241535730739225 |
| GO:0051427 | hormone receptor binding | 0.0241535730739225 |
| GO:0048518 | positive regulation of biological process | 0.0241535730739225 |
| GO:0042975 | peroxisome proliferator activated receptor binding | 0.0241535730739225 |
| GO:0009191 | ribonucleoside diphosphate catabolic process | 0.0241535730739225 |
| GO:0006917 | induction of apoptosis | 0.0251404959497479 |
| GO:0012502 | induction of programmed cell death | 0.0251404959497479 |
| GO:0018076 | N-terminal peptidyl-lysine acetylation | 0.0326867856542673 |
| GO:0006244 | pyrimidine nucleotide catabolic process | 0.0326867856542673 |
| GO:0047756 | chondroitin 4-sulfotransferase activity | 0.0326867856542673 |
| GO:0018394 | peptidyl-lysine acetylation | 0.0326867856542673 |
| GO:0009134 | nucleoside diphosphate catabolic process | 0.0326867856542673 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0406855338775701 |
| GO:0019888 | protein phosphatase regulator activity | 0.0406855338775701 |
| GO:0009185 | ribonucleoside diphosphate metabolic process | 0.041023657906431 |
| GO:0005131 | growth hormone receptor binding | 0.041023657906431 |
| GO:0019208 | phosphatase regulator activity | 0.041023657906431 |
| GO:0005737 | cytoplasm | 0.0477724148508908 |
| GO:0017110 | nucleoside-diphosphatase activity | 0.0477724148508908 |
| GO:0001537 | N-acetylgalactosamine 4-O-sulfotransferase activity | 0.0477724148508908 |
| GO:0008045 | motor axon guidance | 0.0477724148508908 |
| GO:0004718 | Janus kinase activity | 0.0477724148508908 |
| GO:0042981 | regulation of apoptosis | 0.048462135687202 |
| GO:0043067 | regulation of programmed cell death | 0.0496535213762199 |
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 |
|---|---|---|
| hematopoietic system | 9.71e-31 | 102 |
| blood island | 9.71e-31 | 102 |
| hemolymphoid system | 1.70e-27 | 112 |
| bone marrow | 4.91e-21 | 80 |
| adult organism | 5.52e-21 | 115 |
| bone element | 2.73e-19 | 86 |
| immune system | 6.86e-15 | 115 |
| skeletal element | 3.98e-14 | 101 |
| skeletal system | 3.98e-14 | 101 |
| blood | 3.19e-08 | 15 |
| haemolymphatic fluid | 3.19e-08 | 15 |
| organism substance | 3.19e-08 | 15 |
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) |
|---|---|
|
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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
No analysis results for this cluster
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
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