Coexpression cluster:C71
From FANTOM5_SSTAR
Full id: C71_Monocytederived_Macrophage_CD14_Dendritic_Osteoblast_leiomyoma_Prostate
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 |
|---|---|---|---|---|
| 3.8301284794605e-14 | 2.4244713274985e-11 | 8 | 121 | Lysosome (KEGG):04142 |
| 3.34125815597961e-05 | 0.00528754103183774 | 3 | 78 | Antigen processing and presentation (KEGG):04612 |
| 6.61023887274438e-05 | 0.00836856241289439 | 3 | 98 | EGFR1 down reg. targets (Netpath):NetPath_4 |
| 2.05892215321743e-05 | 0.00434432574328877 | 6 | 740 | TGF beta receptor down reg. targets (Netpath):NetPath_7 |
| 1.1735530280982e-06 | 0.000371429533393079 | 3 | 26 | {CTSB,26} (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:0005764 | lysosome | 1.0480335735187e-12 |
| GO:0000323 | lytic vacuole | 1.0480335735187e-12 |
| GO:0005773 | vacuole | 2.55788396001967e-12 |
| GO:0048770 | pigment granule | 2.00977059816662e-05 |
| GO:0042470 | melanosome | 2.00977059816662e-05 |
| GO:0004197 | cysteine-type endopeptidase activity | 0.000144102989006187 |
| GO:0044444 | cytoplasmic part | 0.000543690591520644 |
| GO:0004175 | endopeptidase activity | 0.000543690591520644 |
| GO:0016787 | hydrolase activity | 0.000695068473515278 |
| GO:0008234 | cysteine-type peptidase activity | 0.00148800656465349 |
| GO:0043231 | intracellular membrane-bound organelle | 0.00148800656465349 |
| GO:0043227 | membrane-bound organelle | 0.00148800656465349 |
| GO:0006687 | glycosphingolipid metabolic process | 0.00203212951820557 |
| GO:0016023 | cytoplasmic membrane-bound vesicle | 0.00203212951820557 |
| GO:0031988 | membrane-bound vesicle | 0.00203212951820557 |
| GO:0008233 | peptidase activity | 0.00302605906957373 |
| GO:0006664 | glycolipid metabolic process | 0.00324472019915184 |
| GO:0031410 | cytoplasmic vesicle | 0.00324472019915184 |
| GO:0005737 | cytoplasm | 0.00324472019915184 |
| GO:0031982 | vesicle | 0.00324472019915184 |
| GO:0006508 | proteolysis | 0.00324472019915184 |
| GO:0042007 | interleukin-18 binding | 0.00828775827557786 |
| GO:0030290 | sphingolipid activator protein activity | 0.00828775827557786 |
| GO:0032428 | beta-N-acetylgalactosaminidase activity | 0.00828775827557786 |
| GO:0004213 | cathepsin B activity | 0.00828775827557786 |
| GO:0004192 | cathepsin D activity | 0.00828775827557786 |
| GO:0004215 | cathepsin H activity | 0.00828775827557786 |
| GO:0004229 | gelatinase B activity | 0.00828775827557786 |
| GO:0030984 | kininogen binding | 0.00828775827557786 |
| GO:0006665 | sphingolipid metabolic process | 0.0115021181945284 |
| GO:0043229 | intracellular organelle | 0.0123213930737607 |
| GO:0043226 | organelle | 0.0123213930737607 |
| GO:0004098 | cerebroside-sulfatase activity | 0.0123213930737607 |
| GO:0005889 | hydrogen:potassium-exchanging ATPase complex | 0.0123213930737607 |
| GO:0004557 | alpha-galactosidase activity | 0.0123213930737607 |
| GO:0016004 | phospholipase activator activity | 0.0123213930737607 |
| GO:0045179 | apical cortex | 0.0123213930737607 |
| GO:0030156 | benzodiazepine receptor binding | 0.0123213930737607 |
| GO:0009313 | oligosaccharide catabolic process | 0.0123213930737607 |
| GO:0045177 | apical part of cell | 0.0137390754098811 |
| GO:0005319 | lipid transporter activity | 0.0166542704452397 |
| GO:0004336 | galactosylceramidase activity | 0.0171563837113442 |
| GO:0004563 | beta-N-acetylhexosaminidase activity | 0.0218283282762773 |
| GO:0006689 | ganglioside catabolic process | 0.0218283282762773 |
| GO:0046479 | glycosphingolipid catabolic process | 0.0255355193792421 |
| GO:0008133 | collagenase activity | 0.0255355193792421 |
| GO:0004348 | glucosylceramidase activity | 0.0255355193792421 |
| GO:0006869 | lipid transport | 0.0266617983691264 |
| GO:0044424 | intracellular part | 0.0266617983691264 |
| GO:0008081 | phosphoric diester hydrolase activity | 0.0266617983691264 |
| GO:0007130 | synaptonemal complex assembly | 0.0266617983691264 |
| GO:0004630 | phospholipase D activity | 0.0266617983691264 |
| GO:0009898 | internal side of plasma membrane | 0.0266617983691264 |
| GO:0001509 | legumain activity | 0.0266617983691264 |
| GO:0016042 | lipid catabolic process | 0.0282327712385623 |
| GO:0019377 | glycolipid catabolic process | 0.0294364417697988 |
| GO:0007129 | synapsis | 0.0294364417697988 |
| GO:0005102 | receptor binding | 0.0294364417697988 |
| GO:0005615 | extracellular space | 0.0314492967441854 |
| GO:0019915 | sequestering of lipid | 0.0314492967441854 |
| GO:0001573 | ganglioside metabolic process | 0.0314492967441854 |
| GO:0004767 | sphingomyelin phosphodiesterase activity | 0.0337110872120385 |
| GO:0030547 | receptor inhibitor activity | 0.0337110872120385 |
| GO:0048019 | receptor antagonist activity | 0.0337110872120385 |
| GO:0042578 | phosphoric ester hydrolase activity | 0.0360876906578836 |
| GO:0016788 | hydrolase activity, acting on ester bonds | 0.0371161970695443 |
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | 0.0371161970695443 |
| GO:0030545 | receptor regulator activity | 0.0371161970695443 |
| GO:0003709 | RNA polymerase III transcription factor activity | 0.0371161970695443 |
| GO:0030225 | macrophage differentiation | 0.0371161970695443 |
| GO:0004565 | beta-galactosidase activity | 0.0371161970695443 |
| GO:0042088 | T-helper 1 type immune response | 0.0383185081814939 |
| GO:0017040 | ceramidase activity | 0.0383185081814939 |
| GO:0015925 | galactosidase activity | 0.0383185081814939 |
| GO:0050832 | defense response to fungus | 0.0383185081814939 |
| GO:0000795 | synaptonemal complex | 0.0409522584277374 |
| GO:0016798 | hydrolase activity, acting on glycosyl bonds | 0.0445242020859973 |
| GO:0030149 | sphingolipid catabolic process | 0.0460112216962742 |
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 |
|---|---|---|
| bone marrow | 4.60e-44 | 76 |
| bone element | 1.15e-39 | 82 |
| immune system | 7.74e-38 | 93 |
| hematopoietic system | 6.53e-35 | 98 |
| blood island | 6.53e-35 | 98 |
| skeletal element | 1.01e-34 | 90 |
| skeletal system | 3.28e-34 | 100 |
| hemolymphoid system | 1.09e-31 | 108 |
| musculoskeletal system | 4.84e-22 | 167 |
| lateral plate mesoderm | 1.69e-16 | 203 |
| mesoderm | 3.74e-16 | 315 |
| mesoderm-derived structure | 3.74e-16 | 315 |
| presumptive mesoderm | 3.74e-16 | 315 |
| connective tissue | 3.71e-09 | 371 |
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 | 8.71154e-08 |
| MA0004.1 | 0.0166162 |
| MA0006.1 | 0.0205976 |
| MA0007.1 | 1.01934 |
| MA0009.1 | 0.235113 |
| MA0014.1 | 1.09655e-06 |
| MA0017.1 | 0.0363007 |
| MA0019.1 | 0.367437 |
| MA0024.1 | 0.0466568 |
| MA0025.1 | 0.101013 |
| MA0027.1 | 2.3874 |
| MA0028.1 | 1.47059e-05 |
| MA0029.1 | 0.0172463 |
| MA0030.1 | 0.0152155 |
| MA0031.1 | 0.385497 |
| MA0038.1 | 1.46616 |
| MA0040.1 | 0.0183561 |
| MA0041.1 | 0.000460876 |
| MA0042.1 | 0.000172981 |
| MA0043.1 | 0.111876 |
| MA0046.1 | 0.219742 |
| MA0048.1 | 0.123367 |
| MA0050.1 | 0.0777679 |
| MA0051.1 | 0.328533 |
| MA0052.1 | 0.140172 |
| MA0055.1 | 0.153512 |
| MA0056.1 | 0 |
| MA0057.1 | 0.00894898 |
| MA0058.1 | 0.0236182 |
| MA0059.1 | 0.195022 |
| MA0060.1 | 8.45389e-10 |
| MA0061.1 | 0.52691 |
| MA0063.1 | 0 |
| MA0066.1 | 1.47007 |
| MA0067.1 | 0.0708046 |
| MA0068.1 | 0.00125403 |
| MA0069.1 | 1.53659 |
| MA0070.1 | 0.199443 |
| MA0071.1 | 0.92607 |
| MA0072.1 | 0.193589 |
| MA0073.1 | 1.00648e-05 |
| MA0074.1 | 0.224834 |
| MA0076.1 | 0.000762547 |
| MA0077.1 | 0.777595 |
| MA0078.1 | 0.389838 |
| MA0081.1 | 0.345723 |
| MA0083.1 | 0.246048 |
| MA0084.1 | 0.464164 |
| MA0087.1 | 0.343219 |
| MA0088.1 | 0.0352715 |
| MA0089.1 | 0 |
| MA0090.1 | 1.51222 |
| MA0091.1 | 0.099566 |
| MA0092.1 | 1.05176 |
| MA0093.1 | 0.00358943 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.0630425 |
| MA0101.1 | 0.00794223 |
| MA0103.1 | 0.676297 |
| MA0105.1 | 0.894148 |
| MA0106.1 | 1.30938 |
| MA0107.1 | 0.0158895 |
| MA0108.2 | 0.555551 |
| MA0109.1 | 0 |
| MA0111.1 | 0.903723 |
| MA0113.1 | 0.183483 |
| MA0114.1 | 0.505975 |
| MA0115.1 | 0.0472101 |
| MA0116.1 | 0.0430472 |
| MA0117.1 | 0.499614 |
| MA0119.1 | 0.0689217 |
| MA0122.1 | 0.0639193 |
| MA0124.1 | 0.036779 |
| MA0125.1 | 0.432182 |
| MA0130.1 | 0 |
| MA0131.1 | 0.00803363 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.0499175 |
| MA0136.1 | 0.0572829 |
| MA0139.1 | 0.00418038 |
| MA0140.1 | 0.22034 |
| MA0141.1 | 1.11511 |
| MA0142.1 | 0.649842 |
| MA0143.1 | 1.18534 |
| MA0144.1 | 0.200163 |
| MA0145.1 | 0.199068 |
| MA0146.1 | 2.69848e-05 |
| MA0147.1 | 0.00732749 |
| MA0148.1 | 0.0512685 |
| MA0149.1 | 0.00368955 |
| MA0062.2 | 5.43641e-06 |
| MA0035.2 | 0.31261 |
| MA0039.2 | 2.74833e-15 |
| MA0138.2 | 2.09654 |
| MA0002.2 | 0.385753 |
| MA0137.2 | 0.393516 |
| MA0104.2 | 0.00141789 |
| MA0047.2 | 0.134377 |
| MA0112.2 | 0.718782 |
| MA0065.2 | 0.35417 |
| MA0150.1 | 0.214063 |
| MA0151.1 | 0 |
| MA0152.1 | 0.0297139 |
| MA0153.1 | 0.0812765 |
| MA0154.1 | 0.921495 |
| MA0155.1 | 0.946779 |
| MA0156.1 | 0.0017061 |
| MA0157.1 | 0.37868 |
| MA0158.1 | 0 |
| MA0159.1 | 1.13 |
| MA0160.1 | 0.763189 |
| MA0161.1 | 0 |
| MA0162.1 | 3.85731e-16 |
| MA0163.1 | 9.5431e-05 |
| MA0164.1 | 0.452999 |
| MA0080.2 | 0.0845029 |
| MA0018.2 | 0.021815 |
| MA0099.2 | 0.0136834 |
| MA0079.2 | 0 |
| MA0102.2 | 0.513649 |
| MA0258.1 | 0.313745 |
| MA0259.1 | 0.0015415 |
| 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 |
|---|---|---|---|---|
| BCL3#602 | 15 | 2.04018323644124 | 0.0077165485199933 | 0.0317624487005707 |
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
