Coexpression cluster:C1766
From FANTOM5_SSTAR
Full id: C1766_CD14_CD14CD16_Hair_CD8_CD19_xeroderma_CD4
Phase1 CAGE Peaks
| Hg19::chr16:67970711..67970770,- | p1@PSMB10 |
| Hg19::chr6:32806506..32806579,- | p1@TAP2 |
| Hg19::chr6:32811771..32811831,- | p1@PSMB8 |
| Hg19::chr6:32821924..32821931,+ | p3@PSMB9 |
| Hg19::chr6:32821956..32821975,+ | p1@PSMB9 |
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 |
|---|---|---|---|---|
| 1.46259452862696e-08 | 9.05665559813991e-06 | 3 | 45 | Proteasome (KEGG):03050 |
| 4.292253837981e-08 | 9.05665559813991e-06 | 3 | 64 | Proteasome Degradation (Wikipathways):WP183 |
| 2.67613900622899e-07 | 4.23498997735737e-05 | 3 | 117 | Cell Cycle Checkpoints (Reactome):REACT_1538 |
| 1.34823063570187e-06 | 9.48255547110314e-05 | 3 | 200 | DNA Replication (Reactome):REACT_383 |
| 5.28055171391627e-06 | 0.0003342589234909 | 3 | 315 | Cell Cycle, Mitotic (Reactome):REACT_152 |
| 7.41609277987709e-07 | 7.82397788277033e-05 | 3 | 164 | Metabolism of RNA (Reactome):REACT_21257 |
| 4.292253837981e-08 | 9.05665559813991e-06 | 3 | 64 | Signaling by Wnt (Reactome):REACT_11045 |
| 5.33165031389329e-07 | 6.7498692973889e-05 | 3 | 147 | Apoptosis (Reactome):REACT_578 |
| 1.23011302483476e-06 | 9.48255547110314e-05 | 3 | 194 | HIV Infection (Reactome):REACT_6185 |
| 1.24930054759413e-06 | 9.48255547110314e-05 | 3 | 195 | Metabolism of amino acids and derivatives (Reactome):REACT_13 |
| 6.99828407380497e-06 | 0.000402719438065322 | 3 | 346 | {CDC2,351} (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:0004298 | threonine endopeptidase activity | 4.45890006046998e-07 |
| GO:0005839 | proteasome core complex (sensu Eukaryota) | 4.45890006046998e-07 |
| GO:0000502 | proteasome complex (sensu Eukaryota) | 1.67734810946468e-06 |
| GO:0005829 | cytosol | 2.45545651619859e-06 |
| GO:0006955 | immune response | 3.17272568259787e-05 |
| GO:0006511 | ubiquitin-dependent protein catabolic process | 3.17272568259787e-05 |
| GO:0043632 | modification-dependent macromolecule catabolic process | 3.17272568259787e-05 |
| GO:0019941 | modification-dependent protein catabolic process | 3.17272568259787e-05 |
| GO:0051603 | proteolysis involved in cellular protein catabolic process | 3.17272568259787e-05 |
| GO:0044257 | cellular protein catabolic process | 3.17272568259787e-05 |
| GO:0002376 | immune system process | 3.18547758936163e-05 |
| GO:0030163 | protein catabolic process | 4.79337041589452e-05 |
| GO:0043285 | biopolymer catabolic process | 9.17363901730058e-05 |
| GO:0044265 | cellular macromolecule catabolic process | 0.000130138439451392 |
| GO:0009057 | macromolecule catabolic process | 0.000207011545222337 |
| GO:0004175 | endopeptidase activity | 0.000372993694047045 |
| GO:0043234 | protein complex | 0.000372993694047045 |
| GO:0044248 | cellular catabolic process | 0.000372993694047045 |
| GO:0009056 | catabolic process | 0.000612888261624961 |
| GO:0004409 | homoaconitate hydratase activity | 0.000747674555516307 |
| GO:0032991 | macromolecular complex | 0.00103080130692212 |
| GO:0016787 | hydrolase activity | 0.00103483066727459 |
| GO:0008233 | peptidase activity | 0.00103483066727459 |
| GO:0006508 | proteolysis | 0.00119483757108028 |
| GO:0046967 | cytosol to ER transport | 0.00119622646674452 |
| GO:0044444 | cytoplasmic part | 0.00149521705842028 |
| GO:0015440 | peptide-transporting ATPase activity | 0.00149521705842028 |
| GO:0042825 | TAP complex | 0.00149521705842028 |
| GO:0046980 | tapasin binding | 0.00149521705842028 |
| GO:0015433 | peptide antigen-transporting ATPase activity | 0.00149521705842028 |
| GO:0046978 | TAP1 binding | 0.00175900121882525 |
| GO:0046977 | TAP binding | 0.00175900121882525 |
| GO:0042824 | MHC class I peptide loading complex | 0.00175900121882525 |
| GO:0046979 | TAP2 binding | 0.00175900121882525 |
| GO:0042301 | phosphate binding | 0.00249169833156373 |
| GO:0015198 | oligopeptide transporter activity | 0.00249169833156373 |
| GO:0019538 | protein metabolic process | 0.00303212289754489 |
| GO:0015197 | peptide transporter activity | 0.00314713046787477 |
| GO:0042288 | MHC class I protein binding | 0.00344958683718131 |
| GO:0002483 | antigen processing and presentation of endogenous peptide antigen | 0.00583164475744578 |
| GO:0019885 | antigen processing and presentation of endogenous peptide antigen via MHC class I | 0.00583164475744578 |
| GO:0006857 | oligopeptide transport | 0.00604832873003494 |
| GO:0042605 | peptide antigen binding | 0.00611274679452986 |
| GO:0019883 | antigen processing and presentation of endogenous antigen | 0.00611274679452986 |
| GO:0005737 | cytoplasm | 0.00663599333603718 |
| GO:0042287 | MHC protein binding | 0.00746948551180881 |
| GO:0043231 | intracellular membrane-bound organelle | 0.011881802746805 |
| GO:0043227 | membrane-bound organelle | 0.011881802746805 |
| GO:0015833 | peptide transport | 0.011881802746805 |
| GO:0005788 | endoplasmic reticulum lumen | 0.0190872887198677 |
| GO:0006959 | humoral immune response | 0.0219186774220755 |
| GO:0043229 | intracellular organelle | 0.0241778826458626 |
| GO:0043226 | organelle | 0.0241778826458626 |
| GO:0016836 | hydro-lyase activity | 0.0248247132780344 |
| GO:0043170 | macromolecule metabolic process | 0.0264901850198828 |
| GO:0016835 | carbon-oxygen lyase activity | 0.0264901850198828 |
| GO:0002474 | antigen processing and presentation of peptide antigen via MHC class I | 0.0264901850198828 |
| GO:0046982 | protein heterodimerization activity | 0.0264901850198828 |
| GO:0048002 | antigen processing and presentation of peptide antigen | 0.0264901850198828 |
| GO:0044267 | cellular protein metabolic process | 0.0329518394413252 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0336207880593579 |
| GO:0042803 | protein homodimerization activity | 0.03784391734532 |
| GO:0005634 | nucleus | 0.0395329301440715 |
| GO:0044238 | primary metabolic process | 0.0395329301440715 |
| GO:0003823 | antigen binding | 0.0404041470685052 |
| GO:0044424 | intracellular part | 0.040719536022715 |
| GO:0042277 | peptide binding | 0.0460001800729374 |
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 |
|---|---|---|
| hemolymphoid system | 4.87e-29 | 108 |
| hematopoietic system | 4.24e-27 | 98 |
| blood island | 4.24e-27 | 98 |
| immune system | 9.23e-22 | 93 |
| bone marrow | 2.14e-17 | 76 |
| connective tissue | 2.38e-15 | 371 |
| bone element | 8.44e-14 | 82 |
| skeletal element | 4.86e-12 | 90 |
| lateral plate mesoderm | 2.89e-11 | 203 |
| skeletal system | 2.29e-10 | 100 |
| blood | 1.01e-08 | 15 |
| haemolymphatic fluid | 1.01e-08 | 15 |
| organism substance | 1.01e-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) |
|---|---|
|
{{{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 |
|---|---|---|---|---|
| ELF1#1997 | 5 | 4.25809795880754 | 0.000714241693977684 | 0.00573099940667912 |
| GATA3#2625 | 2 | 10.8946065428824 | 0.012515829121883 | 0.0452830554167652 |
| GTF2F1#2962 | 3 | 7.64379652605459 | 0.0042841549641205 | 0.0203461807238316 |
| IRF1#3659 | 5 | 7.6371637535639 | 3.84754333311872e-05 | 0.000724154943535027 |
| MEF2C#4208 | 2 | 16.5245417970496 | 0.00557985007798205 | 0.0252449299209135 |
| NANOG#79923 | 2 | 11.6979113924051 | 0.0109116495195608 | 0.0402231315887834 |
| NFKB1#4790 | 5 | 5.48806342419384 | 0.000200816284746232 | 0.00239036379788143 |
| PAX5#5079 | 4 | 5.33565242494226 | 0.00222338958618779 | 0.0127783724957003 |
| PRDM1#639 | 3 | 79.0985734664765 | 4.30606791165081e-06 | 0.000136196676748909 |
| RAD21#5885 | 3 | 6.2130203372738 | 0.00775105506881164 | 0.031893169976031 |
| REST#5978 | 3 | 5.79001722967681 | 0.00946878869443394 | 0.0356968856245889 |
| RFX5#5993 | 4 | 9.63832866175608 | 0.00022148012581572 | 0.00249634824736326 |
| SIN3A#25942 | 5 | 5.40888472681514 | 0.000215952267165727 | 0.00248035179044555 |
| SMARCB1#6598 | 4 | 14.6021726249259 | 4.30486693344344e-05 | 0.000768408815009228 |
| SMC3#9126 | 3 | 9.0269597069597 | 0.00265096444946755 | 0.014637276031612 |
| STAT1#6772 | 4 | 16.5652699977594 | 2.61308619905866e-05 | 0.000563626826814306 |
| STAT2#6773 | 4 | 52.2110169491525 | 2.71660181075469e-07 | 1.3976314113961e-05 |
| STAT3#6774 | 3 | 6.31167899829254 | 0.00741117212246054 | 0.0306128541883268 |
| TAF1#6872 | 5 | 3.34304628574529 | 0.00239460009087031 | 0.0135322568524649 |
| TBP#6908 | 5 | 3.70677068709639 | 0.00142875510672112 | 0.00918715395830854 |
| YY1#7528 | 4 | 3.92893659988308 | 0.00719386626991762 | 0.0298403447201496 |
| ZEB1#6935 | 3 | 10.1330592105263 | 0.00189555692435707 | 0.0111614179186406 |
| ZNF143#7702 | 3 | 8.10052593133674 | 0.00362487051209098 | 0.0183304048521895 |
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.
