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PRJNA438478: RNAseq of wild type zebrafish germline
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Results for BX548005.1+smarcc2
Z-value: 2.72
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Transcription factors associated with BX548005.1+smarcc2
| Gene Symbol | Gene ID | Gene Info |
|---|---|---|
| ENSDARG00000077946 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 | |
| ENSDARG00000110907 | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2 |
Activity-expression correlation:
| Gene | Promoter | Pearson corr. coef. | P-value | Plot |
|---|---|---|---|---|
| smarcc2 | dr11_v1_chr6_+_39836474_39836474 | -0.42 | 7.9e-02 | Click! |
| Promoter | Log-likelihood | Transcript | Gene | Gene Info |
|---|---|---|---|---|
| chr11_+_29537756 Show fit | 12.28 |
ENSDART00000103388
|
wu:fi42e03 |
|
| chr23_+_13528550 Show fit | 11.30 |
ENSDART00000099903
|
uridine-cytidine kinase 1-like 1b |
|
| chr11_-_16021424 Show fit | 9.14 |
ENSDART00000193291
ENSDART00000170731 ENSDART00000104107 |
zgc:173544 |
|
| chr7_+_41887429 Show fit | 7.76 |
ENSDART00000115090
|
glutamic pyruvate transaminase (alanine aminotransferase) 2 |
|
| chr5_-_43859148 Show fit | 7.42 |
ENSDART00000162746
ENSDART00000128763 |
si:ch211-204c21.1 |
|
| chr5_+_3891485 Show fit | 7.34 |
ENSDART00000129329
ENSDART00000091711 |
RPA interacting protein |
|
| chr16_-_34285106 Show fit | 7.19 |
ENSDART00000044235
|
phosphatase and actin regulator 4b |
|
| chr8_-_36618073 Show fit | 6.83 |
ENSDART00000047912
|
G patch domain and KOW motifs |
|
| chr6_+_59176470 Show fit | 6.78 |
ENSDART00000161720
|
serine hydroxymethyltransferase 2 (mitochondrial) |
|
| chr5_-_23675222 Show fit | 6.66 |
ENSDART00000135153
|
si:dkey-110k5.6 |
Network of associatons between targets according to the STRING database.
First level regulatory network of BX548005.1+smarcc2
Gene Ontology Analysis
Gene overrepresentation in biological process category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.1 | 15.9 | GO:0016197 | endosomal transport(GO:0016197) |
| 1.7 | 13.4 | GO:0044211 | CTP salvage(GO:0044211) |
| 0.1 | 9.3 | GO:0006821 | chloride transport(GO:0006821) |
| 0.0 | 8.9 | GO:0098609 | cell-cell adhesion(GO:0098609) |
| 0.1 | 8.4 | GO:0051453 | regulation of intracellular pH(GO:0051453) |
| 0.0 | 7.8 | GO:0007265 | Ras protein signal transduction(GO:0007265) |
| 0.4 | 7.4 | GO:0045807 | positive regulation of endocytosis(GO:0045807) |
| 1.0 | 7.2 | GO:2001045 | negative regulation of integrin-mediated signaling pathway(GO:2001045) |
| 0.1 | 7.2 | GO:1902593 | protein import into nucleus(GO:0006606) protein targeting to nucleus(GO:0044744) single-organism nuclear import(GO:1902593) |
| 0.1 | 7.1 | GO:0007030 | Golgi organization(GO:0007030) |
Gene overrepresentation in cellular component category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.0 | 12.3 | GO:0000139 | Golgi membrane(GO:0000139) |
| 0.0 | 11.9 | GO:0005794 | Golgi apparatus(GO:0005794) |
| 0.1 | 8.7 | GO:0005769 | early endosome(GO:0005769) |
| 0.0 | 7.4 | GO:0005912 | adherens junction(GO:0005912) |
| 0.2 | 7.3 | GO:0016605 | PML body(GO:0016605) |
| 0.1 | 7.2 | GO:0030027 | lamellipodium(GO:0030027) |
| 0.3 | 7.1 | GO:0044665 | MLL1/2 complex(GO:0044665) MLL1 complex(GO:0071339) |
| 0.5 | 6.9 | GO:0071782 | endoplasmic reticulum tubular network(GO:0071782) endoplasmic reticulum subcompartment(GO:0098827) |
| 0.8 | 6.8 | GO:0070552 | BRISC complex(GO:0070552) |
| 0.2 | 6.4 | GO:0035097 | histone methyltransferase complex(GO:0035097) |
Gene overrepresentation in molecular function category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 1.7 | 13.4 | GO:0004849 | uridine kinase activity(GO:0004849) |
| 0.9 | 10.2 | GO:0015385 | monovalent cation:proton antiporter activity(GO:0005451) sodium:proton antiporter activity(GO:0015385) potassium:proton antiporter activity(GO:0015386) |
| 0.1 | 9.6 | GO:0004197 | cysteine-type endopeptidase activity(GO:0004197) |
| 0.5 | 9.3 | GO:0005247 | voltage-gated chloride channel activity(GO:0005247) |
| 0.2 | 8.2 | GO:0017022 | myosin binding(GO:0017022) |
| 0.1 | 7.8 | GO:0030170 | pyridoxal phosphate binding(GO:0030170) |
| 0.0 | 7.3 | GO:0005525 | GTP binding(GO:0005525) |
| 0.4 | 7.2 | GO:0072542 | phosphatase activator activity(GO:0019211) protein phosphatase activator activity(GO:0072542) |
| 2.3 | 6.8 | GO:0070905 | glycine hydroxymethyltransferase activity(GO:0004372) serine binding(GO:0070905) |
| 0.0 | 6.8 | GO:0046983 | protein dimerization activity(GO:0046983) |
Gene overrepresentation in curated gene sets: canonical pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 8.3 | PID ATM PATHWAY | ATM pathway |
| 0.2 | 7.8 | PID AURORA B PATHWAY | Aurora B signaling |
| 0.1 | 6.3 | PID SMAD2 3NUCLEAR PATHWAY | Regulation of nuclear SMAD2/3 signaling |
| 0.1 | 6.1 | PID TRKR PATHWAY | Neurotrophic factor-mediated Trk receptor signaling |
| 0.2 | 5.8 | PID MYC PATHWAY | C-MYC pathway |
| 0.5 | 4.1 | PID ANTHRAX PATHWAY | Cellular roles of Anthrax toxin |
| 0.1 | 3.7 | PID RAC1 PATHWAY | RAC1 signaling pathway |
| 0.1 | 3.6 | PID TAP63 PATHWAY | Validated transcriptional targets of TAp63 isoforms |
| 0.0 | 3.5 | WNT SIGNALING | Genes related to Wnt-mediated signal transduction |
| 0.1 | 3.3 | PID RETINOIC ACID PATHWAY | Retinoic acid receptors-mediated signaling |
Gene overrepresentation in curated gene sets: REACTOME pathways category:
| Log-likelihood per target | Total log-likelihood | Term | Description |
|---|---|---|---|
| 0.2 | 11.2 | REACTOME GOLGI ASSOCIATED VESICLE BIOGENESIS | Genes involved in Golgi Associated Vesicle Biogenesis |
| 0.1 | 11.2 | REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES | Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides |
| 0.8 | 7.8 | REACTOME AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION | Genes involved in Amino acid synthesis and interconversion (transamination) |
| 0.2 | 7.1 | REACTOME POST TRANSLATIONAL MODIFICATION SYNTHESIS OF GPI ANCHORED PROTEINS | Genes involved in Post-translational modification: synthesis of GPI-anchored proteins |
| 0.6 | 6.3 | REACTOME SIGNALING BY NODAL | Genes involved in Signaling by NODAL |
| 0.1 | 6.1 | REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION | Genes involved in Factors involved in megakaryocyte development and platelet production |
| 0.4 | 4.8 | REACTOME HDL MEDIATED LIPID TRANSPORT | Genes involved in HDL-mediated lipid transport |
| 0.4 | 4.8 | REACTOME G2 M DNA DAMAGE CHECKPOINT | Genes involved in G2/M DNA damage checkpoint |
| 0.1 | 4.8 | REACTOME CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION | Genes involved in Cyclin E associated events during G1/S transition |
| 0.2 | 4.7 | REACTOME SYNTHESIS OF PA | Genes involved in Synthesis of PA |