Difference between revisions of "Noctua model curation tracking table"
From WormBaseWiki
Jump to navigationJump to searchLine 30: | Line 30: | ||
| Apoptosis | | Apoptosis | ||
| Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways | | Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways | ||
+ | | | ||
| Localization - C. elegans apoptotic cell engulfment | | Localization - C. elegans apoptotic cell engulfment | ||
− | |||
| ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1 | | ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1 | ||
| | | | ||
Line 43: | Line 43: | ||
| Axon regeneration | | Axon regeneration | ||
| Rac module; upstream of JNK-MAPK | | Rac module; upstream of JNK-MAPK | ||
+ | | | ||
| C. elegans regulation of axon regeneration | | C. elegans regulation of axon regeneration | ||
− | |||
| | | | ||
| | | | ||
Line 55: | Line 55: | ||
| Kimberly | | Kimberly | ||
| Dosage Compensation | | Dosage Compensation | ||
+ | | | ||
| | | | ||
| C. elegans X chromosome dosage compensation | | C. elegans X chromosome dosage compensation | ||
Line 95: | Line 96: | ||
| Distal tip cell migration | | Distal tip cell migration | ||
| Glycosylation | | Glycosylation | ||
+ | | | ||
| The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme | | The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme | ||
| | | | ||
− | |||
| | | | ||
| | | | ||
Line 108: | Line 109: | ||
| Dauer | | Dauer | ||
| GPCR Signaling | | GPCR Signaling | ||
+ | | | ||
| Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans. | | Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans. | ||
− | |||
| | | | ||
| | | | ||
Line 121: | Line 122: | ||
| Egg laying | | Egg laying | ||
| GPCR Signaling | | GPCR Signaling | ||
+ | | | ||
| GRK-2 egg laying regulation JM | | GRK-2 egg laying regulation JM | ||
| | | | ||
− | |||
| | | | ||
| | | | ||
Line 134: | Line 135: | ||
| Innate immune response | | Innate immune response | ||
| GPCR Signaling | | GPCR Signaling | ||
+ | | | ||
| The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity. | | The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity. | ||
− | |||
| | | | ||
| | | | ||
Line 147: | Line 148: | ||
| Innate immune response | | Innate immune response | ||
| GPCR Signaling and MAPK signaling | | GPCR Signaling and MAPK signaling | ||
+ | | | ||
| C_elegans_defense_response_to_fungus | | C_elegans_defense_response_to_fungus | ||
| | | | ||
− | |||
| | | | ||
| | | | ||
Line 159: | Line 160: | ||
| Kimberly | | Kimberly | ||
| Heterochronic pathway | | Heterochronic pathway | ||
+ | | | ||
| | | | ||
| Control of C. elegans larval developmental timing - the heterochronic pathway | | Control of C. elegans larval developmental timing - the heterochronic pathway | ||
− | |||
| | | | ||
| | | | ||
Line 173: | Line 174: | ||
| | | | ||
| Insulin Signaling | | Insulin Signaling | ||
+ | | | ||
| Signaling - C. elegans insulin receptor signaling | | Signaling - C. elegans insulin receptor signaling | ||
− | |||
| | | | ||
| | | | ||
Line 186: | Line 187: | ||
| Germ line stem cell maintenance | | Germ line stem cell maintenance | ||
| Notch Signaling | | Notch Signaling | ||
+ | | | ||
| C. elegans germline stem cell maintenance - Notch pathway | | C. elegans germline stem cell maintenance - Notch pathway | ||
− | |||
| | | | ||
| Notch signaling pathway (GO:0007219), positive regulation of stem cell population maintenance (GO:1902459), positive regulation of stem cell proliferation (GO:2000648) | | Notch signaling pathway (GO:0007219), positive regulation of stem cell population maintenance (GO:1902459), positive regulation of stem cell proliferation (GO:2000648) | ||
Line 199: | Line 200: | ||
| Neuronal morphogenesis - AFD thermosensory neuron | | Neuronal morphogenesis - AFD thermosensory neuron | ||
| Receptor guanylyl cyclase | | Receptor guanylyl cyclase | ||
+ | | | ||
| Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape | | Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape | ||
− | |||
| | | | ||
| | | | ||
Line 212: | Line 213: | ||
| Olfactory behavior | | Olfactory behavior | ||
| | | | ||
+ | | | ||
| Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255) | | Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255) | ||
− | |||
| | | | ||
| | | | ||
Line 225: | Line 226: | ||
| Thermosensory behavior | | Thermosensory behavior | ||
| Cyclic nucleotide-gated ion channels | | Cyclic nucleotide-gated ion channels | ||
+ | | | ||
| C. elegans CNG-3 in non-motile cilium of AFD (same reference) | | C. elegans CNG-3 in non-motile cilium of AFD (same reference) | ||
− | |||
| cng-3 | | cng-3 | ||
| | | | ||
Line 238: | Line 239: | ||
| Striated muscle mitochondrial patterning | | Striated muscle mitochondrial patterning | ||
| Receptor tyrosine phosphatase | | Receptor tyrosine phosphatase | ||
+ | | | ||
| The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1 | | The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1 | ||
− | |||
| | | | ||
| | | |
Revision as of 18:00, 19 March 2018
Contributor(s) | Broad Category | Pathway | WBProcess | Noctua Model Title | Genes | GO Term(s), IDs | Module(s) | Noctua Model URL | Model Status | Annotation Issues | To Do | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Kimberly | Apoptosis | Execution phase | Apoptotic process involved in development - C. elegans NSM sister cell death | http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001432 | Development | |||||||
Kimberly | Apoptosis | Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways | Localization - C. elegans apoptotic cell engulfment | ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1 | http://noctua.berkeleybop.org/editor/graph/gomodel:56aac7ad00000175 | Development | ||||||
Kimberly | Axon regeneration | Rac module; upstream of JNK-MAPK | C. elegans regulation of axon regeneration | http://noctua.berkeleybop.org/editor/graph/gomodel:591f58ab00000003 | Development | |||||||
Kimberly | Dosage Compensation | C. elegans X chromosome dosage compensation | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000147 | Development | ||||||||
EGF Signaling | ||||||||||||
FGF Signaling | ||||||||||||
Kimberly | Distal tip cell migration | Glycosylation | The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme | http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000138 | Development | |||||||
Kimberly | Dauer | GPCR Signaling | Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans. | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000454 | Development | |||||||
Jae, Jane, Kimberly | Egg laying | GPCR Signaling | GRK-2 egg laying regulation JM | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000287 | Development | 1 | Finish up annotations for other genes in the paper | |||||
Kimberly | Innate immune response | GPCR Signaling | The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity. | http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000158 | Development | |||||||
Kimberly | Innate immune response | GPCR Signaling and MAPK signaling | C_elegans_defense_response_to_fungus | http://noctua.berkeleybop.org/editor/graph/gomodel:564622cc00000003 | Development | |||||||
Kimberly | Heterochronic pathway | Control of C. elegans larval developmental timing - the heterochronic pathway | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000246 | Development | ||||||||
Kimberly | Insulin Signaling | Signaling - C. elegans insulin receptor signaling | http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696 | Development | ||||||||
Kimberly | Germ line stem cell maintenance | Notch Signaling | C. elegans germline stem cell maintenance - Notch pathway | Notch signaling pathway (GO:0007219), positive regulation of stem cell population maintenance (GO:1902459), positive regulation of stem cell proliferation (GO:2000648) | http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750 | Development | ||||||
Kimberly | Neuronal morphogenesis - AFD thermosensory neuron | Receptor guanylyl cyclase | Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape | http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000192 | Development | |||||||
Kimberly | Olfactory behavior | Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255) | http://noctua.berkeleybop.org/editor/graph/gomodel:59237a3c00000026 | Development | ||||||||
Kimberly | Thermosensory behavior | Cyclic nucleotide-gated ion channels | C. elegans CNG-3 in non-motile cilium of AFD (same reference) | cng-3 | http://noctua.berkeleybop.org/editor/graph/gomodel:5900dc7400001096 | Development | 1) How should we annotate different evidence for CC vs tissue? 2) Annotation extensions that don't use the same evidence code should not appear in the GPAD output. 3) Add relations for positive and negative effect for causally upstream of or within. | |||||
Kimberly | Striated muscle mitochondrial patterning | Receptor tyrosine phosphatase | The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1 | http://noctua.berkeleybop.org/editor/graph/gomodel:5970219a00000566 | Development | |||||||
Kimberly | Germ line stem cell maintenance | TGFbeta Signaling | Linking the environment, DAF-7/TGFβ signaling and LAG-2/DSL ligand expression in the germline stem cell niche | http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000074 | Development | |||||||
Kimberly | DA/DB motor neuron axon outgrowth | Wnt Signaling | The ENU-3 protein family members function in the Wnt pathway parallel to UNC-6/Netrin to promote motor neuron axon outgrowth in C. elegans. | http://noctua.berkeleybop.org/editor/graph/gomodel:598826eb00000296 | Development | |||||||
Chris | Q neuroblast descendant migration | Wnt Signaling | Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration | canonical Wnt signaling pathway (GO:0060070), cell migration (GO:0016477), transcription from RNA polymerase II promoter (GO:0006366) | http://noctua.berkeleybop.org/editor/graph/gomodel:595a9ee700000584 | Development |
Annotations Issues
- What is the correct relation to use between an upstream MF that creates or removes a small molecule that is the input of a downstream MF?
- What is the correct way to evidence a CC when there is experimental data for expression at the tissue- or cellular level, but no subcellular localization?
- Where do the binding activities of a ligand and its receptor occur?
- How should the MFs of protein complexes and their constituent members be represented in GO-CAMs?