Difference between revisions of "Noctua model curation tracking table"
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{|class="wikitable sortable" | {|class="wikitable sortable" | ||
|- | |- | ||
− | ! | + | ! Contributor(s) |
! Broad Category | ! Broad Category | ||
! Pathway | ! Pathway | ||
+ | ! WBProcess | ||
! Noctua Model Title | ! Noctua Model Title | ||
+ | ! Genes | ||
! GO Term(s), IDs | ! GO Term(s), IDs | ||
! Module(s) | ! Module(s) | ||
! Noctua Model URL | ! Noctua Model URL | ||
! Model Status | ! Model Status | ||
+ | ! Annotation Issues | ||
! To Do | ! To Do | ||
|- | |- | ||
| Kimberly | | Kimberly | ||
| Apoptosis | | Apoptosis | ||
+ | | Execution phase | ||
| | | | ||
| Apoptotic process involved in development - C. elegans NSM sister cell death | | Apoptotic process involved in development - C. elegans NSM sister cell death | ||
+ | | | ||
| | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001432 | | http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001432 | ||
| Development | | 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 | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 24: | Line 56: | ||
| Dosage Compensation | | Dosage Compensation | ||
| | | | ||
− | | C. elegans X chromosome dosage compensation | + | | |
+ | | C. elegans X chromosome dosage compensation | ||
+ | | | ||
+ | | | ||
| | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000147 | | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000147 | ||
| Development | | Development | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 34: | Line 70: | ||
| | | | ||
| EGF Signaling | | EGF Signaling | ||
+ | | gonadal sheath cell/ovulation | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | EGF Signaling | ||
+ | | aging | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | EGF Signaling | ||
+ | | quiescence | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | EGF Signaling | ||
+ | | axon maintenance | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | EGF Signaling | ||
+ | | innate immune response | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Ventral enclosure and epidermal morphogenesis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Male tail development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Neuron and axon guidance | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Muscle cell migration | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Oocyte meiotic maturation and oocyte growth | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Germ line apoptosis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Axon regeneration | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Ephrin receptor Signaling | ||
+ | | Hypoxia protection | ||
+ | | | ||
| | | | ||
| | | | ||
Line 44: | Line 228: | ||
| | | | ||
| FGF Signaling | | FGF Signaling | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Cytokinesis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Cell migration | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Pathfinding | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Ciliogenesis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Vulval development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Vesicular trafficking | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Neuronal morphogenesis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | GTPases | ||
+ | | Cell polarity | ||
+ | | | ||
| | | | ||
| | | | ||
Line 54: | Line 344: | ||
| 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 | ||
− | | | + | | |
+ | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000138 | | http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000138 | ||
| Development | | Development | ||
| | | | ||
+ | | | ||
|- | |- | ||
| Kimberly | | Kimberly | ||
| 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. | ||
| | | | ||
+ | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000454 | | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000454 | ||
| Development | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | ERK Signaling | ||
+ | | Immune response | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 74: | Line 382: | ||
| Egg laying | | Egg laying | ||
| GPCR Signaling | | GPCR Signaling | ||
+ | | | ||
| GRK-2 egg laying regulation JM | | GRK-2 egg laying regulation JM | ||
− | | | + | | |
+ | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000287 | | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000287 | ||
| Development | | Development | ||
+ | | 1 | ||
| Finish up annotations for other genes in the paper | | Finish up annotations for other genes in the paper | ||
|- | |- | ||
Line 84: | Line 395: | ||
| 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. | ||
| | | | ||
+ | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000158 | | http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000158 | ||
| Development | | Development | ||
| | | | ||
+ | | | ||
|- | |- | ||
| Kimberly | | Kimberly | ||
| 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 | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | http://noctua.berkeleybop.org/editor/graph/gomodel:564622cc00000003 | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Hedgehog-like signaling pathway | ||
+ | | | ||
| | | | ||
| | | | ||
− | | | + | | |
+ | | | ||
+ | | | ||
| Development | | Development | ||
| | | | ||
+ | | | ||
|- | |- | ||
| 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 110: | Line 442: | ||
| Development | | Development | ||
| | | | ||
+ | | | ||
|- | |- | ||
| Kimberly | | Kimberly | ||
| | | | ||
| Insulin Signaling | | Insulin Signaling | ||
+ | | | ||
| Signaling - C. elegans insulin receptor signaling | | Signaling - C. elegans insulin receptor signaling | ||
+ | | | ||
| | | | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696 | | http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696 | ||
| Development | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Dauer | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | L1 arrest | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Germline proliferation | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Longevity and aging | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Stress resistance | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Immune response | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Fat metabolism | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Reproductive aging | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Insulin Signaling | ||
+ | | Neuronal aging | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | MAPK | ||
+ | | Immune response | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 124: | Line 590: | ||
| 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) | ||
| | | | ||
| http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750 | | http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750 | ||
| Development | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Notch Signaling | ||
+ | | Somatic gonad development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Notch Signaling | ||
+ | | Germline development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Notch Signaling | ||
+ | | Embryonic fate specification/development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Dauer | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Metabolism | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Developmental timing | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Molting | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Cell fate specification | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Spermatheca organogenesis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Nuclear Receptor Signaling | ||
+ | | Nuclear receptors in nutrient sensing, metabolism, and energy homeostasis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | 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. | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | Vulval development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | Excretory duct fate specification/osmoregulation | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | Germline development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | Aging | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | sex muscle differentiation | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | body muscle maintenance | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | axon outgrowth | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | body muscle membrane extension | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | acetylcholine receptor clustering | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | SM migration | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | P12 fate specification | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | uv1 fate specification | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | spicule fate specification | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | RTK Ras MAPK signaling | ||
+ | | male hook specification | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | 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 | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 134: | Line 967: | ||
| Germ line stem cell maintenance | | Germ line stem cell maintenance | ||
| TGFbeta Signaling | | TGFbeta Signaling | ||
+ | | | ||
| Linking the environment, DAF-7/TGFβ signaling and LAG-2/DSL ligand expression in the germline stem cell niche | | 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 | | http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000074 | ||
| Development | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Immune response | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Body size regulation | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Male tail development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Aging and longevity | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Mesodermal patterning | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Chemosensation and neuronal function | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Metabolism | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TGFbeta Signaling | ||
+ | | Cell migration | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | TOLL Signaling | ||
+ | | Immune response | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Wnt Signaling | ||
+ | | Vulval development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Wnt Signaling | ||
+ | | Embryonic development | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Wnt Signaling | ||
+ | | Embryonic development (polarity, fate specification) | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Wnt Signaling | ||
+ | | Cell migration | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Wnt Signaling | ||
+ | | Neurite outgrowth | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
+ | | | ||
+ | |- | ||
+ | | | ||
+ | | | ||
+ | | Wnt Signaling | ||
+ | | Synaptogenesis | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | | ||
+ | | Development | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 144: | Line 1,175: | ||
| DA/DB motor neuron axon outgrowth | | DA/DB motor neuron axon outgrowth | ||
| Wnt Signaling | | 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. | | 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 | | http://noctua.berkeleybop.org/editor/graph/gomodel:598826eb00000296 | ||
| Development | | Development | ||
+ | | | ||
| | | | ||
|- | |- | ||
Line 154: | Line 1,188: | ||
| Q neuroblast descendant migration | | Q neuroblast descendant migration | ||
| Wnt Signaling | | Wnt Signaling | ||
+ | | | ||
| Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration | | 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) | | 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 | | http://noctua.berkeleybop.org/editor/graph/gomodel:595a9ee700000584 | ||
| Development | | 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? |
Latest revision as of 19:03, 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 | gonadal sheath cell/ovulation | |||||||||||
EGF Signaling | aging | |||||||||||
EGF Signaling | quiescence | |||||||||||
EGF Signaling | axon maintenance | |||||||||||
EGF Signaling | innate immune response | |||||||||||
Ephrin receptor Signaling | Ventral enclosure and epidermal morphogenesis | |||||||||||
Ephrin receptor Signaling | Male tail development | |||||||||||
Ephrin receptor Signaling | Neuron and axon guidance | |||||||||||
Ephrin receptor Signaling | Muscle cell migration | |||||||||||
Ephrin receptor Signaling | Oocyte meiotic maturation and oocyte growth | |||||||||||
Ephrin receptor Signaling | Germ line apoptosis | |||||||||||
Ephrin receptor Signaling | Axon regeneration | |||||||||||
Ephrin receptor Signaling | Hypoxia protection | |||||||||||
FGF Signaling | ||||||||||||
GTPases | Cytokinesis | |||||||||||
GTPases | Cell migration | |||||||||||
GTPases | Pathfinding | |||||||||||
GTPases | Ciliogenesis | |||||||||||
GTPases | Vulval development | |||||||||||
GTPases | Vesicular trafficking | |||||||||||
GTPases | Neuronal morphogenesis | |||||||||||
GTPases | Cell polarity | |||||||||||
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 | |||||||
ERK Signaling | Immune response | 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 | |||||||
Hedgehog-like signaling pathway | 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 | ||||||||
Insulin Signaling | Dauer | Development | ||||||||||
Insulin Signaling | L1 arrest | Development | ||||||||||
Insulin Signaling | Germline proliferation | Development | ||||||||||
Insulin Signaling | Longevity and aging | Development | ||||||||||
Insulin Signaling | Stress resistance | Development | ||||||||||
Insulin Signaling | Immune response | Development | ||||||||||
Insulin Signaling | Fat metabolism | Development | ||||||||||
Insulin Signaling | Reproductive aging | Development | ||||||||||
Insulin Signaling | Neuronal aging | Development | ||||||||||
MAPK | Immune response | 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 | ||||||
Notch Signaling | Somatic gonad development | Development | ||||||||||
Notch Signaling | Germline development | Development | ||||||||||
Notch Signaling | Embryonic fate specification/development | Development | ||||||||||
Nuclear Receptor Signaling | Dauer | Development | ||||||||||
Nuclear Receptor Signaling | Metabolism | Development | ||||||||||
Nuclear Receptor Signaling | Developmental timing | Development | ||||||||||
Nuclear Receptor Signaling | Molting | Development | ||||||||||
Nuclear Receptor Signaling | Cell fate specification | Development | ||||||||||
Nuclear Receptor Signaling | Spermatheca organogenesis | Development | ||||||||||
Nuclear Receptor Signaling | Nuclear receptors in nutrient sensing, metabolism, and energy homeostasis | 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. | |||||
RTK Ras MAPK signaling | Vulval development | Development | ||||||||||
RTK Ras MAPK signaling | Excretory duct fate specification/osmoregulation | Development | ||||||||||
RTK Ras MAPK signaling | Germline development | Development | ||||||||||
RTK Ras MAPK signaling | Aging | Development | ||||||||||
RTK Ras MAPK signaling | sex muscle differentiation | Development | ||||||||||
RTK Ras MAPK signaling | body muscle maintenance | Development | ||||||||||
RTK Ras MAPK signaling | axon outgrowth | Development | ||||||||||
RTK Ras MAPK signaling | body muscle membrane extension | Development | ||||||||||
RTK Ras MAPK signaling | acetylcholine receptor clustering | Development | ||||||||||
RTK Ras MAPK signaling | SM migration | Development | ||||||||||
RTK Ras MAPK signaling | P12 fate specification | Development | ||||||||||
RTK Ras MAPK signaling | uv1 fate specification | Development | ||||||||||
RTK Ras MAPK signaling | spicule fate specification | Development | ||||||||||
RTK Ras MAPK signaling | male hook specification | Development | ||||||||||
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 | |||||||
TGFbeta Signaling | Immune response | Development | ||||||||||
TGFbeta Signaling | Body size regulation | Development | ||||||||||
TGFbeta Signaling | Male tail development | Development | ||||||||||
TGFbeta Signaling | Aging and longevity | Development | ||||||||||
TGFbeta Signaling | Mesodermal patterning | Development | ||||||||||
TGFbeta Signaling | Chemosensation and neuronal function | Development | ||||||||||
TGFbeta Signaling | Metabolism | Development | ||||||||||
TGFbeta Signaling | Cell migration | Development | ||||||||||
TOLL Signaling | Immune response | Development | ||||||||||
Wnt Signaling | Vulval development | Development | ||||||||||
Wnt Signaling | Embryonic development | Development | ||||||||||
Wnt Signaling | Embryonic development (polarity, fate specification) | Development | ||||||||||
Wnt Signaling | Cell migration | Development | ||||||||||
Wnt Signaling | Neurite outgrowth | Development | ||||||||||
Wnt Signaling | Synaptogenesis | 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?