Noctua model curation tracking table

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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

  1. 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?
  2. 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?
  3. Where do the binding activities of a ligand and its receptor occur?
  4. How should the MFs of protein complexes and their constituent members be represented in GO-CAMs?