Difference between revisions of "Noctua model curation tracking table"

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Line 1: Line 1:
 
{|class="wikitable sortable"
 
{|class="wikitable sortable"
 
|-
 
|-
! Curator
+
! Contributor(s)
 
! Broad Category
 
! Broad Category
 
! Pathway
 
! Pathway
 +
! WBProcess
 
! Noctua Model Title
 
! Noctua Model Title
 
! Genes
 
! Genes
Line 10: Line 11:
 
! Noctua Model URL
 
! Noctua Model URL
 
! Model Status
 
! Model Status
! Questions/Issues
+
! Annotation Issues
 
! To Do
 
! To Do
 
|-  
 
|-  
Line 16: Line 17:
 
| Apoptosis
 
| Apoptosis
 
| Execution phase
 
| Execution phase
 +
|
 
| Apoptotic process involved in development - C. elegans NSM sister cell death  
 
| Apoptotic process involved in development - C. elegans NSM sister cell death  
 
|
 
|
Line 27: Line 29:
 
| Kimberly
 
| Kimberly
 
| Apoptosis
 
| Apoptosis
| Cell corpse engulfment
+
| 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 40: 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 51: Line 55:
 
| Kimberly
 
| Kimberly
 
| Dosage Compensation
 
| Dosage Compensation
 +
|
 
|
 
|
 
| C. elegans X chromosome dosage compensation
 
| C. elegans X chromosome dosage compensation
 +
|
 
|  
 
|  
 
|
 
|
Line 64: Line 70:
 
|
 
|
 
| EGF Signaling
 
| EGF Signaling
 +
| gonadal sheath cell/ovulation
 +
|
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|
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|
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|
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|-
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| EGF Signaling
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| aging
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|
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|
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|
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|
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|-
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| EGF Signaling
 +
| quiescence
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|
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|
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|
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|
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|
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|
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|
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|-
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| EGF Signaling
 +
| axon maintenance
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|
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|
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|
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|-
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| EGF Signaling
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| innate immune response
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|
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|
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|
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|
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|
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|-
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|
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|
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| Ephrin receptor Signaling
 +
| Ventral enclosure and epidermal morphogenesis
 +
|
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|
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|
 +
|
 +
|
 +
|
 +
|
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|-
 +
|
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|
 +
| Ephrin receptor Signaling
 +
| Male tail development
 +
|
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|
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|
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|
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|
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|
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|
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|-
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|
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|
 +
| Ephrin receptor Signaling
 +
| Neuron and axon guidance
 +
|
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|
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|
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|
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|
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|
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|
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|-
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|
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|
 +
| Ephrin receptor Signaling
 +
| Muscle cell migration
 +
|
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|
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|
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|
 +
|
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
| 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 76: Line 228:
 
|
 
|
 
| FGF Signaling
 
| FGF Signaling
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
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|-
 +
|
 +
|
 +
| GTPases
 +
| Cytokinesis
 +
|
 +
|
 +
|
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|
 +
|
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|
 +
|
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|
 +
|-
 +
|
 +
|
 +
| GTPases
 +
| Cell migration
 +
|
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|
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|
 +
|
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|
 +
|
 +
|
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|
 +
|-
 +
|
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|
 +
| GTPases
 +
| Pathfinding
 +
|
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|
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|
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|
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|
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|
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|
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|-
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|
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|
 +
| GTPases
 +
| Ciliogenesis
 +
|
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|
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|
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|
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|
 +
|
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|
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|
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|-
 +
|
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|
 +
| GTPases
 +
| Vulval development
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
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|-
 +
|
 +
|
 +
| GTPases
 +
| Vesicular trafficking
 
|
 
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|
 +
|
 +
| GTPases
 +
| Neuronal morphogenesis
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
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|-
 +
|
 +
|
 +
| GTPases
 +
| Cell polarity
 
|
 
|
 
|
 
|
Line 88: 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  
|  
+
|
 
|
 
|
 
|
 
|
Line 100: Line 357:
 
| 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 108: Line 366:
 
|  
 
|  
 
|
 
|
 +
|-
 +
|
 +
|
 +
| ERK Signaling
 +
| Immune response
 +
|
 +
|
 +
|
 +
|
 +
| Development
 +
|
 +
|
 
|-
 
|-
 
| Jae, Jane, Kimberly
 
| Jae, Jane, Kimberly
 
| 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
| What is the correct relation to use between the amine oxidase and the serotonin receptor?
+
| 1
 
| Finish up annotations for other genes in the paper
 
| Finish up annotations for other genes in the paper
 
|-
 
|-
Line 124: 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.  
 
|  
 
|  
Line 136: Line 408:
 
| 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
 +
|
 
|  
 
|  
 
|
 
|
 
|
 
|
| http://noctua.berkeleybop.org/editor/graph/gomodel:564622cc00000003
+
|
 +
|
 
| Development
 
| Development
 
|  
 
|  
Line 147: Line 433:
 
| 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 160: Line 447:
 
|  
 
|  
 
| Insulin Signaling
 
| Insulin Signaling
 +
|
 
| Signaling - C. elegans insulin receptor signaling  
 
| Signaling - C. elegans insulin receptor signaling  
 
|
 
|
Line 165: Line 453:
 
|
 
|
 
| http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696
 
| 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
 
| Development
 
|
 
|
Line 172: 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
 
|
 
|
Line 177: Line 596:
 
|
 
|
 
| http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750
 
| 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
 
| Development
 
|
 
|
Line 184: Line 733:
 
| 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 196: Line 746:
 
| 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 208: Line 759:
 
| 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 215: Line 767:
 
| Development
 
| 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.
 
| 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
 +
|
 
|
 
|
 
|-
 
|-
Line 220: Line 954:
 
| 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  
 
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| Germ line stem cell maintenance
 
| Germ line stem cell maintenance
 
| TGFbeta Signaling
 
| TGFbeta Signaling
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| 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
 
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| http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000074
 
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| Development
 
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| DA/DB motor neuron axon outgrowth
 
| DA/DB motor neuron axon outgrowth
 
| Wnt Signaling
 
| Wnt Signaling
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| 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.  
 
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| Q neuroblast descendant migration
 
| Q neuroblast descendant migration
 
| Wnt Signaling
 
| Wnt Signaling
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| Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration
 
| Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration
 
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=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

  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?