Difference between revisions of "Process page mock-ups"

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=Processes in ''C. elegans''=
 
=Processes in ''C. elegans''=
  
 +
==[[Cell division]]==
 +
*[Cell division in male]
 +
*[Cell division in hermaphrodite]
 +
*[Asymmetric cell division]
  
 
==[[Cell death]]==
 
==[[Cell death]]==
Line 21: Line 25:
 
|-valign="top"  
 
|-valign="top"  
 
|
 
|
* [Programmed cell death: Developmental]
+
*[Programmed cell death: Developmental]
* [Programmed cell death: Germ line]
+
*[Programmed cell death: Germ line]
 +
*[Necrosis]
 
|
 
|
* [Necrosis]
+
*[Autophagy]
* [Autophagy]
+
*[Cell death in hermaphrodite]
 
|}
 
|}
  
==[[Autophagy]]==
+
==[[Axis formation]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Asymmetric cell division]
 +
*[Establishing polarity: A/P axis]
 +
*[Establishing polarity: D/V axis]
 +
*[Establishing polarity; L/R Axis]
 +
|
 +
*[Maintaining polarity]
 +
|}
  
==[[Dauer arrest]]==
+
==[[Cell migration]]==
 
{|
 
{|
 
|-valign="top"
 
|-valign="top"
 
|
 
|
*[Regulation of dauer arrest]
+
*[Neuronal migration]
*[Dauer morphological changes]
+
*[Sex Myoblast positioning]
*[Dauer metabolism]
+
*[DTC migration]
 +
*[LC migration]
 +
|}
 +
 
 +
==[[Cell specification and differentiation]]==
 +
{|
 +
|-valign="top"
 
|
 
|
*[Neuronal processes in dauer arrest]
+
*[P11/P12 specification]
*[Steroids/hormones]
+
*[Embryonic blastomere specification]
*[Quiescence]
+
*[Cell differentiation in hermaphrodite]
 +
*[Cell differentiation in male]
 
|}
 
|}
  
==[[L1 arrest]]==
+
==[[Sex determination]]==
 
+
*[Dosage compensation]
==[[Embryonic blastomere specification]]==
 
 
 
==[[Embryonic mesendoderm development]]==
 
 
 
==[[Pharynx development]]==
 
 
 
==[[Gonad development]]==
 
  
==[[Germ line development]]==
+
==[[Tissue morphogenesis]]==
 +
*[Embryonic mesendoderm development]
 +
*[Muscle morphogenesis]
  
==[[Male-specific development]]==
+
==[[Organ development]]==
 
{|
 
{|
 
|-valign="top"
 
|-valign="top"
 
|
 
|
*[Hook Equivalence Group development]
+
*[Pharynx development]
*[Spicule development]
+
*[Gonad development]
*[Male muscle development]
+
*[Duct development]
 +
*[Muscle development]
 
|}
 
|}
 
  
 
==[[Vulval development]]==
 
==[[Vulval development]]==
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|-valign="top"
 
|-valign="top"
 
|
 
|
*[Generation of VPC's]
+
*[[Generation of VPC's]]
 
*[Vulval Precursor Patterning]
 
*[Vulval Precursor Patterning]
 
*[Generation of the adult]
 
*[Generation of the adult]
 +
*[Anchor cell invasion]
 
|
 
|
*[Anchor cell invasion]
 
 
*[Morphogenesis of the vulva]
 
*[Morphogenesis of the vulva]
 
*[Generation of the anchor cell: AC/UV decision]
 
*[Generation of the anchor cell: AC/UV decision]
 
*[Uterine patterning: pi cell induction]
 
*[Uterine patterning: pi cell induction]
 +
*[Uterine patterning: uv1 induction]
 
|
 
|
*[Uterine patterning: uv1 induction]
 
 
*[Patterning of adult cell types: 1° lineage]
 
*[Patterning of adult cell types: 1° lineage]
 
*[Patterning of adult cell types: Polarity of 2° lineage]
 
*[Patterning of adult cell types: Polarity of 2° lineage]
 
|}
 
|}
  
==[[P11/P12 specification]]==
+
==[[Germ line development]]==
  
==[[duct development]]==
+
==[[Spermatogenesis]]==
  
==[[Cell migration]]==
+
==[[Oogenesis]]==
 +
 
 +
==[[L1 development]]==
 +
*[L1 arrest]
 +
 
 +
==[[Molting]]==
 +
 
 +
==[[Male-specific development]]==
 
{|
 
{|
 
|-valign="top"
 
|-valign="top"
 
|
 
|
*[Neuronal migration]
+
*[Hook Equivalence Group development]
*[Sex Myoblast positioning]
+
*[Spicule development]
*[DTC migration]
+
*[Male muscle development]
*[LC migration]
 
 
 
 
|}
 
|}
  
==[[Neuronal regeneration]]==
+
==[[Dauer formation/arrest]]==
 
 
==[[Neuronal migration]]==
 
 
 
==[[Molting]]==
 
 
 
==[[Cell specification]]==
 
 
 
==[[Axis formation]]==
 
 
{|
 
{|
 
|-valign="top"
 
|-valign="top"
 
|
 
|
*[Asymmetric cell division]
+
*[Regulation of dauer arrest]
*[Establishing polarity: A/P axis]
+
*[Dauer morphological changes]
*[Establishing polarity: D/V axis]
+
*[Dauer metabolism]
 +
*[Neuronal processes in dauer arrest]
 
|
 
|
*[Establishing polarity; L/R Axis]
+
*[Steroids/hormones]
*[Maintaining polarity]
+
*[Quiescence]
 +
*[Exit from dauer stage]
 
|}
 
|}
 +
 +
==[[Neuronal regeneration]]==
 +
 
==[[Chemosensation]]==
 
==[[Chemosensation]]==
 
{|
 
{|
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*[Oxygen sensing]
 
*[Oxygen sensing]
 
*[Mating]
 
*[Mating]
|
 
 
*[Integrating signals]
 
*[Integrating signals]
 
|}
 
|}
 
==[[Mechanosensation]]==
 
==[[Mechanosensation]]==
 +
 +
==[[Synaptic transmission]]==
  
 
==[[Behavioral plasticity]]==
 
==[[Behavioral plasticity]]==
 +
*[Habituation]
 +
*[Adaptation]
  
 
==[[Locomotion]]==
 
==[[Locomotion]]==
Line 140: Line 162:
 
|}
 
|}
  
==[[Feeding (Pharyngeal pumping)]]==
+
==[[Feeding]]==
 +
 
 +
*[Pharyngeal pumping]
 +
*[Foraging]
  
 
==[[Defecation]]==
 
==[[Defecation]]==
 +
*[Defecation cycle]
  
 
==[[Ovulation]]==
 
==[[Ovulation]]==
 
+
*[Egg-laying]
==[[Egg-laying]]==
+
*[Egg-laying cycle]]
  
 
==[[Male Mating]]==
 
==[[Male Mating]]==
Line 156: Line 182:
 
*[Turning]
 
*[Turning]
 
*[Vulval Location]
 
*[Vulval Location]
 +
|
 
*[Spicule protraction]
 
*[Spicule protraction]
 
*[Sperm Transfer]
 
*[Sperm Transfer]
Line 170: Line 197:
 
*[Pathogen Avoidance]
 
*[Pathogen Avoidance]
 
|}
 
|}
 +
==[[Behavior]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Locomotion]
 +
*[Pathogen Avoidance]
 +
*[Foraging]
 +
*[Feeding]
 +
*[Defecation]
 +
|
 +
*[Egg laying]
 +
*[Dauer larva formation]
 +
*[Male mating]
 +
*[Social behavior]
 +
*[Learning and memory]
 +
|
 +
*[Sensory response to touch]
 +
*[Sensory response to smell]
 +
*[Sensory response to taste]
 +
*[Sensory response to temperature]
 +
|}
 +
 +
[[Category:Process page]]

Latest revision as of 20:52, 24 September 2010

back to Caltech SOPs

Notes for process pages

  • Pathway databases
    • BioCyc: Peter Karp, SRI, PathoLogic tools,
    • KEGG:
    • C. elegans specific db, Armand Leroi's, NMR-based metabolomic data using MetaShark for assigning enzyme classification
    • WikiPathways: Alex Pico, Gladstone, GenMAPP Pathway Markup Language (GPML), PathVisio
    • Reactome: Peter D'Eustachio, Lisa Matthews
    • NEMAPATH: Makedonka Mitreva, nematode.net, nonelegans
  • Visualization software
    • Cytoscape
    • GenMAPP
    • PathVisio

Processes in C. elegans

Cell division

  • [Cell division in male]
  • [Cell division in hermaphrodite]
  • [Asymmetric cell division]

Cell death

  • [Programmed cell death: Developmental]
  • [Programmed cell death: Germ line]
  • [Necrosis]
  • [Autophagy]
  • [Cell death in hermaphrodite]

Axis formation

  • [Asymmetric cell division]
  • [Establishing polarity: A/P axis]
  • [Establishing polarity: D/V axis]
  • [Establishing polarity; L/R Axis]
  • [Maintaining polarity]

Cell migration

  • [Neuronal migration]
  • [Sex Myoblast positioning]
  • [DTC migration]
  • [LC migration]

Cell specification and differentiation

  • [P11/P12 specification]
  • [Embryonic blastomere specification]
  • [Cell differentiation in hermaphrodite]
  • [Cell differentiation in male]

Sex determination

  • [Dosage compensation]

Tissue morphogenesis

  • [Embryonic mesendoderm development]
  • [Muscle morphogenesis]

Organ development

  • [Pharynx development]
  • [Gonad development]
  • [Duct development]
  • [Muscle development]

Vulval development

  • Generation of VPC's
  • [Vulval Precursor Patterning]
  • [Generation of the adult]
  • [Anchor cell invasion]
  • [Morphogenesis of the vulva]
  • [Generation of the anchor cell: AC/UV decision]
  • [Uterine patterning: pi cell induction]
  • [Uterine patterning: uv1 induction]
  • [Patterning of adult cell types: 1° lineage]
  • [Patterning of adult cell types: Polarity of 2° lineage]

Germ line development

Spermatogenesis

Oogenesis

L1 development

  • [L1 arrest]

Molting

Male-specific development

  • [Hook Equivalence Group development]
  • [Spicule development]
  • [Male muscle development]

Dauer formation/arrest

  • [Regulation of dauer arrest]
  • [Dauer morphological changes]
  • [Dauer metabolism]
  • [Neuronal processes in dauer arrest]
  • [Steroids/hormones]
  • [Quiescence]
  • [Exit from dauer stage]

Neuronal regeneration

Chemosensation

  • [Chemotaxis]
  • [Oxygen sensing]
  • [Mating]
  • [Integrating signals]

Mechanosensation

Synaptic transmission

Behavioral plasticity

  • [Habituation]
  • [Adaptation]

Locomotion

  • [Pirouettes]
  • [Foraging]
  • [Taxis]

Feeding

  • [Pharyngeal pumping]
  • [Foraging]

Defecation

  • [Defecation cycle]

Ovulation

  • [Egg-laying]
  • [Egg-laying cycle]]

Male Mating

  • [Mate-Finding]
  • [Response to contact]
  • [Turning]
  • [Vulval Location]
  • [Spicule protraction]
  • [Sperm Transfer]
  • [Spicule retraction]

Sleep

Pathogen Response

  • [Innate Immune Response]
  • [Pathogen Avoidance]

Behavior

  • [Locomotion]
  • [Pathogen Avoidance]
  • [Foraging]
  • [Feeding]
  • [Defecation]
  • [Egg laying]
  • [Dauer larva formation]
  • [Male mating]
  • [Social behavior]
  • [Learning and memory]
  • [Sensory response to touch]
  • [Sensory response to smell]
  • [Sensory response to taste]
  • [Sensory response to temperature]