Difference between revisions of "Process page mock-ups"

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<h1>Programmed Cell Death in ''C. elegans''</h1>
+
[http://www.wormbase.org/wiki/index.php/Caltech_documentation back to Caltech SOPs]
<h2>[http://www.wormbook.org/chapters/www_programcelldeath/programcelldeath.html Developmental Cell Death in ''C. elegans'']</h2>
+
=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
  
[[image:Pcdfig2_s.png]]
+
*Visualization software
 +
**Cytoscape
 +
**GenMAPP
 +
**PathVisio
  
----
+
=Processes in ''C. elegans''=
  
<h2>Steps and processes</h2> 
+
==[[Cell division]]==
<h3>[[Specification]]</h3>
+
*[Cell division in male]
"...a cell is instructed to undergo programmed cell death..."
+
*[Cell division in hermaphrodite]
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00001324;class=Gene eor-1]''
+
*[Asymmetric cell division]
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00001325;class=Gene eor-2]''
 
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00006604;class=Gene tra-1]''
 
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00001949;class=Gene hlh-2]''
 
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00001950;class=Gene hlh-3]''
 
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00000469;class=Gene ces-2]''
 
**''[http://www.wormbase.org/db/gene/gene?name=WBGene00000468;class=Gene ces-1]''
 
  
<h3>[[Killing Phase]]</h3>
+
==[[Cell death]]==
"...the apoptotic program is activated in the cell instructed to die..."
+
{|
 +
|-valign="top"
 +
|
 +
*[Programmed cell death: Developmental]
 +
*[Programmed cell death: Germ line]
 +
*[Necrosis]
 +
|
 +
*[Autophagy]
 +
*[Cell death in hermaphrodite]
 +
|}
  
<h3>[[Execution Phase]]</h3>
+
==[[Axis formation]]==
"...cells are dismantled and subsequently engulfed by neighboring cells..."
+
{|
 +
|-valign="top"
 +
|
 +
*[Asymmetric cell division]
 +
*[Establishing polarity: A/P axis]
 +
*[Establishing polarity: D/V axis]
 +
*[Establishing polarity; L/R Axis]
 +
|
 +
*[Maintaining polarity]
 +
|}
  
**[[DNA Degradation Pathway]]
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==[[Cell migration]]==
**[[Corpse Engulfment Pathway]]
+
{|
 +
|-valign="top"
 +
|
 +
*[Neuronal migration]
 +
*[Sex Myoblast positioning]
 +
*[DTC migration]
 +
*[LC migration]
 +
|}
  
<h3>Cells</h3>
+
==[[Cell specification and differentiation]]==
*'''links to anatomy pages'''
+
{|
 +
|-valign="top"
 +
|
 +
*[P11/P12 specification]
 +
*[Embryonic blastomere specification]
 +
*[Cell differentiation in hermaphrodite]
 +
*[Cell differentiation in male]
 +
|}
  
<h3>Pathways</h3>
+
==[[Sex determination]]==
*'''[807 Paseo del Mar, Palos Verdes Estates, Los Angeles, California 90274 reactome]'''
+
*[Dosage compensation]
*'''[http://www.biocyc.org biocyc.org pathway tools]'''
 
  
<h3>Map onto animal</h3>
+
==[[Tissue morphogenesis]]==
 +
*[Embryonic mesendoderm development]
 +
*[Muscle morphogenesis]
  
<h2>[http://www.wormbook.org/chapters/www_germlinesurvival/germlinesurvival.html Germline Cell Death in ''C. elegans'']</h2>
+
==[[Organ development]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Pharynx development]
 +
*[Gonad development]
 +
*[Duct development]
 +
*[Muscle development]
 +
|}
  
 +
==[[Vulval development]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[[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]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Hook Equivalence Group development]
 +
*[Spicule development]
 +
*[Male muscle development]
 +
|}
 +
 
 +
==[[Dauer formation/arrest]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Regulation of dauer arrest]
 +
*[Dauer morphological changes]
 +
*[Dauer metabolism]
 +
*[Neuronal processes in dauer arrest]
 +
|
 +
*[Steroids/hormones]
 +
*[Quiescence]
 +
*[Exit from dauer stage]
 +
|}
 +
 
 +
==[[Neuronal regeneration]]==
 +
 
 +
==[[Chemosensation]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Chemotaxis]
 +
*[Oxygen sensing]
 +
*[Mating]
 +
*[Integrating signals]
 +
|}
 +
==[[Mechanosensation]]==
 +
 
 +
==[[Synaptic transmission]]==
 +
 
 +
==[[Behavioral plasticity]]==
 +
*[Habituation]
 +
*[Adaptation]
 +
 
 +
==[[Locomotion]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Pirouettes]
 +
*[Foraging]
 +
*[Taxis]
 +
|}
 +
 
 +
==[[Feeding]]==
 +
 
 +
*[Pharyngeal pumping]
 +
*[Foraging]
 +
 
 +
==[[Defecation]]==
 +
*[Defecation cycle]
 +
 
 +
==[[Ovulation]]==
 +
*[Egg-laying]
 +
*[Egg-laying cycle]]
 +
 
 +
==[[Male Mating]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Mate-Finding]
 +
*[Response to contact]
 +
*[Turning]
 +
*[Vulval Location]
 +
|
 +
*[Spicule protraction]
 +
*[Sperm Transfer]
 +
*[Spicule retraction]
 +
|}
 +
 
 +
==[[Sleep]]==
 +
 
 +
==[[Pathogen Response]]==
 +
{|
 +
|-valign="top"
 +
|
 +
*[Innate Immune Response]
 +
*[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]