User:Anat Levit/Sandbox 1: Difference between revisions

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The phosphovariants can now be identified when the phosphorylation sites or interacting kinases were altered between subtype sequences.

The identified sites were classified according to one of the following types, defined by Ryu et al. 2009:

# In <scene name='User:Anat_Levit/Sandbox_1/Type_i/2'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-).

# In <scene name='User:Anat_Levit/Sandbox_1/Type_i/2'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-) ('''colored green''').

# In <scene name='User:Anat_Levit/Sandbox_1/Type_ii/2'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-).

# In <scene name='User:Anat_Levit/Sandbox_1/Type_ii/2'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-) ('''colored blue''').

# <scene name='User:Anat_Levit/Sandbox_1/Type_iii/1'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself.

# <scene name='User:Anat_Levit/Sandbox_1/Type_iii/1'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself ('''colored red''').

<scene name='User:Anat_Levit/Sandbox_1/Type_i/3'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are colored yellow (<scene name='User:Anat_Levit/Sandbox_1/All_phosphosites/1'>view all predictions</scene>).

<scene name='User:Anat_Levit/Sandbox_1/Type_i/3'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are '''colored yellow''' (<scene name='User:Anat_Levit/Sandbox_1/All_phosphosites/1'>view all predictions</scene>).

== Binding site analysis ==

@@ Line 36: / Line 36: @@
 The phosphovariants can now be identified when the phosphorylation sites or interacting kinases were altered between subtype sequences.
 The identified sites were classified according to one of the following types, defined by Ryu et al. 2009:
-# In <scene name='User:Anat_Levit/Sandbox_1/Type_i/2'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-).
+# In <scene name='User:Anat_Levit/Sandbox_1/Type_i/2'>type I</scene> the phosphorylation site is in the same location as the variation, and can either create a new phosphorylation site (Type I+) or eliminate an existing site (Type I-) (<font color='green'>'''colored green'''</font>).
-# In <scene name='User:Anat_Levit/Sandbox_1/Type_ii/2'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-).
+# In <scene name='User:Anat_Levit/Sandbox_1/Type_ii/2'>type II</scene> the variation is not in the same location as the phosphorylation site, and can either create a new phosphorylation site (Type II+) or eliminate an existing site (Type II-) (<font color='blue'>'''colored blue'''</font>).
-# <scene name='User:Anat_Levit/Sandbox_1/Type_iii/1'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself.
+# <scene name='User:Anat_Levit/Sandbox_1/Type_iii/1'>Type III</scene> are variations that change only the type of kinase involved, without affecting the phosphorylation site itself (<font color='red'>'''colored red'''</font>).
-<scene name='User:Anat_Levit/Sandbox_1/Type_i/3'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are colored yellow (<scene name='User:Anat_Levit/Sandbox_1/All_phosphosites/1'>view all predictions</scene>).
+<scene name='User:Anat_Levit/Sandbox_1/Type_i/3'>Identical</scene> phosphor-acceptor residues predicted to be phosphorylated by the same kinases are <font color='yellow'>'''colored yellow'''</font> (<scene name='User:Anat_Levit/Sandbox_1/All_phosphosites/1'>view all predictions</scene>).
 == Binding site analysis ==