From 54b1b794bed075967b0de3f9e6699269f2c57410 Mon Sep 17 00:00:00 2001 From: khanspers Date: Fri, 22 Nov 2024 13:45:23 -0800 Subject: [PATCH] update text --- stages/sig-cascade/index.html | 2 +- stages/sig-phosphorylation/index.html | 4 ++-- stages/sig-start/index.html | 11 +++++------ stages/sig-transcription/index.html | 14 ++++++-------- stages/sig-transport/index.html | 11 ++++++----- 5 files changed, 20 insertions(+), 22 deletions(-) diff --git a/stages/sig-cascade/index.html b/stages/sig-cascade/index.html index fe8b347..d0e03bd 100644 --- a/stages/sig-cascade/index.html +++ b/stages/sig-cascade/index.html @@ -38,7 +38,7 @@

Background

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+

A signaling cascade is a series of chemical reactions that occur within cells when in response to a stimulus, for example a ligand binding a receptor. The signal is transduced to the cell interior through second messengers which amplify the signal and transfer it to effector molecules, causing the cell to respond to the initial stimulus. Most signaling cascades are composed of series of events, in which one event triggers the next, in a linear way. Signaling cascades commonly result in effects on transcription factors, which in turn affect transcription of specific genes. In our pathway, the binding of Insulin to the Insulin receptor triggers the PI3K/Akt pathway, which leads to several downstream effects.

Your Mission

Draw the part of the pathway outlined in red below:

diff --git a/stages/sig-phosphorylation/index.html b/stages/sig-phosphorylation/index.html index d75627a..5940f08 100644 --- a/stages/sig-phosphorylation/index.html +++ b/stages/sig-phosphorylation/index.html @@ -40,11 +40,11 @@

Background

Protein phosphorylation is a common post-translational modification of proteins, which involves the addition of a phosphate group to specific amino acids of a - protein by enzymes called kinases. The phosphorylation of proteins affects their activity, either activating or inactivating them, and is a common theme in signal transduction cascades. In the case of the Glucose-insulin signaling pathway, the binding of Insulin to the insulin receptor (INSR) causes conformational changes and autophosphorylion which activates the insulin receptor. The Insulin receptor substrate (IRS1) can then bind the insulin receptor and is subsequently phosphorylated by INSR, which activates the protein, thus transmitting the signal to downstream pathways. Although the pathway figure appears to show phosphorylation of INSR, the article text actually mentions IRS1: "Insulin controls glucose metabolism and results in glucose uptake through the phosphorylation of insulin receptor substrate....", so we will model this phosphorylation. It is not uncommon that information in pathway figures in publications differ from the information in the article text, so it is important to read the article in full and cross-check all information.

+ protein by enzymes called kinases. The phosphorylation of proteins affects their activity, either activating or inactivating them, and is a common theme in signal transduction cascades. In the case of the Glucose-insulin signaling pathway, the binding of Insulin to the insulin receptor (INSR) causes conformational changes and autophosphorylion which activates the insulin receptor. The Insulin receptor substrate (IRS1) can then bind the insulin receptor and is subsequently phosphorylated by INSR, which activates the protein, thus transmitting the signal to downstream pathways. Although the pathway figure appears to show phosphorylation of INSR, the article text actually mentions IRS1: "Insulin controls glucose metabolism and results in glucose uptake through the phosphorylation of insulin receptor substrate....", so we will model this phosphorylation. It is not uncommon that information in pathway figures in publications differ from the information in the article text, so it is important to read the article in full and cross-check all information.

WikiPathways models allow for the addition of a number of State objects to any DataNode, which can be used to depict not only phosphorylation of specific amino acid residues, but also other post-translational modifications. In addition to indicating that a protein is phosphorylated, we have developed a method for - adding specific site information to states on nodes in a way that is amenable to data mapping in tools like Cytoscape. The information is added as a structured comment. The process of protein phosphorylation by a kinase can be depicted in different ways, with varying degrees of detail. We will use a simplified style to indicate the phosphorylation of IRS1 by INSR usinf an arrow interaction directly from the INSR to IRS1 to indicate the activation caused by the phosphorylation, and a State node added to the IRS1 node.

+ adding specific site information to states on nodes in a way that is amenable to data mapping in tools like Cytoscape. The information is added as a structured comment. The process of protein phosphorylation by a kinase can be depicted in different ways, with varying degrees of detail. We will use a simplified style to indicate the phosphorylation of IRS1 by INSR using an arrow interaction directly from the INSR to IRS1 to indicate the activation caused by the phosphorylation, and a State node added to the IRS1 node. For more detailed information on describing protein phosphorylation in pathways, see Protein Phosphorylation.

Your Mission

diff --git a/stages/sig-start/index.html b/stages/sig-start/index.html index 81c8612..4f5790e 100644 --- a/stages/sig-start/index.html +++ b/stages/sig-start/index.html @@ -41,20 +41,19 @@

Background

- This path desribes the process of authoring a pathway model from a published pathway figure. In this case, we will use a pathway figure from the Pathway Figure OCR (PFOCR) project. Pathway Figure OCR is an open science project dedicated to extracting pathway information from the published literature. These instructions assume that you have everything you need to work with WikiPathways. [add links to setup and account creation] -

-

We will focus on a pathway figure below, describing Glucose-Insulin signaling, from a publication by Mahmoudi et al. To model this pathway, we will use the corresponding Pathway Figure OCR page for the figure as well as the publication itself, and other resources. The first step, described below, is to access the genes and chemicals extracted by PFOCR to jump-start the pathway drawing process.

- + This path describes the process of authoring a pathway model from a published pathway figure. In this case, we will use a pathway figure from the Pathway Figure OCR project. Pathway Figure OCR (PFOCR) is an open science project dedicated to extracting pathway information from the published literature. These instructions assume that you have everything you need to work with WikiPathways, including PathVisio and a WikiPathways account.

+

We will focus on a pathway figure below, describing Glucose-Insulin signaling, from a publication by Mahmoudi et al. To model this pathway, we will use the corresponding Pathway Figure OCR page as well as the publication itself, and other resources. The first step, described below, is to access the genes and chemicals extracted by PFOCR to jump-start the pathway drawing process.

+

Getting Started


diff --git a/stages/sig-transcription/index.html b/stages/sig-transcription/index.html index 866bf4c..1923b23 100644 --- a/stages/sig-transcription/index.html +++ b/stages/sig-transcription/index.html @@ -32,13 +32,12 @@

Organized training challenges for new WikiPathways authors

Background

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@@ -50,7 +49,7 @@

Your Mission

  • Launch PathVisio and open the dowloaded file or your draft pathway file via File > Open.
  • Perform the challenge tasks:
    • --> -
  • When you have completed the challenge, save your work as a GPML file under File > Save As.
    • -
  • Drag-and-drop the GPML file below to check if it is correct.
    • +
  • When you have completed the challenge, save your work as a GPML file under File > Save As.
    • +
  • Drag-and-drop the GPML file below to check if it is correct.
    • diff --git a/stages/sig-transport/index.html b/stages/sig-transport/index.html index 70be240..b36f75b 100644 --- a/stages/sig-transport/index.html +++ b/stages/sig-transport/index.html @@ -39,6 +39,7 @@

    Background

    + The first step in this pathway is two-fold; the binding of Insulin to the Insulin receptor and the transport of Glucose into the cell aided by the glucose transporter SLC2A2 (GLUT2). In the figure, the receptor are illustrated by graphical objects that are perfectly interpretable by the human brain, but since they are not labeled, they can't be interepted/found by the OCR method that was used to extract information from this pathway. We will need to add data nodes for the receptor and the transporter.

    Your Mission

    @@ -47,18 +48,18 @@

    Your Mission

    -
  • Save your work as a GPML file under File > Save As.
    • -
  • Drag-and-drop the GPML file below to check if it is correct.
    • -