From 1c9aaafff0863a753fe6df063b5a6eb39e37e758 Mon Sep 17 00:00:00 2001 From: Octopus <21128258+anastasiiaNG@users.noreply.github.com> Date: Thu, 29 Dec 2022 19:42:29 +0400 Subject: [PATCH] Update README.md --- README.md | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index b6fff65..0b73ac3 100755 --- a/README.md +++ b/README.md @@ -5,18 +5,10 @@ > GAM-clustering provides metabolic variability within dataset using a novel network-based computational approach that utilizes cellular transcriptional profiles as proxies. The metabolic network of reactions from KEGG database is presented as a graph that has vertices corresponding to metabolites and the edges corresponding to the reactions with the expressed genes. In the graph the method tries to find a set of connected subgraphs, with each corresponding well to a certain gene expression pattern. Curret analysis reveals the major metabolic features associated with different subpopulations and highlights a number of metabolic modules that are specific to individual cell types, tissues of residence, or developmental stages. -To explore data visit the following links: -- [Gene expression heatmap](https://artyomovlab.wustl.edu/phantasus/?preloaded=ImmGen_total_Eduw0mei4) -- [PCA with samples annotation](http://artyomovlab.wustl.edu/publications/supp_materials/Immgen/PCADatasetOverview.html) -- [Heatmap of metabolic modules](https://artyomovlab.wustl.edu/phantasus/?session=x039baa087a35e7) - -## Requirments -- [R](https://www.r-project.org/) -- [sgmwcs-solver](https://github.com/ctlab/sgmwcs-solver) -- [KEGG mouse metabolic network](GAM) +To explore data visit the following [interactive browser](https://artyomovlab.wustl.edu/immgen-met/). ## Input data -[Raw counts](Data/OSMNP_unnormalized_genes_count_10_3_18.count_table) are processed by [rawDataProcessing.R]() script and the output object `es.top12k` has the following structure: +[Raw counts](Data/OSMNP_unnormalized_genes_count_10_3_18.count_table) are processed by [`rawDataProcessing.R`](rawDataProcessing.R) script and the output object `es.top12k` has the following structure: ``` r > load("Data/337_es.top12k.Rda") @@ -33,7 +25,7 @@ To explore data visit the following links: ``` ## Modules deriving -The initial patterns are defined using k-means clustering on gene expression matrix and then are refined in an iterative process using the network connections ([modulesDeriving.R]()). +The initial patterns are defined using k-means clustering on gene expression matrix and then are refined in an iterative process using the network connections ([`modulesDeriving.R`](modulesDeriving.R)). The final output presents a set of specific subnetworks (also called metabolic modules) that reflect metabolic variability within a given transcriptional dataset. Each metabolic module is a piece of metabolic network whose gene expression has correlated expression pattern across all dataset. The following graph and heatmap represent network and constituting genes' expression for module 5, correspondingly: ![module5](/readmePics/github.pic.m5.png "network and gene expression heatmap for module 5") @@ -41,7 +33,7 @@ Averaged gene expression of all modules is represented at the following summary ![centers](/readmePics/github.m.centers.png "centers heatmap") ## Modules annotation -Functional annotation of obtained modules is based on KEGG and Reactome canonical pathways ([modulesAnnotation.R]()). +Functional annotation of obtained modules is based on KEGG and Reactome canonical pathways ([`modulesAnnotation.R`](modulesAnnotation.R)). The following example is devoted to module 5 (k - number of module genes in a particular pathway, K - number of genen in a particular pathway): ``` r > paths <- data.table::fread("Data/m.5.pathways_mod.tsv") @@ -50,4 +42,4 @@ The following example is devoted to module 5 (k - number of module genes in a pa ## 1: R-MMU-191273 1.009604e-48 17 24 1.237774e-45 Cholesterol biosynthesis Hmgcs1 Hmgcr Msmo1 Cyp51 Mvd ... ## 2: R-MMU-8957322 9.801101e-39 17 67 6.008075e-36 Metabolism of steroids Hmgcs1 Hmgcr Msmo1 Cyp51 Mvd ... ## 3: R-MMU-556833 1.406903e-27 18 395 5.749543e-25 Metabolism of lipids Hmgcs1 Hmgcr Msmo1 Cyp51 Aacs ... -``` \ No newline at end of file +```