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README.md

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-# Microarray_Mtb
+# Microarray gene expression analysis of Mycobacterium tuberculosis (Mtb)
+
+
+
+## Project description:
+
+Our project investigated 177 genes across 287 conditions using different treatments, 
+antibiotics, and chemical agents to identify the genes involved in a biological process that 
+could be inferred the similar expression levels and the regulatory networks between the genes 
+among the conditions.
+
+
+
+## Analysis workflow:
+
+#### 1. Initial analysis:
+
+We imported data into R for analysis. We determined the number for genes and conditions in our 
+data. We made a Q-Qplot to test for normality in our data. We identified and imputed missing 
+data points using impute R package.
+
+#### 2. PCA and Gene Correlation analysis:
+
+We analysed variance-covariance structure and determined percent of variance explained by each 
+Principal component. We also analysed the degree of association between genes using a heatmap 
+of gene correlation.
+
+#### 3. Gene distance Clustering Analysis:
+
+We performed hierarchical Euclidean distance clustering of genes and made a dendrogram to 
+visualize the grouping of genes in our data.
+
+#### 4. Network Inference Analysis:
+
+We used minet package for constructing networks. We used three methods for comparison; clr, 
+mrnet, and aracne. We wrote out the resulting networks to a table for further analysis in 
+CytoScape.
+
+#### 5. Network Property Analysis with CytoScape:
+
+We imported the network table into CytoScape, we optimised the threshold for each network 
+until we obtained an easily interpretable network. We settled on a threshold of 0.25 for clr, 
+0.1 for mrnet, for some reason changing threshold did not seem to affect aracne network. For 
+this reason, we did not proceed with network from aracne.
+
+#### 6. Network Cluster Analysis:
+
+We explored network properties using analyse network tool in CytoScape. We used clusterONE app 
+to determine clusters in our network.
+
+#### 7. GO Biological Processes:
+
+We analysed the GO biological processes and molecular functions associated with the clusters 
+using Bingo.