BioNet-Finder Files

#### FTD NETWORK ANALYSIS PROJECTS ####

Copyright (c) 2017-2018 Fernando Palluzzi, Mario Grassi, Valentina Saba

Index:
1. Methods references
2. Lincense
3. ItalianFTD-GWAS_data_PlosOne2017 NETWORK ANALYSIS - DATA LOADING [Reference 1]
4. ItalianFTD-fMRI_data_2018 NETWORK ANALYSIS - DATA LOADING [Reference 2]

1. METHOD REFERENCES.

# Reference 1

  Title: A Novel Network Analysis Approach Reveals DNA Damage,
         Oxidative Stress and Calcium/cAMP Homeostasis-Associated
         Biomarkers in Frontotemporal Dementia
Journal: Plos One, 2017

Developers: Fernando Palluzzi (1,2), Mario Grassi (1)

(1) Università di Pavia, Pavia, Italy
    Department of Brain and Behavioural Sciences
    Via Bassi 21, 27100, Pavia (PV), Italy

(2) Istituto Europeo di Oncologia (IEO), Milano, Italy
    Department of Experimental Oncology
    Via Adamello 16, 20139, Milano (MI), Italy

Contacts: fernando.palluzzi@gmail.com; Fernando.Palluzzi@ieo.it

# Reference 2

Title: 	Brain connectivity and information-flow breakdown 
		revealed by a minimum spanning tree-based model 
		of MRI data in behavioural variant Frontotemporal Dementia
Journal: [forthcoming]

Developers: Valentina Saba , Mario Grassi

	Università di Pavia, Pavia, Italy
    Department of Brain and Behavioural Sciences
    Via Bassi 21, 27100, Pavia (PV), Italy

	Contacts: valentina.saba01@universitadipavia.it; mario.grassi@unipv.it


2. LICENSE.

    This file is part of the genomic data analysis project BioNet-Finder
    
    (BNF).
    
    BNF is free software: you can redistribute it and/or modify it
    
    under the terms of the GNU General Public License as published by the
    
    Free Software Foundation, either version 3 of the License, or
    
    (at your option) any later version.


    BNF software is distributed in the hope that it will be useful,

    but WITHOUT ANY WARRANTY; without even the implied warranty of

    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

    GNU General Public License for more details.
    
    
    You should have received a copy of the GNU General Public License

    along with BNF.  If not, see <http://www.gnu.org/licenses/>.



3. ItalianFTD-GWAS_data_PlosOne2017 NETWORK ANALYSIS - DATA LOADING [Reference 1].

3.1. Install R

1) Download and install the R statistical software from
   https://www.r-project.org/

2) Start R

3) Install and load the igraph package, using the R commands:
   
   install.packages("igraph")
   library(igraph)


3.2. FTD Input Data (computable R version)

1) Download the ItalianFTD-GWAS_Oct2017 zip archive from the BioNet-Finder project:
    
    https://sourceforge.net/projects/bionet-finder/

2) Load the Italian FTD-GWAS data following the R commands in GWAS_ItalianFTD_data.R


3.3. Raw tab-delimited genotype file

Download ItalianFTD_PC1_genotypes.txt (raw PC1-transformed genotypes)
   
The raw data matrix of PC1-transformed genotypes, for FTD cases and controls,
can be extracted from R in a tab-delimited file with the following command:


  write.table(dataFTD, "ItalianFTD_PC1_genotypes.txt", row.names = TRUE, sep = "/t")


It will produce the ItalianFTD_PC1_genotypes.txt file, containing Entrez gene
IDs as rows, and the 1458 subjects as columns.

The total file size is 368.4 MB.

Each subject is numbered from i1 to i1458:
 i.  subjects from i1 to i926 are controls;
 ii. subjects from i927 to i1458 are FTD cases.

 
 
4. ItalianFTD-fMRI_data_2018 NETWORK ANALYSIS - DATA LOADING [Reference 2].

4.1. Input Data 

1) Download the zip archive in ItalianFTD-fMRI_May2018 folder from
   https://sourceforge.net/projects/bionet-finder/

2) Uncrompress the zip file. Two folders are stored inside it:
   i.  ItalianbvFTD-fMRI_data (41 bvFTD patients) 
   ii. ItalianHC-fMRI_data (39 healthy controls)

3) To reproduce the analyses in Reference 2 (Materials and methods, section 2),
   you need to install the R libraries igraph, brainwaver, and brainGraph
	
4.2. Tables of pre-proccessed fMRI data

For each subject, a data table in csv format is provided, containing 193 time series (rows)
grouped by 116 brain regiorns (columns), defined by the automated anatomical labelling (AAL) atlas
(Reference 2, Materials and methods: Neuroimaging pre-processing and Brain parcellation).

Table files for bvFTD and healthy-control (HC) subjects are numbered bvFTD1-41 and HC1-39, respectively
(total file size 42.3 MB).