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| !!!Procedure |
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| !!Useful Resource: |
| !!!Processing data |
| vPECA model requires input as sample matched time-series RNA-seq, and ATAC-seq, and individual matched DNA-seq data together with selection scores calculated for each SNP from public data. For RNA-seq and ATAC-seq data, first we processed raw reads into an expression matrix with row genes and column samples. And chromatin accessibility data as a matrix with element by sample dimensions. The candidate RE and TG pairs based on distance are collected into a Element_gene in Data_prior.mat. Then the SNPs locate on REs and their corresponding selection scores are in a text file named element_SNP_use.txt. The prior (TF-TG, TG-RE) learned from public data could be set to certain number if it is not available. TF binding strength are calculated from motif scan algorithm. |
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| Download 25 bio-sample matched RNA-seq and DNase-seq data from mouse ENCODE project. |
| !!!Running vPECA |
| All the main programs are in main_PECA.m file. Please run the script and get the result from the folder called Output. All the selection status of each RE, and TF-RE-TG triplets are listed |
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| Download regulatoryElement-targetGene association. |
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| Download PECA predicted whole network and context specific network for 25 tissues or cell type. |
| !!!Requirements |
| MATLAB 2018a |
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| !!!Time |
| It usually takes several seconds on each gene. In total, about 24 hours are required to processing all the genes, and write all text output files. |
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| !!Using PECA Tools: |
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| PECA-TNet: Matlab tool for context specific network |
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| Input: paired expression of genes (Exp) and chromatin accessibility of regulatory elements (Opn) on your interested cellular context. |
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| Output: context specific network (TissueSpecificNet). |
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| Usage: TissueSpecificNet=PECATool1(Exp,Opn,GeneName,ElementName); |
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| Where GeneName and ElementName are name of gene and regulatory elements. |
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| PECA-Anno: Matlab tool for genomic region annotation by network |
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| Input: Bed file of the genomic region you interested (region.bed’). |
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| Output: annotation network of your region (RegionNet). |
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| Usage: RegionNet=PECATool2(‘region.bed’); |
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| * [PECA|http://web.stanford.edu/~zduren/PECA/] |
| * [vPECA.zip|vPECA.zip] |
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| Category: [Software] |
| Category: [Supplementary] [Software] |
