Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

The central goal of XGR by Fang et al. (2016) is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.


News

CHANGES IN VERSION 1.1.1

NEW FEATURES

o Modify functions ('xEnricher', 'xEnricherGenes', 'xEnricherSNPs', 'xEnricherYours', 'xGRviaGenomicAnno') enabling two-side p-value calculation and inclusion of odds ratio (confidence intervals)

o Add a new function 'xEnricherGenesAdv' for conducting enrichment analysis given a list of gene sets and a list of ontologies

o Add a new function 'xGRviaGeneAnnoAdv' for conducting enrichment analysis given a list of genomic region sets and a list of ontologies

o Add a new function 'xEnrichForest' for visualising enrichment results in a forest plot

o Add a new function 'xVisInterpAnimate' for animating irregular data interpolation and visualisation

o Modify 'xDAGpropagate' allowing for keeping all children

o Modify 'xSNP2nGenes' and 'xSNP2GeneScores' allowing for inclusion of a TAD dataset to pre-filter SNP-nGene pairs

o Modify 'xEnrichBarplot', 'xEnrichCompare', 'xVisNet', 'xVisInterp', 'xVisInterpAnimate' and 'xVisEvidence' allowing for inclusion of font family

o Populate the primary source KEGG into 'xEnricherGenes', 'xGRviaGeneAnno', 'xDefineNet', 'xSubneterGenes', 'xSubneterSNPs' and 'xSubneterGR'

o Add a new function 'xCombineNet' for combining networks

o Modify 'xGR2nGenes' allowing for user-defined 'GR.Gene' (a GR object)

o Modify 'xEnrichDAGplot' only visualising nodes within a user-defined graph (an igraph object)

o Populate annotations (KEGG and REACTOME)

o Add a new function 'xGraphML' for creating a graphml file

o Add a new function 'xVolcano' for drawing a volcano plot

o Add a new function 'xAddCoords' for adding coordinates into a graph by a node attribute

o Add a new function 'xGraphSplit' for splitting a graph by a node attribute

o Add a new function 'xRegress' for regressing out data by principle components

o Add functions ('xGGnetwork' and 'xOBOcode') enabling ggplot-like visualisation

o Add functions ('xGScore' and 'xGScoreAdv') enabling extraction of genomic scores  

o Add functions ('xBigraph' and 'xBiheatmap') supporting bigraph analysis

o Add functions ('xGR2xGenes', 'xGR2xGeneScores' and 'xGR2xNet') supporing genomic region analysis using the crosslink info

CHANGES IN VERSION 1.0.10

NEW FEATURES

o Add a new function 'xVisInterp' for irregular data interpolation and visualisation

o Populate annotations

o Modify 'xSymbol2GeneID' allowing for converting into gene info
    
o Define S3 classes ('eTerm')

o Add a new function 'xDefineNet' for defining built-in network

CHANGES IN VERSION 1.0.9

NEW FEATURES

o Add a new function 'xSymbol2GeneID' for converting gene symbols to entrez geneid

o Add a new function 'xDAGpropagate' for propagating annotations

CHANGES IN VERSION 1.0.8

NEW FEATURES

o Add a new function 'xCheckParallel' for checking and using parallel computing on Unix-like systems and on Windows

o Enable parallel computing on Windows ('xDAGsim', 'xSocialiser' and 'xGRviaGenomicAnnoAdv')

o Populate annotations

CHANGES IN VERSION 1.0.6

NEW FEATURES

o Fix bugs (such as in 'xGRviaGeneAnno', 'xGRviaGenomicAnno' and 'xGRviaGenomicAnnoAdv')

o Get published in Genome Medicine (see http://dx.doi.org/10.1186/s13073-016-0384-y)

CHANGES IN VERSION 1.0.5

NEW FEATURES

o Change functions ('xEnrichBarplot' and 'xEnrichCompare') caused by the major ggplot2 update (2.2.0)

o Add a new function 'xColormap' for defining color palette (including those used by ggplot2)

o Add new functions ('xSubneterGR', 'xGR2GeneScores', 'xGR2nGenes' and 'xGRscores') to conduct region-based network analysis

o Populate annotations

CHANGES IN VERSION 1.0.4

NEW FEATURES

o Add infrastructure functions ('xSNPlocations' and 'xSM2DF')

o Populate annotations

CHANGES IN VERSION 1.0.3

NEW FEATURES

o Fix bugs in the function 'xRDataLoader' for Windows users

o Enable choosing analysis resolution done by 'xGRviaGenomicAnno'

CHANGES IN VERSION 1.0.2

NEW FEATURES

o Add new functions ('xEnrichConciser', 'xEnrichBarplot', 'xEnrichDAGplot', 'xEnrichCompare' and 'xEnrichDAGplotAdv') to visualise and compare enrichment analysis results

o Add new functions ('xSocialiserDAGplot' and 'xSocialiserDAGplotAdv') to visualise and compare similarity analysis results

o Add new functions ('xVisKernels', 'xSNPscores', 'xSNP2nGenes', 'xSparseMatrix' and 'xSNP2GeneScores') to control how to define and score seed genes from a list of GWAS SNPs

o Add new annotation functions ('xGRviaGeneAnno', 'xGRviaGenomicAnno' and 'xGRviaGenomicAnnoAdv') to interpret user-defined list of genomic regions either via looking at nearby gene annotations by ontologies or via looking at co-localised functional genomic annotations

CHANGES IN VERSION 1.0.0

NEW FEATURES

o A new data interpretation system by comprehensively utilising ontology and network information to make a user-defined gene or SNP list more interpretable

o Enrichment analysis using either built-in or custom ontologies

o Similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles

o Network analysis for identifying gene networks given a query list of (significant) genes or SNPs

Reference manual

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