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Protocols

LRpath specifications

Information


Unique identifier OMICS_04057
Name LRpath
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • RNA-Enrich

Documentation


Maintainer


  • person_outline Snehal Patil

Information


Unique identifier OMICS_04057
Name LRpath
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • RNA-Enrich

Versioning


No version available

Documentation


Maintainer


  • person_outline Snehal Patil

Publications for LRpath

LRpath citations

 (23)
call_split

Loss of microRNA 128 promotes cardiomyocyte proliferation and heart regeneration

2018
Nat Commun
PMCID: 5816015
PMID: 29453456
DOI: 10.1038/s41467-018-03019-z
call_split See protocol

[…] performed using the negative binomial statistical model of read counts as implemented in the edgeR Bioconductor package. The KEGG pathways and MSigDb gene sets enrichment analysis was performed using LRpath methodology as implemented in the CLEAN package, and ranked by the enrichment P-value. Functional enrichment analysis of the genes that are both downregulated in miR-128OE hearts and are predic […]

library_books

Solute carriers affect Anopheles stephensi survival and Plasmodium berghei infection in the salivary glands

2017
Sci Rep
PMCID: 5522484
PMID: 28733628
DOI: 10.1038/s41598-017-06317-6

[…] SGs of from each condition were grouped to obtain the quantity needed to perform high throughput sequencing. Sequencing was performed at Parque Científico de Madrid (FPCM, Spain). From 1 µg of total-RNA, enrich poly (A) mRNA were used to bead with magnetic beads with Oligo (dT) to construct the cDNA library. Next, from purified mRNAs, two different fragmentation conditions were applied so that a […]

library_books

Differential expression analysis for RNAseq using Poisson mixed models

2017
Nucleic Acids Res
PMCID: 5499851
PMID: 28369632
DOI: 10.1093/nar/gkx204

[…] e original continuous predictor variable in DE analysis.Several lines of evidence support the biological validity of the genes detected by MACAU. First, we performed gene ontology (GO) analysis using LRpath () on T2D and GL associated genes identified by MACAU, as in the FUSION study () (). The GO analysis results for T2D and GL are consistent with previous studies (,) and are also similar to each […]

library_books

An integrative study on the impact of highly differentially methylated genes on expression and cancer etiology

2017
PLoS One
PMCID: 5298317
PMID: 28178311
DOI: 10.1371/journal.pone.0171694

[…] RET oncogene expression with a large methylation decrease, contributing to an improved understanding of the etiology of thyroid cancer.In contrast to previously applied methods, such as MethylMix and LRpath, our approach integrates protein-protein interaction information in the identification of methylation-driven genes. Additionally, compared to the work of Jiao et al. [], which also integrates p […]

call_split

Immune adaptation to chronic intense exercise training: new microarray evidence

2017
BMC Genomics
PMCID: 5216585
PMID: 28056786
DOI: 10.1186/s12864-016-3388-5
call_split See protocol

[…] old-changes for enrichment analysis. Enriched Gene Ontology (GO) Biological Process terms [] and Kyoto Encyclopaedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathways [] were tested by LRpath [], a logistic regression -based gene set enrichment method. LRpath relates the odds of gene set membership with the significance of differential expression (p values from IBMT). LRpath’s abili […]

library_books

Genomic binding of PAX8 PPARG fusion protein regulates cancer related pathways and alters the immune landscape of thyroid cancer

2016
Oncotarget
PMCID: 5351587
PMID: 28008156
DOI: 10.18632/oncotarget.14050

[…] Gene IDs, p-values and fold changes from RNA-seq differential expression analyses were used as input in LRpath [, ] to perform gene set enrichment testing. We tested GO terms and KEGG pathways with the directional test option, which identifies gene sets enriched with up-regulated or down-regulated genes […]


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LRpath institution(s)
Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, USA

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