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Protocols

OrderedList specifications

Information


Unique identifier OMICS_03525
Name OrderedList
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.52.0
Stability Stable
Requirements
methods, stats, graphics, Biobase, R(>=2.1.0), Biobase(>=1.5.12), twilight(>=1.9.2), twilight
Maintained Yes

Versioning


No version available

Documentation


Publication for OrderedList

OrderedList citations

 (16)
library_books

Integrated omics dissection of proteome dynamics during cardiac remodeling

2018
Nat Commun
PMCID: 5760723
PMID: 29317621
DOI: 10.1038/s41467-017-02467-3

[…] ed Stouffer’s Z score test. Significance of correlation was reported as asymptotic P of Spearman’s ρ. The similarity of gene lists in the meta-analysis of multi-omics data sets was compared using the OrderedList package (v.2.4) in R/Bioconductor. Significance of functional enrichment was reported as hypergeometric test P with Benjamini–Hochberg adjustment. The significance of protein–protein corre […]

library_books

Comprehensive transcriptional map of primate brain development

2016
Nature
PMCID: 5325728
PMID: 27409810
DOI: 10.1038/nature18637

[…] s (419 * 418 = 175,142 comparisons). For each gene list comparison, we found the number of overlapping genes and calculated an overlap similarity score based on the weighted rank order of the lists (“OrderedList” package in R). We then generated a null distribution of similarity scores by shuffling gene lists 10 million times and calculated P values for observed similarity scores. We found that 56 […]

call_split

Identification of epigenetic modifications that contribute to pathogenesis in therapy related AML: Effective integration of genome wide histone modification with transcriptional profiles

2015
BMC Med Genomics
PMCID: 4460748
PMID: 26043758
DOI: 10.1186/1755-8794-8-S2-S6
call_split See protocol

[…] ]. The significance of the similarity between the two statistics (coefficient and fold change) was estimated using an empirical p-value based on permutation (n = 1000), using the Bioconductor package OrderedList []. We also tested the differential expression between -q/del(7q) t-AML (n = 8) and normal controls to determine whether a regulatory biomodule for t-AML is consistent despite loss of chro […]

library_books

Increased Expression of Interferon Signaling Genes in the Bone Marrow Microenvironment of Myelodysplastic Syndromes

2015
PLoS One
PMCID: 4372597
PMID: 25803272
DOI: 10.1371/journal.pone.0120602

[…] EGs was created in Cytoscape [] and its MultiColoredNodes plug-in []. The overall similarity of differential expression signatures between RCMD vs. control and RAEB vs. control was assessed using the OrderedList R package [], which does not rely on a simple overlap of DEGs but instead considers the complete ordering of all genes in the two differential expression signatures to assess their overall […]

library_books

Blood Protein Markers of Neocortical Amyloid β Burden: A Candidate Study Using SOMAscan Technology

2015
PMCID: 4923714
PMID: 25881911
DOI: 10.3233/JAD-150020

[…] r analysis using standard linear regression on our serum samples from the AIBL cohort. Within each cohort (TwinsUK and AIBL) the proteins were ranked by p-value from the regressions and the R package OrderedList was used to compare the rank of proteins present on both versions of the platform [].To assess the concordance of proteomic signal between SOMAscan and RBM MAP, we implemented an identical […]

library_books

Hidden Treasures in “Ancient” Microarrays: Gene Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue

2014
PMCID: 4178426
PMID: 25325012
DOI: 10.3389/fonc.2014.00251

[…] d one based on AUC. A statistical methods based on differentially weighting overlaps among lists depending by whether they occur at the extremes of in the middle of the lists [Bioconductor’s package “OrderedList,” ()] was employed to test and measure the similarity between the lists of each ordering scheme. […]

Citations

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OrderedList institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

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