ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer (Q41491896)

1 October 2017

ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer (English)

1 reference

1 October 2017

0 references

0 references

1 reference

1 reference

4

1 reference

1 October 2017

Panu Jaakkola

3

0 references

author name string

Fatemeh Seyednasrollah

series ordinal

1

1 reference

PMC publication ID

4705679

1 October 2017

Krista Rantanen

series ordinal

2

1 reference

1 October 2017

11 August 2015

1 reference

1 October 2017

Nucleic Acids Research

1 reference

1 October 2017

44

1 reference

1 October 2017

1

1 reference

1 October 2017

e1

1 reference

Creative Commons Attribution 4.0 International

1 October 2017

start time

14 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/4705679

based on heuristic

inferred from PubMed Central ID database lookup

cites work

limma powers differential expression analyses for RNA-sequencing and microarray studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

HTSeq--a Python framework to work with high-throughput sequencing data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Detecting and correcting systematic variation in large-scale RNA sequencing data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Translating a gene expression signature for multiple myeloma prognosis into a robust high-throughput assay for clinical use.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

voom: Precision weights unlock linear model analysis tools for RNA-seq read counts

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Comparison of software packages for detecting differential expression in RNA-seq studies

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Integrated molecular analysis of clear-cell renal cell carcinoma

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Comprehensive molecular characterization of clear cell renal cell carcinoma

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

A comparison of methods for differential expression analysis of RNA-seq data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Differential analysis of gene regulation at transcript resolution with RNA-seq

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Genetic and functional studies implicate HIF1α as a 14q kidney cancer suppressor gene

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Differential expression in RNA-seq: a matter of depth

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Synthetic spike-in standards for RNA-seq experiments

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Differential expression analysis for sequence count data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Absence of VHL gene alteration and high VEGF expression are associated with tumour aggressiveness and poor survival of renal-cell carcinoma

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

External validation of the Mayo Clinic stage, size, grade, and necrosis (SSIGN) score for clear-cell renal cell carcinoma in a single European centre applying routine pathology

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Surveillance strategies for renal cell carcinoma patients following nephrectomy.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Contrasting properties of hypoxia-inducible factor 1 (HIF-1) and HIF-2 in von Hippel-Lindau-associated renal cell carcinoma.

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Significance analysis of microarrays applied to the ionizing radiation response

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

Reproducibility-optimized test statistic for ranking genes in microarray studies

11 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4705679

19 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKV806

VHL tumor suppressor gene alterations associated with good prognosis in sporadic clear-cell renal carcinoma

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26264667

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKV806

1 reference

1 October 2017

1 reference

PMC publication ID

4705679

1 October 2017

PubMed publication ID

26264667

1 reference

PMC publication ID

4705679