4.7 Article

Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level

Related references

Note: Only part of the references are listed.
Article Cell Biology

Proteogenomics of glioblastoma associates molecular patterns with survival

Gali Yanovich-Arad et al.

Summary: This study utilized high-resolution mass spectrometry proteomics and RNA sequencing to analyze 87 GBM patients, identifying specific immune, metabolic, and developmental processes associated with survival. The findings revealed a stronger association between proteomic profiles and survival, establishing proteomic heterogeneity in GBM as a key factor in understanding poor survival.

CELL REPORTS (2021)

Article Genetics & Heredity

Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways

Maxim Sorokin et al.

Summary: High-throughput molecular and genomic analyses have allowed for the reconstruction of thousands of human molecular pathways, enabling the investigation of pathway activation levels (PALs) using bioinformatic algorithms. Understanding the functional roles of pathway components is crucial for comprehensive analysis of pathway activation profiles. Annotation of functional roles is necessary for the direct calculation of PALs and establishment of large scale profiles of pathway regulation using gene expression data.

FRONTIERS IN GENETICS (2021)

Article Biochemistry & Molecular Biology

Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology

Marianna A. Zolotovskaia et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Multidisciplinary Sciences

Glioma-initiating cells at tumor edge gain signals from tumor core cells to promote their malignancy

Soniya Bastola et al.

NATURE COMMUNICATIONS (2020)

Article Multidisciplinary Sciences

Atlas of RNA sequencing profiles for normal human tissues

Maria Suntsova et al.

SCIENTIFIC DATA (2019)

Article Biochemistry & Molecular Biology

The Reactome Pathway Knowledgebase

Antonio Fabregat et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Predicting proteome dynamics using gene expression data

Krzysztof Kuchta et al.

SCIENTIFIC REPORTS (2018)

Article Biotechnology & Applied Microbiology

Reduced changes in protein compared to mRNA levels across non-proliferating tissues

Kobi Perl et al.

BMC GENOMICS (2017)

Article Multidisciplinary Sciences

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues

Idit Kosti et al.

SCIENTIFIC REPORTS (2016)

Article Biochemical Research Methods

The CPTAC Data Portal: A Resource for Cancer Proteomics Research

Nathan J. Edwards et al.

JOURNAL OF PROTEOME RESEARCH (2015)

Article Biotechnology & Applied Microbiology

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

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

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

Marie-Agnes Dillies et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biotechnology & Applied Microbiology

RNA-Seq improves annotation of protein-coding genes in the cucumber genome

Zhen Li et al.

BMC GENOMICS (2011)

Article Biotechnology & Applied Microbiology

Correlations between RNA and protein expression profiles in 23 human cell lines

Marcus Gry et al.

BMC GENOMICS (2009)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)