ArticleProceedings of the National Academy of Sciences of the United States of America2013
Multiplatform single-sample estimates of transcriptional activation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Loss of Wave1 gene defines a subtype of lethal prostate cancer.Oncotarget · 2015Pooled it
- A Novel PTPN2 Isoform Differentially Regulates Immune Response.European journal of immunology · 2026Article
- Development and validation of a 23-gene expression signature for molecular subtyping of medulloblastoma in a long-term Chinese cohort.Acta neurochirurgica · 2024Article
- Fibronectin Type III Domain Containing 3B as a Potential Prognostic and Therapeutic Biomarker for Glioblastoma.Biomedicines · 2023Article
- Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns.Frontiers in molecular biosciences · 2023Article
- Deciphering Tumour Microenvironment of Liver Cancer through Deconvolution of Bulk RNA-Seq Data with Single-Cell Atlas.Cancers · 2022Article
- Differential dependency of human glioblastoma cells on vascular endothelial growth factor‑A signaling via neuropilin‑1.International journal of oncology · 2022Article
- Transcriptomic Harmonization as the Way for Suppressing Cross-Platform Bias and Batch Effect.Biomedicines · 2022Review
- A Knowledge-Based Discovery Approach Couples Artificial Neural Networks With Weight Engineering to Uncover Immune-Related Processes Underpinning Clinical Traits of Breast Cancer.Frontiers in immunology · 2022Article
- KDM6B is an androgen regulated gene and plays oncogenic roles by demethylating H3K27me3 at cyclin D1 promoter in prostate cancer.Cell death & disease · 2021Article
- Extra-domain B of fibronectin as an alternative target for drug delivery and a cancer diagnostic and prognostic biomarker for malignant glioma.Theranostics · 2021Article
- A hierarchical Bayesian mixture model for inferring the expression state of genes in transcriptomes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- MyoMiner: explore gene co-expression in normal and pathological muscle.BMC medical genomics · 2020Article
- Cell-of-Origin Subtyping of Diffuse Large B-Cell Lymphoma by Using a qPCR-based Gene Expression Assay on Formalin-Fixed Paraffin-Embedded Tissues.Frontiers in oncology · 2020Article
- African American Specific Gene Panel Predictive of Poor Prostate Cancer Outcome.The Journal of urology · 2019Article
- L1TD1 - a prognostic marker for colon cancer.BMC cancer · 2019Article
- Gene expression signature of atypical breast hyperplasia and regulation by SFRP1.Breast cancer research : BCR · 2019Article
- Distinct transcriptional repertoire of the androgen receptor in ETS fusion-negative prostate cancer.Prostate cancer and prostatic diseases · 2019Article
- Blockade of integrin α3 attenuates human pancreatic cancer via inhibition of EGFR signalling.Scientific reports · 2019Article
- Ambient Pollution-related Reprogramming of the Human Small Airway Epithelial Transcriptome.American journal of respiratory and critical care medicine · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Over the past two decades, many biotechnology platforms have been developed for high-throughput gene expression profiling. However, because each platform is subject to technology-specific biases and produces distinct raw-data distributions, researchers have experienced difficulty in integrating data across platforms. Data integration is crucial to data-generating consortiums, researchers transitioning to newer profiling technologies, and individuals seeking to aggregate data across experiments. We address this need with our Universal exPression Code (UPC) approach, which corrects for platform-specific background noise using models that account for the genomic base composition and length of target regions; this approach also uses a mixture model to estimate whether a gene is active in a particular profiling sample. The latter produces standardized UPC values on a zero-to-one scale, so that they can be interpreted consistently, irrespective of profiling technology, thus enabling downstream analysis pipelines to be developed in a platform-agnostic manner. The UPC method can be applied to one- and two-channel expression microarrays and to next-generation sequencing data (RNA sequencing). Furthermore, UPCs are derived using information from within a given sample only--no ancillary samples are required at processing time. Thus, UPCs are suitable for personalized-medicine workflows where samples must be processed individually rather than in batches. In a variety of analyses and comparisons, UPCs perform comparably to other methods designed specifically for microarrays or RNA sequencing in most settings. Software for calculating UPCs is freely available at www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.