DriverMap Predesigned Targeted Expression Profiling Panels
DriverMap Targeted Expression Profiling Panels specifically amplify selected sets of genes whose expression provides insights on cancer and inflammatory diseases, cell signaling, cell lineages, processes of differentiation and immune activation.
- Expertly curated key genes associated with specific human diseases or cell phenotypes
- Ultra-sensitive quantitation of genes most likely to be involved in cellular processes and disease progression
- Targeted gene sets increase NGS read numbers for gene targets, which improves profiling statistics, specificity and sensitivity
Five DriverMap Panels Target Biologically Relevant Gene Sets
DriverMap Human Cell Marker Panel
The DriverMap Human Cell Marker Panel measures the expression level of 1,285 human protein-coding genes associated with immune and stromal cell types. The cell marker gene sets summarize and characterize gene signatures for 64 distinct cell types, spanning multiple adaptive and innate immunity cells, hematopoietic progenitors, epithelial cells, and extracellular matrix cells derived from thousands of published gene expression signatures. To generate the compendium of gene-specific signatures for human cell types, we used data from ENCODE, FANTOM, ImmGen, and the Human Primary Cells Atlas (HPCA). Also, we collected gene expression profiles from the Blueprint project, from which we annotated 144 samples from 28 cell types, and the IRIS project, from which we annotated 95 samples from 13 cell types. We collected and curated gene expression profiles from ~2,310 samples of pure cell types and annotated 64 distinct cell types and cell subsets.
DriverMap Human Hallmark Signatures Panel
The DriverMap Human Hallmark Signatures Panel measures the expression level of 4,304 human genes encompassing well-defined molecular pathways, biological states, or disease processes as described in the Molecular Signatures Database (MSigDB).
DriverMap Human LINCS 1000x Panel
The DriverMap Human LINCS 1000x Panel assays the expression level of 1,573 human from the Library of Integrated Network-based Cellular Signatures (LINCS – http://www.lincsproject.org) and Drugbank (https://www.drugbank.ca). The LINCS program aims to create a network-based understanding of biology by cataloging gene expression changes and other cellular processes that occur when cells are exposed to perturbing agents –drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Gene expression signatures in response to such perturbations were used to identify the minimal subset of universally informative transcripts termed “landmark genes.”
Also, to provide further insight into trends in the discovery of new drug targets, we analyzed the drugs approved by the US Food and Drug Administration (FDA) during the past three decades and examined the interactions of these drugs with therapeutic targets encoded by the human genome, using the DrugBank database and extensive manual curation. We identified 575 direct effect-mediating drug targets in the human genome, which are modulated by 1071 unique drugs and included in LINCSx.
DriverMap Human Pan-Cancer Pathway Panel
The DriverMap Human Pan-Cancer Pathway Panel measures the expression level of 2,094 genes associated with tumor formation and progression. Tumorigenesis is a complex and dynamic process consisting of three stages: initiation, progression, and metastasis. The DriverMap Pan-Cancer Pathway Assay targets genes related to DNA repair, angiogenesis, cell adhesion, extracellular matrix, cell cycle, and apoptosis. Many genes encoding transcription factors and protein kinases can be found to be differentially expressed during tumor progression and metastasis. Novel gene signatures of molecular pathways that are often disregulated in cancer were included based on expert curation from scientific publications, directly from transcriptome data from NCBI GEO, and from internal unpublished profiling experiments which involved perturbation of known cancer genes (DECIPHER – http://www.decipherproject.net). The DriverMap Pan-Cancer panel also measures the expression of genes involved in tumor-immune responses, including markers associated with different stromal cells, leukocyte subsets, antigen presentation, cancer immunotherapy, and immune checkpoint pathways.
DriverMap Human Transcription Factor Signature Panel
The DriverMap Human Transcription Factor Signature Panel enables gene signature-based inference and quantitative evaluation of 343 key transcription factors by providing expression data for 2,649 human genes. The panel provides expression data on both transcription factors and their known target genes. The panel was assembled by integrating data from the literature using a natural language processing (NLP) framework, expert manual curation, and open-access databases linking transcription factors to their target genes. As a result, the DriverMap Human Transcription Assay provides expression data for 6,401 possible regulation pathways linking 343 distinct transcription factors.
All the benefits of the DriverMap Technology
The DriverMap Targeted Profiling Panels utilize the same single-tube multiplex assay approach as the DriverMap Genome-Wide Expression Profiling Assay, which provides robust, quantitative, and reproducible measurements of each expressed gene over as much as 5-orders of magnitude. The DriverMap approach overcomes the low sensitivity and specificity challenges of current RNA sequencing technologies. It greatly simplifies the protocols for data generation and analysis while providing robust specificity, sensitivity and reproducibility of differentially expressed, protein-coding genes. For rapid analysis, it also comes with the DriverMap Deconvolution Software that enables visualization of gene-specific expression data in an Excel spreadsheet format directly from Illumina NGS Fastq raw reads.
DriverMap kits include all necessary reagents and components required to generate 96 targeted RNA-Seq libraries. The DriverMap technology can effectively be used with total RNA derived from blood, cell culture, or fresh frozen or formalin-fixed paraffin-embedded (FFPE) tissue.
Murine orthologs of 4,700 key human genes included in the Pan-Cancer, LINCSx and Hallmark Signatures panels are available as a separate DriverMap mouse panel.