SurfaceGenie: a web-based application for prioritizing cell-type specific marker candidates.

07:00 EST 13th February 2020 | BioPortfolio

Summary of "SurfaceGenie: a web-based application for prioritizing cell-type specific marker candidates."

Cell-type specific surface proteins can be exploited as valuable markers for a range of applications including immunophenotyping live cells, targeted drug delivery, and in vivo imaging. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. A significant challenge in analyzing 'omic' discovery datasets is the selection of candidate markers that are most applicable for downstream applications.


Journal Details

This article was published in the following journal.

Name: Bioinformatics (Oxford, England)
ISSN: 1367-4811


DeepDyve research library

PubMed Articles [48848 Associated PubMed Articles listed on BioPortfolio]

Annotations capturing cell-type-specific TF binding explain a large fraction of disease heritability.

Regulatory variation plays a major role in complex disease and that cell-type-specific binding of transcription factors (TF) is critical to gene regulation. However, assessing the contribution of gene...

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns.

Transcription factors (TFs) selectively bind distinct sets of sites in different cell types. Such cell type-specific binding specificity is expected to result from interplay between the TF's intrinsic...

Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution.

The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not captu...

Translation of genome to glycome: role of the Golgi apparatus.

Glycans are one of the four biopolymers of the cell and they play important roles in cellular and organismal physiology. They consist of both linear and branched structures and are synthesized in a no...

SCMarker: Ab initio marker selection for single cell transcriptome profiling.

Single-cell RNA-sequencing data generated by a variety of technologies, such as Drop-seq and SMART-seq, can reveal simultaneously the mRNA transcript levels of thousands of genes in thousands of cells...

Clinical Trials [24728 Associated Clinical Trials listed on BioPortfolio]

Alpha-Type 1 Dendritic Cell (DC)-Based Vaccines Loaded With Allogeneic Prostate Cell Lines in Combination With Androgen Ablation in Patients With Prostate Cancer

Dendritic cells or "DCs" are special white blood cells that stimulate the immune system. This study is being done to test the feasibility, safety and efficacy of a specific type of dendrit...

DCLK1 as a Marker/Indicator of Stem Cell Response in Barrett's Esophagus/Esophageal Adenocarcinoma

The hypotheses are: 1) the intestinal stem cell marker, DCLK1, which is increased in both the epithelium and stroma in colon cancer is also increased in BE (Barrett's esophagus) with HGD (...

Detection of Human Beta Cell Death in Type 1 Diabetes Mellitus (T1DM) by Methylation Specific Polymerase Chain Reaction (PCR)

To investigate the use of methylation-specific PCR (MSP) assays to detect human beta cell-specific gene methylation patterns in serial blood samples drawn from newly diagnosed Type 1 diabe...

Study of IGRP-specific T Cell in Peripheral Blood of Type 1 Diabetes Mellitus

10 type 1 diabetes, 10 type 2 diabetes and 10 healthy controls matched with age and sex were enrolled in our study and their periphera blood mononuclear cells (PBMC) were isolated. We impl...

Red Cell Distribution Width (RDW) as a Prognostic Marker in ICU

The aim of this study is to verify if high values of RDW are useful prognostic marker for ICU mortality and 90-days mortality. Moreover, we will investigate the prognostic value of RDW in ...

Medical and Biotech [MESH] Definitions

A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.

A hexosaminidase specific for non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. It acts on GLUCOSIDES; GALACTOSIDES; and several OLIGOSACCHARIDES. Two specific mammalian isoenzymes of beta-N-acetylhexoaminidase are referred to as HEXOSAMINIDASE A and HEXOSAMINIDASE B. Deficiency of the type A isoenzyme causes TAY-SACHS DISEASE, while deficiency of both A and B isozymes causes SANDHOFF DISEASE. The enzyme has also been used as a tumor marker to distinguish between malignant and benign disease.

Adaptive antiviral defense mechanisms, in archaea and bacteria, based on DNA repeat arrays called CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS (CRISPR elements) that function in conjunction with CRISPR-ASSOCIATED PROTEINS (Cas proteins). Several types have been distinguished, including Type I, Type II, and Type III, based on signature motifs of CRISPR-ASSOCIATED PROTEINS.

Cells of the lymphoid series that can react with antigen to produce specific cell products called antibodies. Various cell subpopulations, often B-lymphocytes, can be defined, based on the different classes of immunoglobulins that they synthesize.

Cell surface receptors that are specific for INTERLEUKIN-8. Two specific receptor subtypes (type A and B) have been found and bind IL-8 with high affinity.

Quick Search

DeepDyve research library

Relevant Topic

Drug Delivery
<!--LGfEGNT2Lhm-->Drug delivery is the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals.  <!--LGfEGNT2Lhm-->Drug delivery technologies are <!--LGfEGNT2Lhm-->patent pr...

Searches Linking to this Article