CITRUS is a supervised machine learning algorithm designed to analyze single cell data, identify cell populations, and identify changes in the frequencies or functional marker expression patterns of those populations that are significantly associated with an outcome. The algorithm is a black box that includes steps to cluster cell populations, characterize these populations, and identify the significant characteristics. This chapter describes how to optimize the use of CITRUS by combining it with upstream and downstream data analysis and visualization tools.

01 Jul 2018·Cancer Research

Abstract 2265: viSNE in Cytobank enables rapid exploratory data analysis for RNA-seq biomarker discovery

Author: Polikowsky, Hannah ; Drake, Katherine A. ; Sethi, Ashu

AbstractBiomarkers provide great potential for understanding and predicting patient outcomes. However, the large numbers of putative biomarkers assayed by many discovery technologies can be difficult to parse quickly to understand their potential as predictors of an outcome of interest. viSNE is a non-linear dimensionality reduction algorithm available on the Cytobank informatics platform that can rapidly assess whether a set of biomarkers can meaningfully group samples. We establish a method for applying viSNE to RNA-seq data. We demonstrate this method using data from The Cancer Genome Atlas for 1,011 samples from 5 different types of kidney cancer and matched normal tissue samples for 139 of the subjects. The tumors ranged from stage I to stage IV, and subjects varied by age, gender, and whether they were living when the sample was taken. Using FPKM data from the 806 most variable transcripts in these samples, viSNE was able to group the samples into six distinct “islands” that separated cancer samples from each of the five disease types and the matched normal tissue. We demonstrate that viSNE is robust to noise and is able to group the samples even when variables that do not contribute to the signal are present in the data, and illustrate how this can be leveraged as part of a larger biomarker discovery workflow with RNA-seq and other data types. viSNE allows rapid exploratory data analysis that helps to build understanding of correlations between biomarkers and patient outcomes and improve overall time-to-results in biomarker discovery pipelines.Citation Format: Ashu Sethi, Hannah Polikowsky, Katherine A. Drake. viSNE in Cytobank enables rapid exploratory data analysis for RNA-seq biomarker discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2265.

01 Dec 2015·BMC BioinformaticsQ4 · BIOLOGY

NetworkPainter: dynamic intracellular pathway animation in Cytobank

Q4 · BIOLOGY

ArticleOA

Author: Chen, Edward Y ; Guturu, Harendra ; Irish, Jonathan M ; Karr, Jonathan R ; Kotecha, Nikesh ; Blair, Stuart L ; Covert, Markus W

BACKGROUNDHigh-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data.RESULTSWe developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point.CONCLUSIONNetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.

100 Deals associated with Cytobank, Inc.

100 Translational Medicine associated with Cytobank, Inc.

Corporation Tree

Boost your research with our corporation tree data.

view full example data

Pipeline

Pipeline Snapshot as of 20 May 2025

No data posted

Deal

Boost your decision using our deal data.

view full example data

Translational Medicine

Boost your research with our translational medicine data.

view full example data

Profit

Explore the financial positions of over 360K organizations with Synapse.

view full example data

Grant & Funding(NIH)

Access more than 2 million grant and funding information to elevate your research journey.

view full example data

Investment

Gain insights on the latest company investments from start-ups to established corporations.

view full example data

Financing

Unearth financing trends to validate and advance investment opportunities.

view full example data

AI Agents Built for Biopharma Breakthroughs

Accelerate discovery. Empower decisions. Transform outcomes.

Get started for free today!

Accelerate Strategic R&D decision making with Synapse, PatSnap’s AI-powered Connected Innovation Intelligence Platform Built for Life Sciences Professionals.

Start your data trial now!

Synapse data is also accessible to external entities via APIs or data packages. Empower better decisions with the latest in pharmaceutical intelligence.

Bio

Bio Sequences Search & Analysis

Chemical

Chemical Structures Search & Analysis

Cytobank, Inc.

Overview

Related

Corporation Tree

Pipeline

Pipeline Snapshot as of 20 May 2025

Deal

Translational Medicine

Profit

Grant & Funding(NIH)

Investment

Financing