Recent advances in sequencing technology have led to a tremendous surge in generation genomics and transcriptomics data. The Cancer Genome Atlas (TCGA) consortium has utilized such modern technologies to sequence samples from thousands of cancer patients, with a wide variety of cancers.
Big data analysis from the project has led to the comprehensive molecular characterization of multiple cancer types and identification of potential biomarkers. Such high volume of data present an excellent opportunity for cancer researchers and clinicians to raise questions associated with tumor heterogeneity, racial disparity and to unearth novel cancer subtype specific markers. Systematic cancer data exploration by cancer researchers and clinicians requires analysis platforms with user-friendly features.
While there are computational tools available to aid researchers in carrying out specific TCGA data analyses, there is a need for a resource to facilitate the analysis of gene expression and survival profiles for tumor subgroups and for molecular subtypes of cancers.
In order to address this issue, a group at the UAB Department of Pathology led by Sooryanarayana Varambally, Ph.D., Associate Professor, Molecular and Cellular Pathology and Director, Translational Oncologic Pathology Research, and the UAB Comprehensive Cancer Center developed the University of Alabama Cancer Database, or UALCAN, an easy to use, interactive web-portal to perform to in-depth analyses of TCGA gene expression data.
UALCAN uses TCGA RNA-sequencing and patients' clinical data from 33 different cancer types, including several metastatic tumors. The web-based platform's user-friendly features facilitate:
1) relative expression analysis of a query gene(s) across tumor and normal samples, as well as in various tumor sub-groups based on individual cancer stages, tumor grade, race, body weight or other clinico-pathologic features
2) understanding the combined impact of gene expression level and clinico-pathologic features on patient survival
3) identification of the top over- and under-expressed genes in individual cancer types
This resource aids in in silico validation of target genes and for identifying tumor sub-group specific candidate biomarkers.
UALCAN allows users to export results of gene expression and survival analysis as publication-ready graphical images in png, jpeg, and PDF formats. The precompiled list of the top 250 over-/under-expressed genes for major cancers (with large sample size) as well as popular cancer subtypes (e.g. triple negative breast cancer [TNBC], prostate tumors with ETS-fusion) is provided via heatmap feature. This serves as a ready-to-use list of potential markers for further exploration.
Using UALCAN, it is possible to explore/validate the pan cancer expression pattern of hundreds of use-defined gene via “Scan by gene classes” option. UALCAN serves as a one-stop-shop by providing easy access to external resources such as GeneCards, Human Protein Reference Database (HPRD) (to explore relevant protein interactions), PubMed, TargetScan (to find predicted microRNA that potentially regulate the gene of interest) and Human Protein Atlas (to investigate protein expression in various cancers).
Since its release to the public in 2017, UALCAN has been visited over 50,000 times all across the world and is being highly cited. We believe that UALCAN will be extremely helpful in accelerating cancer biomarker and therapeutic target identification. We will add new functionality to UALCAN including non-coding RNA and microRNA expression analyses in the future.
This work was supported by UAB Pathology, the UAB Comprehensive Cancer Center, UAB Heersink School of Medicine and the Breast Cancer Research Foundation of Alabama (BCRFA).
Others contributors to this project include: Darshan Chandrashekar, Ph.D., Bioinformatics; Bhuwan Bashel, software engineer, Planet Fundraiser; Sai Akashaya Hodigere Balasubramanya; Israel Ponce-Rodriguez, IT Manager, UAB; Balabhadrapatruni Chakravarthi, Ph.D., UAB; and Chad Creighton, Ph.D., Baylor College of Medicine.
UALCAN is publicly available at: http://ualcan.path.uab.edu.
An article in the journal Neoplasia describing this web portal is here: https://www.ncbi.nlm.nih.gov/pubmed/28732212
UALCAN has been featured in RNA-Seq blog site: http://www.rna-seqblog.com/tag/ualcan/
Congratulations to our Chairman, George Netto, M.D., on receiving the third UAB School of Medicine Featured Discovery award. This initiative celebrates the important research from UAB School of Medicine faculty members, in particular those published in prominent scientific journals.
Netto, an internationally recognized clinician-scientist, was selected for his study titled, “Non-invasive detection of urothelial cancer through the analysis of driver gene mutation and aneuploidy” (eLife, 2018; 7:e32143). Dr. Netto conducted research that found a new test for urothelial cancers, which is less invasive and more accurate.
From the announcement by Selwyn Vickers, M.D., FACS, Senior Vice President for Medicine and Dean, UAB School of Medicine:
On Friday, June 6, several of our Department's faculty were awarded by the UAB Health Services Foundation for their decades of clinical service at the Physician Service Awards event.
Presented by Tony Jones, M.D., COO, Chief Physician Executive; Patricia Pritchett, Executive Vice President; and Billy Connelley, Senior Associate Vice President of Ambulatory Services and held at the Kirklin Clinic, the event had a lighthearted tone as each award recipient was introduced with a witty description of their career at UAB.
The Department's awardees are as follows:
Pat Bucy, M.D., Ph.D., Professor, Laboratory Medicine--celebrating 30 years
It was a lovely evening for a reception on Thursday, May 24, at the Renaissance Birmingham Ross Bridge Golf Resort & Spa as the Department celebrated its outgoing residents and fellows with a dinner and awards at the 2018 Outgoing Reception.
Host James Hackney, M.D., Director of the Pathology Residency Programs, emceed the event which included refreshments and dinner, followed by comments from Chair George Netto, M.D., and the presentation of awards.
George Netto, M.D., Chair of the Department of Pathology, welcomes guests at the Residents and Fellows Outgoing Reception
Two faculty awards came first. Alexander Feldman, M.D., Chief Resident in Anatomic Pathology, presented Frida Rosenblum, M.D., Assistant Professor in Cytopathology, with the Leonard H. Robinson Award for Resident Education in Anatomic Pathology.
Joseph Drwiega, M.D., Clinical Pathology Chief Resident, presented Lawrence Williams, M.D., Associate Professor, Laboratory Medicine with the Shu T. Huang Award for Excellence in Laboratory Medicine Education. These were followed by the presentation of resident awards.
- Research Progresses in Rare Disease TTP as Pathology Hosts Third Annual Fair June 9
- Inaugural Pilot Awards Given Supporting Translational and Clinical Research
- Büttner Delivers Lecture on Integrating Molecular Pathology and Clinical Oncology into Practice
- Pathology Faculty Marques and Wende are 2018 Dean's Excellence Award Winners
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