scholarly journals ProCanBio: a database of manually curated biomarkers for Prostate Cancer

2021 ◽  
Author(s):  
Dikscha Sapra ◽  
Harpreet Kaur ◽  
Anjali Dhall ◽  
Gajendra P.S. Raghava
Keyword(s):  
Prostate Cancer ◽  
Cancer Biomarkers ◽  
Research Community ◽  
Web Browsers ◽  
Detailed Data ◽  
Research Groups ◽  
Web Based ◽  
The Past ◽  
Diagnosis And Prognosis ◽  
User Friendly

Background: Prostate Cancer is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of prostate cancer. However, information related to the biomarkers is widely scattered across numerous resources in complex textual format, which poses hindrance to understand the tumorigenesis of this malignancy and scrutinization of robust signature. To the best of authors knowledge, there is no resource that can consolidate the information contained in all the published literature. Results: Here, we present ProCanBio, a manually curated database that maintains detailed data on 2053 entries of potential prostate cancer biomarkers obtained from 412 publications in user friendly tabular format. Among them, 766 protein-based, 488 RNA-based, 157 genomic mutations, 261 miRNA-based, and 122 are metabolites-based biomarkers. To explore the information in the resource, a web-based interactive platform was developed with searching, and browsing facilities. ProCanBio is freely available and is compatible with most web browsers and devices. Eventually, we anticipated this resource will be highly useful for the research community involved in the area of prostate malignancy.

scholarly journals Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform

2021 ◽  
Vol 6 ◽  
Author(s):  
Ellen G. Dow ◽  
Elisha M. Wood-Charlson ◽  
Steven J. Biller ◽  
Timothy Paustian ◽  
Aaron Schirmer ◽  
...  
Keyword(s):  
Energy Systems ◽  
Department Of Energy ◽  
Student Survey ◽  
Teaching Resources ◽  
Web Based ◽  
The Past ◽  
Instructional Units ◽  
Bioinformatics Education ◽  
User Friendly

Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.

Abstract 2391: Computation of a user-friendly composite score from three prostate cancer biomarkers

2021 ◽  
Author(s):  
Gargi Pal ◽  
Emmanuel Asante-Asamani ◽  
Leslie Liu ◽  
Olorunseun O. Ogunwobi
Keyword(s):  
Prostate Cancer ◽  
Cancer Biomarkers ◽  
Composite Score ◽  
User Friendly

Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS

2020 ◽  
Author(s):  
Zhixu Qiu ◽  
Siyuan Chen ◽  
Yuhong Qi ◽  
Chunni Liu ◽  
Jingjing Zhai ◽  
...  
Keyword(s):  
High Throughput ◽  
Stress Responses ◽  
Large Scale ◽  
Model Organisms ◽  
Rna Seq ◽  
Research Groups ◽  
Web Based ◽  
Rich Functionality ◽  
Transcriptional Switch ◽  
User Friendly

Abstract Transcriptional switch (TS) is a widely observed phenomenon caused by changes in the relative expression of transcripts from the same gene, in spatial, temporal or other dimensions. TS has been associated with human diseases, plant development and stress responses. Its investigation is often hampered by a lack of suitable tools allowing comprehensive and flexible TS analysis for high-throughput RNA sequencing (RNA-Seq) data. Here, we present deepTS, a user-friendly web-based implementation that enables a fully interactive, multifunctional identification, visualization and analysis of TS events for large-scale RNA-Seq datasets from pairwise, temporal and population experiments. deepTS offers rich functionality to streamline RNA-Seq-based TS analysis for both model and non-model organisms and for those with or without reference transcriptome. The presented case studies highlight the capabilities of deepTS and demonstrate its potential for the transcriptome-wide TS analysis of pairwise, temporal and population RNA-Seq data. We believe deepTS will help research groups, regardless of their informatics expertise, perform accessible, reproducible and collaborative TS analyses of large-scale RNA-Seq data.

scholarly journals Human Tissue Kallikreins: A Family of New Cancer Biomarkers

2002 ◽  
Vol 48 (8) ◽  
pp. 1198-1205 ◽  
Author(s):  
Eleftherios P Diamandis ◽  
George M Yousef
Keyword(s):  
Prostate Cancer ◽  
Steroid Hormone ◽  
Specific Antigen ◽  
Serum Biomarkers ◽  
Protein Levels ◽  
The Past ◽  
Diagnosis And Prognosis ◽  
Glandular Kallikrein ◽  
Protease Enzyme ◽  
Enzymatic Pathways

Abstract Kallikreins are a subgroup of the serine protease enzyme family. Until recently, it was thought that the human kallikrein gene family contained only three members. In the past 3 years, the entire human kallikrein gene locus was discovered and found to contain 15 kallikrein genes. Kallikreins are expressed in many tissues, including steroid hormone-producing or hormone-dependent tissues such as the prostate, breast, ovary, and testis. Most, if not all, kallikreins are regulated by steroid hormones in cancer cell lines. There is strong but circumstantial evidence linking kallikreins and cancer. Prostate-specific antigen (PSA; hK3) and, more recently, human glandular kallikrein (hK2) are widely used tumor markers for prostate cancer. Three other kallikreins, hK6, hK10, and hK11, are emerging new serum biomarkers for ovarian and prostate cancer diagnosis and prognosis. Several other kallikreins are differentially expressed at both the mRNA and protein levels in various endocrine-related malignancies, and they have prognostic value. The coexpression of many kallikreins in the same tissues (healthy and malignant) points to the possible involvement of kallikreins in cascade enzymatic pathways. In addition to their diagnostic/prognostic potential, kallikreins may also emerge as attractive targets for therapeutics.

scholarly journals PSA and Beyond: The Past, Present, and Future of Investigative Biomarkers for Prostate Cancer

2010 ◽  
Vol 10 ◽  
pp. 1919-1931 ◽  
Author(s):  
Jeffrey Tosoian ◽  
Stacy Loeb
Keyword(s):  
Prostate Cancer ◽  
Acid Phosphatase ◽  
Early Diagnosis ◽  
Prostate Cancer Screening ◽  
Specific Antigen ◽  
Cancer Biomarkers ◽  
Prostatic Acid Phosphatase ◽  
The Past ◽  
Free Psa ◽  
Life Threatening

The discovery of prostate-specific antigen (PSA) as a biomarker represented a major discovery in the early diagnosis and monitoring of prostate cancer. However, the use of PSA is limited by the lack of specificity and an inability to differentiate indolent from life-threatening disease reliably at the time of diagnosis. A multitude of studies have aimed to improve the performance of PSA as well as identify additional biomarkers. The purpose of this study is to review available data on prostate cancer biomarkers for prostate cancer screening and prognostication, including prostatic acid phosphatase, PSA, PSA derivatives (PSA density, free PSA, pro PSA, and PSA kinetics), PCA3, GSTP1, AMACR, and other newly emerging molecular and genetic markers.

scholarly journals PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Morad M. Mokhtar ◽  
Achraf El Allali ◽  
Mohamed-Elamir F. Hegazy ◽  
Mohamed A. M. Atia
Keyword(s):  
Web Based ◽  
Plant Genomes ◽  
The Past ◽  
Plant Trait ◽  
Pathway Gene ◽  
Efficient Gene ◽  
Visualization Tools ◽  
User Friendly ◽  
Specific Pathway ◽  
Radical Shift

AbstractOver the past decade, the problem of finding an efficient gene-targeting marker set or signature for plant trait characterization has remained challenging. Many databases focusing on pathway mining have been released with one major deficiency, as they lack to develop marker sets that target only genes controlling a specific pathway or certain biological process. Herein, we present the PlantPathMarks database (PPMdb) as a comprehensive, web-based, user-friendly, and interactive hub for pathway-based markers in plant genomes. Based on our newly developed pathway gene set mining approach, two novel pathway-based marker systems called pathway gene-targeted markers (PGTMs) and pathway microsatellite-targeted markers (PMTMs) were developed as a novel class of annotation-based markers. In the PPMdb database, 2,690,742 pathway-based markers reflecting 9,894 marker panels were developed across 82 plant genomes. The markers include 691,555 PGTMs and 1,999,187 PMTMs. Across these genomes, 165,378 enzyme-coding genes were mapped against 126 KEGG reference pathway maps. PPMdb is furnished with three interactive visualization tools (Map Browse, JBrowse and Species Comparison) to visualize, map, and compare the developed markers over their KEGG reference pathway maps. All the stored marker panels can be freely downloaded. PPMdb promises to create a radical shift in the paradigm of the area of molecular marker research. The use of PPMdb as a mega-tool represents an impediment for non-bioinformatician plant scientists and breeders. PPMdb is freely available at http://ppmdb.easyomics.org.

The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

2017 ◽  
Vol 1 (1) ◽  
pp. 44-49
Author(s):  
Nur Azizah ◽  
Dedeh Supriyanti ◽  
Siti Fairuz Aminah Mustapha ◽  
Holly Yang
Keyword(s):  
Financial Management ◽  
Accounting System ◽  
Bank Account ◽  
Web Based ◽  
Online System ◽  
Version 2.0 ◽  
User Friendly ◽  
The Impact ◽  
A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements.   Keywords:​Accounting Online System, Financial Management, Cash and Bank

Exercise Capacity in Chronic Heart Failure

2012 ◽  
Vol 9 (1) ◽  
pp. 57-60 ◽  
Author(s):  
Gina G Mentzer ◽  
Alex J Auseon
Keyword(s):  
Quality Of Life ◽  
Heart Failure ◽  
Exercise Training ◽  
Exercise Capacity ◽  
Positive Impact ◽  
Pharmacologic Therapy ◽  
The Past ◽  
Diagnosis And Prognosis ◽  
Future Therapy

Heart failure (HF) affects more than 5 million people and has an increasing incidence and cost burden. Patients note symptoms of dyspnea and fatigue that result in a decreased quality of life, which has not drastically improved over the past decades despite advances in therapies. The assessment of exercise capacity can provide information regarding patient diagnosis and prognosis, while doubling as a potential future therapy. clinically, there is acceptance that exercise is safe in hf and can have a positive impact on morbidity and quality of life, although evidence for improvement in mortality is still lacking. specific prescriptions for exercise training have not been developed because many variables and confounding factors have prevented research trials from demonstrating an ideal regimen. Physicians are becoming more aware of the indices and goals for hf patients in exercise testing and therapy to provide comprehensive cardiac care. it is further postulated that a combination of exercise training and pharmacologic therapy may eventually provide the most benefits to those suffering from hf.

Web-Based Peer and Self-Assessment System Design and Development for Elementary School Students

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Mehmet EMIN KORTAK
Keyword(s):  
Elementary School ◽  
Elementary School Students ◽  
Primary Schools ◽  
Peer Assessment ◽  
Assessment System ◽  
Assessment Process ◽  
School Students ◽  
Self Assessment ◽  
Web Based ◽  
User Friendly

This research aimed at designing and improving the web-based integrated peer and self- assessment. WesPASS (web-based peer-assessment system), developed in this research, allows students to assess their own or their peers’ performance and project assignments and to report about the result of these assessments so that they correct their assignments. This study employed design-based research. The participants included 102 fourth grade primary school students and their 4 teachers from 2 state and 2 private primary schools in Ankara, Kecioren (Turkey) who employed the system and were engaged in a questionnaire survey to assess its quality. The findings were analyzed through quantitative data analysis. The findings revealed that the system can be used by elementary school students for peer and self-assessment system. The participants stated that WesPASS is simple and user-friendly, and it accelerates the assessment process by employing information technology and allows to share opinions 

Sign in / Sign up

Export Citation Format

Share Document