Documents

GeneLinker Online Help

In keeping with our philosophy of providing customers--current and prospective--with as much information as possible about out products, we have made the full GeneLinker Online Help Documents available. A PDF version of the GeneLinker Gold 3.1/GeneLinker Platinum 2.1 documentation is also available.

Protein Biomarker/Proteomics Examples

The GeneLinker products are well suited for Protein Biomarker data. The protein biomarker dataset used in Protein Biomarker Discovery with GeneLinker Platinum is the NIH/NCI Center for Cancer Research Ovarian dataset 8-7-02.

An earlier Proteomics Data Analysis Example is also available.

Selected Citations

Below is a selection of book chapters, refereed publications and posters that feature the GeneLinker products.

The following published book chapter includes analysis using GeneLinker and nine images exported from GeneLinker:

• Modularity in Development and Evolution. Chapter 10: Systematic Exploration and Mining of Gene Expression Data Provides Evidence for Higher-Order, Modular Regulation. University of Chicago Press. Gerhard Schlosser and Gunter P. Wagner, editors. Roland Somogyi, Stefanie Fuhrman, Gary Anderson, Chris Madill, Larry D. Greller, and Bernard Chang.

GeneLinker Online Colour Figures from Chapter 10

Copyright 2004 by The University of Chicago. All Rights Reserved.

The following papers include images and results produced by GeneLinker:

• Chang B, Somogyi R, Fuhrman S Evidence for Shared Genetic Programs from Cluster Analysis of Hippocampal Gene Expression Dynamics in Development and Response to Injury. Restor Neurol Neurosci. 2001;18(2-3):115-25.
• Kotlyar M, Fuhrman S, Ableson A, Somogyi R (2002) Spearman correlation identifies statistically significant gene expression clusters in spinal cord development and injury. Neurochem Res 27(10):1129–1136
• Somogyi R, McMichael J, Baranzini S, Mousavi P, Greller L (2004 in press) Advanced data mining and predictive modeling at the core of personalized medicine, in R. Paton, ed., Multidisciplinary Approaches to Theory in Medicine
• Masami Yokota Hirai, Mitsuru Yano, Dayan B. Goodenowe, Shigehiko Kanaya, Tomoko Kimura, Motoko Awazuhara, Masanori Arita, Toru Fujiwara and Kazuki Saito Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana PNAS July 6, 2004 Vol. 101 no. 27 10205-10210.
• Bernhard Juurlink. The Beginning of the Nutri-Geno-Proteo-Metabolo-mics Era of Nutritional Studies PBI Bulletin, 2003 Issue 1.
• Sergio E. Baranzini, Parvin Mousavi, Jordi Rio, Stacy J. Caillier, Althea Stillman, Pablo Villoslada, Matthew M. Wyatt, Manuel Comabella, Larry D. Greller, Roland Somogyi, Xavier Montalban, Jorge R. Oksenberg. Transcription-Based Prediction of Response to IFNß [interferon beta] Using Supervised Computational Methods, PLoS Bioloogy, Volume 3, Issue 1, January 2005.

The following poster from Amersham Biosciences illustrates the use of GeneLinker(TM) Gold's Matrix Plots:

• LaFramboise WA, Bombach KL, George JD, Cullen RF, Pogozelski AR, Guthrie RD, Magovern JA Expression Profiling of the Compensatory Response to Myocardial Infarct

Additional References for Proprietary Algorithms

SLAM is protected by an extensive patent portfolio (including U.S. Patent No. 6,493,637) covering the original Coincidence method and several applications. U.S., Canadian and International patent applications on IBIS are currently pending.

• Steeg, E.W, Robinson, D.A. and Willis, E., “Coincidence Detection: A Fast Method for Discovering Higher-Order Correlations in Multidimensional Data”, Proceedings of KDD '98, New York, August 1998.
• Steeg, E.W. and Pham, H., “Application of a Novel and Fast Information-Theoretic Method to the Discovery of Higher-Order Correlations in Protein Databases”, Proceedings of the Pacific Symposium on Biocomputing, PSB ‘98, Hawaii, 1998.
• Roland Somogyi, Alan Ableson, Larry D. Greller. Exploration, Inference, Prediction: A Step-Wise Approach to Gene Networks for Understanding Drug Action, Invited workshop, IBC In Silico Technologies Drug Discovery conference, 21 May 2001.

Publication Submission

Please email us any publications that feature the GeneLinker products. We love to see the different ways that the product is being used and hear about how our products are being used.

New Citations

If you are going to include results or visualizations produced by GeneLinker in a paper or poster, please mention the product that was used to produce them.

• Improved Outcomes' GeneLinker(TM) Gold 4.6 was used to produce the hierarchical clustering results.

• Authors: Mark Chatterley and Tom Radcliffe
• Year Published: 2005
• Title: GeneLinker Gold (or Platinum)
• Version: 4.6
• Place Published: Kingston, ON, Canada
• Publisher: Improved Outcomes Software Inc.