1. Input format

• Input can be multiple genes or pathways;
• Input Terms should be delimited by comma (e.g. 850295, 850334, 850338);
• Two types of identifiers are allowed for gene input: Entrez ID or official gene symbol; any other IDs have to be converted into Entrez ID or official gene symbol; DAVID ID conversion tool is suggested;
• Gene lists or pathway names can be uploaded as query input.

2. Output format

• Table output is organized according to output selection and popped up in a new window;
• Output in Cytoscape format can be imported and opened in Cytoscape software to display the interaction data in a graph;
• Both table and Cytoscape output can be downloaded as .txt files.

3. Terminology

• Candidate genes are the discovered new genes from OntoFing network that may have functional relevance to the query genes set or pathways based on the network connectivity
• Pathway name filtering refers to excluding the candidate genes whose linked PubMed abstracts containing the query pathway name, resulting in novel candidate genes with no publications linking the gene and the query pathway.

  Please contact us for further questions:
        W. Jim Zheng, Ph.D.
        Associate Professor
        Center for Computational Biomedicine
        School of Biomedical Informatics
        University of Texas Health Science Center at Houston
        7000 Fannin St. Suite 600
        Houston, TX 77030
        Phone: (713) 500-3641
        email: wenjin.j.zheng@uth.tmc.edu