D3.js - Data-Driven Documents. Network2Canvas. Enrichr. Tutorial Step 1. Uploading a list Enrichr uses a list of Entrez gene symbols as input. Each symbol in the input must be on its own line. You can upload the list by either selecting the text file that contains the list or just simply pasting in the list into the text box. It is recommended to enter a description for your list so that multiple lists can be differentiated from each other if you choose to save or share your list. If you are using a touch device, you can swipe left or right to navigate between the different tabs at the top.
Step 2. On the results page, the analysis is divided into different categories of enrichment; in the example, the transcription category is shown. You can open a particular analysis by tapping on the name of the gene-set library, presenting a multitude of visualizations. Step 3. The first visualization is the bar graph. X2K: Expression2Kinases.
Hepatic fibrosis is a scarring response to liver damage often due to chronic liver disease.
In fibrogenesis, hepatic stellate cells (HSCs) activate and transdifferentiate into ECM-producing myofibroblasts. To better understand the gene expression changes that occur during such a process, De Minicis et al.[1] conducted a microarray study to examine differences in gene expression profiles between cultured and in vivo activated HSCs. Using the study as a source of microarray data for X2K, we attempted to identify the upstream transcription factors, intermediate proteins, and protein kinases that may potentially regulate the fibrosis response in HSCs. The differentially expressed genes found from the microarray study were split into two groups of up-regulated and down-regulated genes and sorted based on their fold change. We set the cut-off for up-regulated genes to have at least a fold change of 2 or greater, and for down-regulated genes to have at least a fold change of 0.7 or lower.
Mount Sinai - Iyengar Laboratory - Department of Pharmacology and Systems Therapeutics. Large Network Visualization Tool. Flash Network Viewer. Download: FNV_1.0.zip The download contains the FNV.swf file, a source code package for embedding, the viewer in a PDF document, documentation, and sample network XML files.
Make sure that you extract all the files from the zipped archive before attempting to run FNV. Paper If you use FNV we ask that you cite our article published in Oxford Bioinformatics. Dannenfelser, Ruth et al. “FNV: Light-weight Flash-based network and pathway viewer.” Abstract Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses, and drugs.
About FNV was designed and implemented in Avi Ma'ayan's laboratory at the Mount Sinai School of Medicine in New York. Documentation A user manual and additional sample files can be found on the documentation page. Flash Network Viewer. Graphviz - Graph Visualization Software. Pajek [Pajek Wiki] The Gene Ontology. Lists2Networks-Ma'ayan Lab-MSSM. DAVID Functional Annotation Bioinformatics Microarray Analysis.
FANMOD: a tool for fast network motif detection. Introduction From this page you can download a tool to detect network motifs as described in S.
Wernicke and F. Rasche. FANMOD: a tool for fast network motif detection. S. And is much faster than any other available motif detection tool, especially for larger motifs of size >4. License You may use FANMOD for all of your research purposes as long as you do the following: You acknowledge its use in any published work that fully or in part derives its results from its usage.
Absolutely no guarantees or warranties are made concerning the suitability, correctness, or any other aspect of the distributed files. Downloads Last updated on December 23rd, 2006. Some testdata is available from the webpage of Uri Alon at the Weizmann Institute here. Source We had some people experience problems with the Linux version of FANMOD because different distributions contain different libraries.
By downloading the source of FANMOD, you agree to use it for the sole purpose of compiling it on your machine. NetEvo - Tools for Complex Dynamical Network Evolution. Sets2Networks. Genes2FANs. Citation and Further Information Quick Start Instructions (More detailed instructions can be found on the instructions/about page.)
This program draws from one or more selected background networks. It will take a list of genes you provide as seed genes and identify all interacting genes that fall on paths through the background network(s) between them. STRING: functional protein association networks. Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization. Genes2Networks. A command-line version of this program is available at: This program draws from a large background network consisting of several protein interaction datasets.
It will take a list of genes you provide as seed genes and identify all interacting genes that fall on paths through the background network between them. Instructions 1. Specify your gene list. This is a list of primary human entrez gene symbols which will be used to find interacting nodes. If you use Genes2Networks, please cite: Berger SI, Posner JM, Ma'ayan A.