BioPax is collaborative effort to create a data exchange format for biological pathway data. BioPax is an open source project.
The candidate gene list for the sarcoma sequencing effort was compiled from a variety of curated lists, cancer and sarcoma reviews, and Entrez Gene queries, followed by a additional curation (in progress). The resulting gene list includes the gene symbol, gene name, description, chromosome, location, Entrez GeneID, Entrez HyperLink, COSMIC Hyperlink, gene ontology (GO) terms, InterPro Descriptions, and data source.
The Cancer Cell Map contains selected cancer related signaling pathways which you can browse or search.
The Cancer Cell Map was created by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center and the Institute of Bioinformatics. Powered by the cPath pathway database software.
The Clinical Tissue Microarray Database combines and annotates scanned tissue microarray images currently generated in the Department of Surgical Pathology's tissue microarray unit. Tissue microarrays (TMAs) are microscopic slides upon which sections of hundreds of small tissue cores (from many different tissue sources) have been reproducibly gridded. These slides may be stained using a variety of chemical and immunohistochemical (antibody) stains. TMAs are typically used to screen hundreds of tissue samples with a single antibody. These data sets will be retrospectively and prospectively annotated with clinical data. ClinTMA is a resource from which these TMA data can be shared, searched, retrieved and analyzed for research purposes. It is operated by the Bioinformatics Core.
Objectives:
- Combine TMA data.
- Consistently and prospectively annotate genomic datasets with biological, clinical and outcome information.
- Implement a system to effectively and efficiently share, search, retrieve and analyze TMA data for research purposes.
cPath aims to be a freely available cancer pathway database. Currently, only information about protein-protein interactions collected from major interaction databases that support the PSI-MI format is available. cPath is open-source and is easy to locally install for private management of protein-protein interactions. Future directions include support for the BioPAX format so that entire pathways can be stored, queried and presented.
Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.
This plug-in loads an expression data file (consult the Cytoscape manual to learn about the format of this type of file) and then allows the user to color the nodes in a network according to their expression values. The GUI works like a VCR, with play, pause, and stop buttons. If the user presses the play button, the plug-in will iterate over all the conditions in the expression file and color the nodes according to their corresponding expression values.
Released by: Iliana Avila-Campillo, Galitski Group, Institute for Systems Biology.
This plugin enables Cytoscape to import data formatted in the GEO Simple Omnibus Format in Text (SOFT). SOFT is a text file format used to represent and exchange Gene Expression Data.
For an earlier version of this Plugin, which works in Cytoscape 1.1, refer to the Data Services Plugin on the Cytoscape 1.1 Plugins page.
Released by: Sander Group, Computational Biology Center, Memorial Sloan-Kettering Cancer Center.
The Database & Reagent Registry is an online system for registering and searching for databases and reagent collections owned by investigators, services, or departments. In other words, it is an institutional "yellow pages" that may be used to locate databases as well as biological and chemical reagents that have been collected throughout MSKCC. It is hoped that this registry will ultimately facilitate and stimulate interdisciplinary collaboration among MSKCC's basic and clinical researchers.
Within the registry, databases and reagent collections may be described as clinical database, cell line collection, small molecule library, slide presentation, supplementary website or tissue/sample bank.
GeneQuiz is a tool that, given a DNA or protein sequence from a known or unknown gene, runs numerous queries and calculations in batch and then integrates the alternate transcript, sequence comparison, function and structure predictions into a single report.
A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. We report the development of an information system that provides this network as a natural way of accessing the more than ten million abstracts in PubMed. By employing genes and proteins as hyperlinks between sentences and abstracts, we convert the information in PubMed into one navigable resource and bring all the advantages of the internet to scientific literature investigation. Moreover, this literature network can be superimposed upon experimental interaction data (e.g. yeast-two hybrid data from Drosophila and C.elegans) to make possible a simultaneous analysis of novel and existing knowledge. The network presented in iHOP contains half a million sentences and 30000 different genes from human, mouse, Drosophila, C. elegans, zebrafish, Arabidopsis, yeast and E. coli.
miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander ( 
).
Although hundreds of miRNAs have been discovered, the functions of these miRNAs are not known. This viewer allows access to the predicted protein coding gene targets. Searching by miRNA will display a ranked list of gene targets and allow you to analyze each conserved target gene/sites in detail. Similarly, searching by gene name/identifier will display the sequence of the three prime UTR and the positions of the miRNA sites along the sequence, allowing you to analyze the target sites in detail.
Pathguide contains information about hundreds of internet pathway resources.
Pathlite is a de-identified query portal for diagnostic records for the paraffin-embedded, formalin-fixed tissue archive of the Department of Pathology. It is accessible by MSK personnel and is intended to assist investigators in the development of clinical and basic research studies by providing information about the extent of this tissue archive.
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes.
ProteinKeys is a tool that, given a protein family multiple sequence alignment and optional protein structure, predicts functional residues in a protein based on entropy analysis. ProteinKeys includes a multiple alignment and an integrated 3D protein structure viewer (JMol).
In order to support multi-institutional studies the Bioinformatics Core is developing a multi-institution, human subject accrual system called "Study Tracker". The Study Tracker will allow the PI of the Administrative Core to track subject accruals to individual study arms, and will be designed to address the following use cases:
- How many patients have been accrued to the individual arms, and which arms need additional accruals?
- How many patients have responded to therapy?
- How many patients have had adverse events?
- Which patients need additional data?
