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https://portals.broadinstitute.org/cmap/
Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Connectivity Map 02 (RRID:SCR_015674) Copy
http://www.broadinstitute.org/gsea/
Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy
http://www.broad.mit.edu/cancer/software/genecluster2/gc2.html
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A software package for analyzing gene expression and other bioarray data, giving users a variety of methods to build and evaluate class predictors, visualize marker lists, cluster data and validate results. GeneCluster 2.0 greatly expands the data analysis capabilities of GeneCluster 1.0 by adding supervised classification, gene selection, class discovery and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbor (KNN) algorithms, a module for systematically finding and evaluating clustering via self-organizing maps, and modules for marker gene selection and heat map visualization that allow users to view and sort samples and genes by many criteria. It enhances the clustering capabilities of GeneCluster 1.0 by adding a module for batch SOM clustering, and also includes a marker gene finder based on a KNN analysis and a visualization module. GeneCluster 2.0 is a stand-alone Java application and runs on any platform that supports the Java Runtime Environment version 1.3.1 or greater.
Proper citation: GeneCluster 2: An Advanced Toolset for Bioarray Analysis (RRID:SCR_008446) Copy
Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines.
Proper citation: CMap (RRID:SCR_016204) Copy
http://software.broadinstitute.org/gsea/msigdb/index.jsp
Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.
Proper citation: Molecular Signatures Database (RRID:SCR_016863) Copy
http://www.broad.mit.edu/mpr/lung
Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.
Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy
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