Research article
Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
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* Corresponding author: Richard H Scheuermann scheuerm@utsw.swmed.edu
- † Equal contributors
1 Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
2 Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
3 San Diego Supercomputer Center, University of California, San Diego, California 92122, USA
4 Department of Bioengineering, University of California, San Diego, California 92122, USA
5 Division of Biology, California Institute of Technology, Pasadena, CA, USA
BMC Bioinformatics 2006, 7:237 doi:10.1186/1471-2105-7-237
Published: 2 May 2006Additional files
Additional File 1:
CLASSIFI input file. The CLASSIFI input file was generated following microarray data clustering. It lists probe IDs, Gene names, and Cluster IDs resulting from categorical clustering of processed data from B cells stimulated with anti-CD40, LPS, and AIG. This input file was uploaded at the CLASSIFI website [28], which provides a web interface for the use of CLASSIFI.
Format: XLS Size: 282KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 2:
CLASSIFI output file. Complete output file resulting from CLASSIFI analysis of the data set. Clusterid = gene clusters resulting from categorical clustering of processed data from B cells stimulated with anti-CD40, LPS, and AIG. GO id = a unique Gene Ontology identifier that corresponds to a GO term, which is used to describe gene products based on molecular function, biological process, or cellular component. g = number of probes in the data set, f = number of probes with associated GO id in the data set, c = number of probes in the gene cluster, n = number of probes with associated GO id in the gene cluster. Expt = the expected number of occurrences of a given GO id in a given cluster of size (n) based on a random distribution. Prob = the probability that the GO id co-cluster pattern has occurred by chance.
Format: XLS Size: 802KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional File 3:
CLASSIFI GO file. Complete list of all GO ids (representing the entire GO ancestry) associated with each probe ID.
Format: XLS Size: 478KB Download file
This file can be viewed with: Microsoft Excel Viewer