Virulence
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Tyrosine
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Tumor Suppressor Proteins
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Tumor Markers, Biological
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Tumor Cells, Cultured
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Transcription, Genetic
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Transcription Factors
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Trans-Activators
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Tissue Distribution
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Thymus Gland
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
T-Lymphocytes
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Survival Rate
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Staphylococcus aureus
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Signal Transduction
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Sequence Analysis, DNA
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
RNA, Messenger
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
RNA
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Receptors, IgE
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Receptors, Estrogen
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Receptors, Antigen, T-Cell
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Rats
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Pyrimidines
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Proto-Oncogene Proteins c-abl
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Proteins
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Protein Transport
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Protein Sorting Signals
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Protein Kinase C
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Piperazines
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Phosphorylation
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Phosphoproteins
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Paired Box Transcription Factors
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Ovarian Neoplasms
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
Oligonucleotide Array Sequence Analysis
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Nuclear Proteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
NFATC Transcription Factors
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Neoplasm Proteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Mutation
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Multigene Family
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Molecular Sequence Data
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Models, Biological
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Mice
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Membrane Glycoproteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Mast Cells
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
MAP Kinase Signaling System
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Lymphoma, Large B-Cell, Diffuse
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Lymphoma, Follicular
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Lymphocyte Activation
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Lipopolysaccharides
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Ligands
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Leukocytes, Mononuclear
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Jurkat Cells
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Interleukin-4
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Interleukin-11
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Information Storage and Retrieval
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
In Vitro Techniques
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Immunoprecipitation
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Immunohistochemistry
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Immunoglobulin E
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Immunity
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Humans
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Homeodomain Proteins
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Histamine Release
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
GPI-Linked Proteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Glioblastoma
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Genomics
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Genome, Human
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Genome
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Genes, myc
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Gene Expression Regulation, Neoplastic
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Gene Expression Regulation
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Gene Expression Profiling
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Gene Expression
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
GATA3 Transcription Factor
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Flow Cytometry
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Female
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Extracellular Signal-Regulated MAP Kinases
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Escherichia coli
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Ephrin-B1
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Enzyme-Linked Immunosorbent Assay
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Enzyme Activation
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Dose-Response Relationship, Immunologic
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
DNA-Binding Proteins
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
DNA, Complementary
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
DNA Topoisomerases, Type II
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
DNA Primers
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Databases, Genetic
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Cytosol
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Computational Biology
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Cluster Analysis
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Chromosome Mapping
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Cells, Cultured
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Cell Separation
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Cell Proliferation
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Cell Nucleus
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Cell Movement
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Cell Membrane
M. Diehn, Bhattacharya, R., Botstein, D., and Brown, P. O.,
“Genome-scale identification of membrane-associated human mRNAs.”,
PLoS Genet, vol. 2, no. 1, p. e11, 2006.
Cell Line
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Cation Transport Proteins
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Carrier Proteins
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Carcinoma, Papillary
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Breast Neoplasms
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Brain Neoplasms
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Bordetella pertussis
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Blotting, Western
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Blotting, Northern
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Benzamides
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Base Sequence
I. S. Lossos, Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., and Levy, R.,
“Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.”,
Proc Natl Acad Sci U S A, vol. 99, no. 13, pp. 8886-91, 2002.
Bacterial Toxins
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
Bacteria
J. C. Boldrick, Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. Long, Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., and Relman, D. A.,
“Stereotyped and specific gene expression programs in human innate immune responses to bacteria.”,
Proc Natl Acad Sci U S A, vol. 99, no. 2, pp. 972-7, 2002.
B-Lymphocytes
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
Antigens, Neoplasm
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Antigens, CD28
M. Diehn, Alizadeh, A. A., Rando, O. J., Liu, C. Long, Stankunas, K., Botstein, D., Crabtree, G. R., and Brown, P. O.,
“Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation.”,
Proc Natl Acad Sci U S A, vol. 99, no. 18, pp. 11796-801, 2002.
Antibodies, Anti-Idiotypic
K. Sayama, Diehn, M., Matsuda, K., Lunderius, C., Tsai, M., Tam, S. - Y., Botstein, D., Brown, P. O., and Galli, S. J.,
“Transcriptional response of human mast cells stimulated via the Fc(epsilon)RI and identification of mast cells as a source of IL-11.”,
BMC Immunol, vol. 3, p. 5, 2002.
Anoxia
Y. Liang, Diehn, M., Watson, N., Bollen, A. W., Aldape, K. D., M Nicholas, K., Lamborn, K. R., Berger, M. S., Botstein, D., Brown, P. O., and Israel, M. A.,
“Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme.”,
Proc Natl Acad Sci U S A, vol. 102, no. 16, pp. 5814-9, 2005.
Animals
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
I. - P. Tu, Schaner, M., Diehn, M., Sikic, B. I., Brown, P. O., Botstein, D., and Fero, M. J.,
“A method for detecting and correcting feature misidentification on expression microarrays.”,
BMC Genomics, vol. 5, p. 64, 2004.
M. Diehn, Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., J Cherry, M., Botstein, D., Brown, P. O., and Alizadeh, A. A.,
“SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.”,
Nucleic Acids Res, vol. 31, no. 1, pp. 219-23, 2003.
Adenocarcinoma, Clear Cell
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Adenocarcinoma
M. E. Schaner, Ross, D. T., Ciaravino, G., Sorlie, T., Troyanskaya, O., Diehn, M., Wang, Y. C., Duran, G. E., Sikic, T. L., Caldeira, S., Skomedal, H., Tu, I. - P., Hernandez-Boussard, T., Johnson, S. W., O'Dwyer, P. J., Fero, M. J., Kristensen, G. B., Borresen-Dale, A. - L., Hastie, T., Tibshirani, R., van de Rijn, M., Teng, N. N., Longacre, T. A., Botstein, D., Brown, P. O., and Sikic, B. I.,
“Gene expression patterns in ovarian carcinomas.”,
Mol Biol Cell, vol. 14, no. 11, pp. 4376-86, 2003.
Adaptor Proteins, Signal Transducing
J. P. Roose, Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., and Weiss, A.,
“T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression.”,
PLoS Biol, vol. 1, no. 2, p. E53, 2003.
