Differential coexpression analysis using microarray data and its application to human cancer

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206 · see citing works

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

Sørlie, T., Perou, C., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M., van de Rijn, M., Jeffrey, S., et al. (2001) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.191367098 · Cited by 11,695 · see citing works

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling

Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., et al. (2000) · Nature · doi:10.1038/35000501 · Cited by 9,925 · see citing works

An automated method for finding molecular complexes in large protein interaction networks

Bader, G. D., & Hogue, C. W. V. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-2 · Cited by 6,112 · see citing works

Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses

Bhattacharjee, A., Richards, W. G., Staunton, J. E., Li, C., Monti, S., Vasa, P. P., Ladd, C., Beheshti, J., Bueno, R., Gillette, M. A., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191502998 · Cited by 2,580 · see citing works

Gene expression correlates of clinical prostate cancer behavior

Singh, D., Febbo, P. G., Ross, K. N., Jackson, D. G., Manola, J. B., Ladd, C., Tamayo, P., Renshaw, A. A., D'Amico, A. V., Richie, J. P., et al. (2002) · Cancer Cell · doi:10.1016/s1535-6108(02)00030-2 · Cited by 2,513 · see citing works

A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules

Stuart, J. M., Segal, E., Koller, D., & Kim, S. K. (2003) · Science · doi:10.1126/science.1087447 · Cited by 2,235 · see citing works

Multiclass cancer diagnosis using tumor gene expression signatures

Ramaswamy, S., Tamayo, P., Rifkin, R. M., Mukherjee, S., Yeang, C., Angelo, M., Ladd, C., Reich, M. M., Latulippe, É., Mesirov, J. P., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.211566398 · Cited by 2,029 · see citing works

Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression

Rhodes, D. R., Yu, J., Sundaram, S. K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T. R., Pandey, A., & Chinnaiyan, A. M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401994101 · Cited by 1,010 · see citing works

Gene Expression Patterns in Human Liver Cancers

Chen, X., Cheung, S., So, S. K., Fan, S. T., Barry, C. T., Higgins, J., Lai, K.-M., Ji, J., Dudoit, S., Ng, I. O., et al. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.02-02-0023 · Cited by 879 · see citing works

Energy Substrate Modulates Mitochondrial Structure and Oxidative Capacity in Cancer Cells

Rossignol, R., Gilkerson, R., Aggeler, R., Yamagata, K., Remington, S., & Capaldi, R. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-1101 · Cited by 865 · see citing works

Dynamic imaging of collagen and its modulation in tumors in vivo using second-harmonic generation

Brown, E. B., McKee, T. D., DiTomaso, E., Pluen, A., Seed, B., Boucher, Y., & Jain, R. K. (2003) · Nature Medicine · doi:10.1038/nm879 · Cited by 836 · see citing works

Coexpression Analysis of Human Genes Across Many Microarray Data Sets

Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J., & Pavlidis, P. (2004) · Genome Research · doi:10.1101/gr.1910904 · Cited by 770 · see citing works

A module map showing conditional activity of expression modules in cancer

Segal, E., Friedman, N., Koller, D., & Regev, A. (2004) · Nature Genetics · doi:10.1038/ng1434 · Cited by 685 · see citing works

Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays.

Notterman, D. A., Alon, U., Sierk, A. J., & Levine, A. J. (2001) · PubMed · Cited by 602 · see citing works

Exploration of Global Gene Expression Patterns in Pancreatic Adenocarcinoma Using cDNA Microarrays

Iacobuzio–Donahue, C. A., Maitra, A., Olsen, M. N., Lowe, A. W., van Heek, N. T., Rosty, C., Kim, W., Sato, N., Parker, A. R., Ashfaq, R., et al. (2003) · American Journal Of Pathology · doi:10.1016/s0002-9440(10)63911-9 · Cited by 471 · see citing works

Combining multiple microarray studies and modeling interstudy variation

Choi, J. K., Yu, U.-S., Kim, S. S., & Yoo, O. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg1010 · Cited by 415 · see citing works

Similarities and Differences in Genome-Wide Expression Data of Six Organisms

Bergmann, S., Ihmels, J., & Barkai, N. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0020009 · Cited by 348 · see citing works

Variation in Gene Expression Patterns in Human Gastric Cancers

Chen, X., Leung, S. Y., Yuen, S. T., et al. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-12-0833 · Cited by 321 · see citing works

Autonomous regulation of the anaphase-promoting complex couples mitosis to S-phase entry

Rapé, M., & Kirschner, M. W. (2004) · Nature · doi:10.1038/nature03023 · Cited by 302 · see citing works

The yeast coexpression network has a small‐world, scale‐free architecture and can be explained by a simple model

van Noort, V., Snel, ‎., & Huynen, M. A. (2004) · EMBO Reports · doi:10.1038/sj.embor.7400090 · Cited by 256 · see citing works

Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500-Element cDNA ArrayPreprint

Boer, J. M., Huber, W. K., Sültmann, H., Wilmer, F., von Heydebreck, A., Haas, S., Korn, B., Gunawan, B., Vente, A., FÜZESI, L., et al. (2001) · Genome Research · doi:10.1101/gr.184501 · Cited by 206 · see citing works

Genome-wide coexpression dynamics: Theory and application

Li, K.-C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252466999 · Cited by 199 · see citing works

Alteration of the bioenergetic phenotype of mitochondria is a hallmark of breast, gastric, lung and oesophageal cancer

Isidoro, A., Martínez, M., Fernández, P. L., et al. (2004) · Biochemical Journal · doi:10.1042/bj20031541 · Cited by 192 · see citing works

Colorectal carcinogenesis is associated with stromal expression of COL11A1 and COL5A2

Fischer, H. (2001) · Carcinogenesis · doi:10.1093/carcin/22.6.875 · Cited by 188 · see citing works

UbcH10 is the cancer-related E2 ubiquitin-conjugating enzyme.

Okamoto, Y., Ozaki, T., Miyazaki, K., Aoyama, M., Miyazaki, M., & Nakagawara, A. (2003) · PubMed · Cited by 186 · see citing works

Cell cycle regulation of metallothionein in human colonic cancer cells.

Nagel, W. W., & Vallée, B. L. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.2.579 · Cited by 152 · see citing works

Bioinformatic identification of potential autocrine signaling loops in cancers from gene expression profiles

Graeber, T. G., & Eisenberg, D. S. (2001) · Nature Genetics · doi:10.1038/ng755 · Cited by 133 · see citing works

Overexpression, genomic amplification and therapeutic potential of inhibiting the UbcH10 ubiquitin conjugase in human carcinomas of diverse anatomic origin

Wagner, K. W., Sapinoso, L. M., El-Rifai, W. M., Frierson, H. F., Butz, N., Mestan, J., Hofmann, F., Deveraux, Q. L., & Hampton, G. M. (2004) · Oncogene · doi:10.1038/sj.onc.1207861 · Cited by 131 · see citing works

Integrative analysis of multiple gene expression profiles applied to liver cancer study

Choi, J. K., Choi, J. Y., Kim, D. G., Choi, D. W., Kim, B. Y., Lee, K. H., Yeom, Y. I., Yoo, H. S., Yoo, O. J., & Kim, S. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.03.081 · Cited by 96 · see citing works

Overexpression of TGF-β by infiltrated granulocytes correlates with the expression of collagen mRNA in pancreatic cancer

Aoyagi, Y., Oda, T., Kinoshitá, T., Nakahashi, C., Hasebe, T., Ohkohchi, N., & Ochiai, A. (2004) · British Journal of Cancer · doi:10.1038/sj.bjc.6602141 · Cited by 90 · see citing works

CHANGES IN COLLAGEN METABOLISM IN PROSTATE CANCER: A HOST RESPONSE THAT MAY ALTER PROGRESSION

Burns‐Cox, N., Avery, N. C., Gingell, J. C., et al. (2001) · The Journal of Urology · doi:10.1016/s0022-5347(05)65656-x · Cited by 78 · see citing works

A system for enhancing genome-wide coexpression dynamics study

Li, K.-C., Liu, C., Sun, W., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402962101 · Cited by 74 · see citing works

Prognostic significance of metallothionein in human gastrointestinal cancer.

Janssen, A. M. L., van Duijn, W., Kubben, F. J. G. M., et al. (2002) · PubMed · Cited by 55 · see citing works

Transforming growth factor β 1 secreted from scirrhous gastric cancer cells is associated with excess collagen deposition in the tissue

MAHARA, K., Kato, J., Terui, T., et al. (1994) · British Journal of Cancer · doi:10.1038/bjc.1994.147 · Cited by 54 · see citing works

Increased Expression of Metallothionein Is Associated with Irinotecan Resistance in Gastric Cancer

Chun, J. H., Kim, H. K., Kim, E. S., et al. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-1063 · Cited by 54 · see citing works

Correlation of metallothionein expression with apoptosis in nasopharyngeal carcinoma

Jayasurya, A., Bay, B., Yap, W. M., et al. (2000) · British Journal of Cancer · doi:10.1054/bjoc.1999.1063 · Cited by 52 · see citing works

Metallothionein expression in hepatocellular carcinoma

Huang, G. (2002) · World Journal of Gastroenterology · doi:10.3748/wjg.v8.i4.650 · Cited by 46 · see citing works

Breast tumour cell-induced down-regulation of type I collagen mRNA in fibroblasts

Fenhalls, G., Geyp, M., DENT, D. M., et al. (1999) · British Journal of Cancer · doi:10.1038/sj.bjc.6690821 · Cited by 43 · see citing works

Expression of mRNAs for type I and type III procollagens in serous ovarian cystadenomas and cystadenocarcinomas.

Kauppila, S., Saarela, J., Stenbäck, F., et al. (1996) · PubMed · Cited by 39 · see citing works

Expression of Metallothionein in Colorectal Cancers and Synchronous Liver Metastases

Hishikawa, Y., Kohno, H., Ueda, S., et al. (2001) · Oncology · doi:10.1159/000055368 · Cited by 36 · see citing works

Prognostic significance of metallothionein expression in renal cell carcinoma

Mitropoulos, D., Kyroudi‐Voulgari, A., Theocharis, S., et al. (2005) · World Journal of Surgical Oncology · doi:10.1186/1477-7819-3-5 · Cited by 30 · see citing works

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

Parikshak, N. N., Gandal, M. J., & Geschwind, D. H. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3934 · Cited by 430 · see citing works

DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules

Tesson, B. M., Breitling, R., & Jansen, R. C. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-497 · Cited by 244 · see citing works

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

Amar, D., Safer, H., & Shamir, R. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002955 · Cited by 169 · see citing works

Emerging role of microRNAs in major depressive disorder: diagnosis and therapeutic implications

Dwivedi, Y. (2014) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2014.16.1/ydwivedi · Cited by 169 · see citing works

Comparative assessment of differential network analysis methods

Lichtblau, Y., Zimmermann, K., Haldemann, B., Lenze, D., Hummel, M., & Leser, U. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw061 · Cited by 76 · see citing works

Shared probe design and existing microarray reanalysis using PICKY

Chou, H.-H. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-196 · Cited by 25 · see citing works

Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction

Fan, L., Meng, H., Guo, X., Li, X., & Meng, F. (2018) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2017-0075 · Cited by 21 · see citing works

[Study on development of DNA microarrays for human papillomavirus (HPV) diagnosis].

Liu, C., Ma, W., Bao, Z., et al. (2003) · PubMed · Cited by 1 · see citing works

DNA Microarray Technology

Zhou, J. Z., & Thompson, D. K. (2004) · doi:10.1002/0471647527.ch6 · Cited by 62 · see citing works

Deep learning identifies erroneous microarray-based, gene-level conclusions in literature

Qin, Y., Yi, D., Chen, X., & Guan, Y. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab089 · Cited by 1 · see citing works