DAVID: Database for Annotation, Visualization, and Integrated Discovery

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

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232

Database resources of the National Center for Biotechnology Information: update

Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,695

Identifying biological themes within lists of genes with EASE

Hosack, D. A., Dennis, G., Sherman, B. T., Lane, H. C., & Lempicki, R. A. (2003) · Genome biology · doi:10.1186/gb-2003-4-10-r70 · Cited by 1,961

The Ensembl genome database project

Hubbard, T. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.38 · Cited by 1,610

Computational analysis of microarray data

Quackenbush, J. (2001) · Nature Reviews Genetics · doi:10.1038/35076576 · Cited by 1,481

Database resources of the National Center for Biotechnology Information

Wheeler, D. L. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.10 · Cited by 583

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Rebhan, M., Caspi, V. C., Prilusky, J., & Lancet, D. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.8.656 · Cited by 502

NetAffx: Affymetrix probesets and annotations

Liu, G. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg121 · Cited by 487

Chondrogenic Differentiation of Human Mesenchymal Stem Cells in Three-Dimensional Alginate Gels

Xu, J., Wang, W., Ludeman, M., Cheng, K. K., Hayami, T., Lotz, J. C., & Kapila, S. (2008) · Tissue Engineering Part A · doi:10.1089/tea.2007.0272 · Cited by 225

Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

Li, M., Balch, C., Montgomery, J. S., Jeong, M., Chung, J. H., Yan, P. S., Huang, T. H. ‐., Kim, S., & Nephew, K. P. (2009) · BMC Medical Genomics · doi:10.1186/1755-8794-2-34 · Cited by 225

POCUS: mining genomic sequence annotation to predict disease genes

Turner, F. S., Clutterbuck, D. R., & Semple, C. A. M. (2003) · Genome biology · doi:10.1186/gb-2003-4-11-r75 · Cited by 227

Body mass index-independent inflammation in omental adipose tissue associated with insulin resistance in morbid obesity

Hardy, O. T., Perugini, R. A., Nicoloro, S. M. C., Gallagher-Dorval, K. A., Puri, V., Straubhaar, J., & Czech, M. (2010) · Surgery for Obesity and Related Diseases · doi:10.1016/j.soard.2010.05.013 · Cited by 229

Alzheimer’s disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes

Sekar, S., McDonald, J., Cuyugan, L., Aldrich, J., Kurdoglu, A., Adkins, J., Serrano, G., Beach, T. G., Craig, D. W., Valla, J., et al. (2015) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2014.09.027 · Cited by 199

Computational methods for discovering gene networks from expression data

Lee, W.-P., & Tzou, W. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp028 · Cited by 229

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiaePreprint

Herrgård, M. J., Lee, B.-S., Portnoy, V., & Palsson, B. Ø. (2006) · Genome Research · doi:10.1101/gr.4083206 · Cited by 227

COL11A1 promotes tumor progression and predicts poor clinical outcome in ovarian cancer

Wu, Y., Chang, T.-H., Huang, Y.-F., Huang, H.-D., & Chou, C. (2013) · Oncogene · doi:10.1038/onc.2013.307 · Cited by 216

Glucose regulates transcription in yeast through a network of signaling pathways

Zaman, S., Lippman, S. I., Schneper, L. M., Slonim, N., & Broach, J. R. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.2 · Cited by 217

Elucidating the Role of Gonadal Hormones in Sexually Dimorphic Gene Coexpression Networks

van Nas, A., GuhaThakurta, D., Wang, S. S., Yehya, N., Horvath, S., Zhang, B., Ingram-Drake, L. A., Chaudhuri, G., Schadt, E. E., Drake, T. A., et al. (2008) · Endocrinology · doi:10.1210/en.2008-0563 · Cited by 226

miR-125b-2 is a potential oncomiR on human chromosome 21 in megakaryoblastic leukemiaPreprint

Klusmann, J., Li, Z., Böhmer, K., Maroz, A., Koch, M. L., Emmrich, S., Godinho, F. J., Orkin, S. H., & Reinhardt, D. (2010) · Genes & Development · doi:10.1101/gad.1856210 · Cited by 220

Global Identification of Myc Target Genes Reveals Its Direct Role in Mitochondrial Biogenesis and Its E-Box Usage In Vivo

Kim, J., Lee, J. H., & Iyer, V. R. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001798 · Cited by 219

Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions

Ishigaki, S., Masuda, A., Fujioka, Y., Iguchi, Y., Katsuno, M., Shibata, A., Urano, F., Sobue, G., & Ohno, K. (2012) · Scientific Reports · doi:10.1038/srep00529 · Cited by 219

Gene Expression Profiling Following In Utero Exposure to Phthalate Esters Reveals New Gene Targets in the Etiology of Testicular Dysgenesis1

Liu, K., Lehmann, K. P., Sar, M., Young, S. S., & Gaido, K. W. (2005) · Biology of Reproduction · doi:10.1095/biolreprod.104.039404 · Cited by 219

mRNA and microRNA Expression Profiles in Circulating Tumor Cells and Primary Tumors of Metastatic Breast Cancer Patients

Sieuwerts, A. M., Mostert, B., Vries, J. B., Peeters, D. J. E., de Jongh, F. E., Stouthard, J. M., Dirix, L. Y., van Dam, P. A., van Galen, A., de Weerd, V., et al. (2011) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-11-0255 · Cited by 223

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence

Steinbaugh, M. J., Narasimhan, S. D., Robida-Stubbs, S., Mazzeo, L. E. M., Dreyfuss, J. M., Hourihan, J. M., Raghavan, P., Operaña, T. N., Esmaillie, R., & Blackwell, T. K. (2015) · eLife · doi:10.7554/elife.07836 · Cited by 215

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

Khatri, P., Bhavsar, P., Bawa, G., & Drăghici, S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh409 · Cited by 220

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

Cotney, J. L., Leng, J., Yin, J., Reilly, S. K., DeMare, L. E., Emera, D., Ayoub, A. E., RAKIC, P. T., & Noonan, J. P. (2013) · Cell · doi:10.1016/j.cell.2013.05.056 · Cited by 215

NK Cell Terminal Differentiation: Correlated Stepwise Decrease of NKG2A and Acquisition of KIRs

Béziat, V., Descours, B., Parizot, C., Debré, P., & Vieillard, V. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011966 · Cited by 228

Consequences of long-term oral administration of the mitochondria-targeted antioxidant MitoQ to wild-type mice

Rodriguez-Cuenca, S., Cochemé, H. M., Logan, A., Abakumova, I., Prime, T. A., Rose, C., Vidal-Puig, A., Smith, A. C., Rubinsztein, D. C., Fearnley, I. M., et al. (2010) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2009.10.039 · Cited by 218

BMDExpress: a software tool for the benchmark dose analyses of genomic data

Yang, L., Allen, B. C., & Thomas, R. S. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-387 · Cited by 218

Chemical composition and pharmacological mechanism of Qingfei Paidu Decoction and Ma Xing Shi Gan Decoction against Coronavirus Disease 2019 (COVID-19): In silico and experimental study

Yang, R., Liu, H., Bai, C., Wang, Y., Zhang, X., Guo, R., Wu, S., Wang, J., Leung, E. L., Chang, H., et al. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104820 · Cited by 217

Analysis of whole genome biomarker expression in blood and brain

Rollins, B. L., Martin, M. V., Morgan, L. Z., & Vawter, M. P. (2010) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.31062 · Cited by 217

High-Throughput Screening Assay for the Identification of Compounds Regulating Self-Renewal and Differentiation in Human Embryonic Stem Cells

Desbordes, S. C., Placantonakis, D. G., Ciro, A., Socci, N. D., Lee, G., Djaballah, H., & Studer, L. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.05.010 · Cited by 217

Direct Recruitment of Polycomb Repressive Complex 1 to Chromatin by Core Binding Transcription Factors

Yu, M., Mazor, T., Huang, H., Huang, H.-T., Kathrein, K. L., Woo, A. J., Chouinard, C. R., Labadorf, A. T., Akie, T. E., Moran, T. B., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.11.032 · Cited by 230

NRF2 deficiency replicates transcriptomic changes in Alzheimer's patients and worsens APP and TAU pathology

Rojo, A. I., Pajares, M., Rada, P., Núñez, Á., Nevado‐Holgado, A. J., Killick, R., LEUVEN, F. V., Ribé, E. M., Lovestone, S., Yamamoto, M. P., et al. (2017) · Redox Biology · doi:10.1016/j.redox.2017.07.006 · Cited by 220

The proteome of red cell membranes and vesicles during storage in blood bank conditions

Bosman, G. J. C. G. M., Lasonder, E., Luten, M., Roerdinkholder‐Stoelwinder, B., Novotny, V. M. J., Bos, H. J., & DeGrip, W. J. (2008) · Transfusion · doi:10.1111/j.1537-2995.2007.01630.x · Cited by 215

Transcriptome Profiling and Functional Analyses of the Zebrafish Embryonic Innate Immune Response to Salmonella Infection

Stockhammer, O. W., Zakrzewska, A., Hegedüs, Z., Spaink, H. P., & Meijer, A. H. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900082 · Cited by 220

Curcumin Extends Life Span, Improves Health Span, and Modulates the Expression of Age-Associated Aging Genes in Drosophila melanogaster

Lee, K., Lee, B.-S., Semnani, S., Avanesian, A., Um, C.-Y., Jeon, H., Seong, K.-M., Yu, K., Min, K., & Jafari, M. (2010) · Rejuvenation Research · doi:10.1089/rej.2010.1031 · Cited by 217

Friedreich's Ataxia Induced Pluripotent Stem Cells Model Intergenerational GAA⋅TTC Triplet Repeat Instability

Ku, S., Soragni, E., Campau, E., Thomas, E. A., Altun, G., Laurent, L. C., Loring, J. F., Напиерала, М., & Gottesfeld, J. M. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.09.014 · Cited by 221

A central regulatory role for eosinophils and the eotaxin/CCR3 axis in chronic experimental allergic airway inflammation

Fulkerson, P. C., Fischetti, C. A., McBride, M. L., Hassman, L. M., Hogan, S. P., & Rothenberg, M. E. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607863103 · Cited by 213

In vivo actin cross-linking induced by Vibrio cholerae type VI secretion system is associated with intestinal inflammation

Ma, A. T., & Mekalanos, J. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0915156107 · Cited by 208

Neuronal MicroRNA Deregulation in Response to Alzheimer's Disease Amyloid-β

Schonrock, N., Ke, Y. D., Humphreys, D., Staufenbiel, M., Ittner, L. M., Preiss, T., & Götz, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011070 · Cited by 211

A systems view of epithelial–mesenchymal transition signaling states

Thomson, S., Petti, F., Sujka-Kwok, I., Mercado, P., Bean, J. M., Monaghan, M., Seymour, S. L., Argast, G. M., Epstein, D. M., & Haley, J. D. (2010) · Clinical & Experimental Metastasis · doi:10.1007/s10585-010-9367-3 · Cited by 216

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues

Kosti, I., Jain, N., Aran, D., Butte, A. J., & Sirota, M. (2016) · Scientific Reports · doi:10.1038/srep24799 · Cited by 210

Network pharmacology to unveil the mechanism of Moluodan in the treatment of chronic atrophic gastritis

Zhou, W., Zhang, H., Wang, X., Kang, J. G., Guo, W., Zhou, L., Liu, H., Wang, M., Jia, R., Du, X., et al. (2021) · Phytomedicine · doi:10.1016/j.phymed.2021.153837 · Cited by 218

Aberrant Expression of Long Noncoding RNAs in Early Diabetic Retinopathy

Yan, B., Tao, Z.-F., Li, X., Zhang, H., Yao, J., & Jiang, Q. L. (2014) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.13-13221 · Cited by 210

Transcriptomic Characterization of Temperature Stress Responses in Larval Zebrafish

Long, Y., Li, L., Li, Q., He, X., & Cui, Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037209 · Cited by 210

The Macrophage Colony-Stimulating Factor 1 Response Signature in Breast Carcinoma

Beck, A. H., Espinosa, Í., Edris, B., Li, R., Montgomery, K. D., Zhu, S., Varma, S., Marinelli, R. J., van de Rijn, M., & West, R. B. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-08-1283 · Cited by 211

CD140a identifies a population of highly myelinogenic, migration-competent and efficiently engrafting human oligodendrocyte progenitor cells

Sim, F. J., McClain, C. R., Schanz, S. J., Protack, T. L., Windrem, M. S., & Goldman, S. A. (2011) · Nature Biotechnology · doi:10.1038/nbt.1972 · Cited by 208

Histones associated with downregulated genes are hypo-acetylated in Huntington's disease models

Sadri‐Vakili, G., Bouzou, B., Benn, C., Kim, M.-O., Chawla, P., Overland, R. P., Glajch, K. E., Xia, E., Qiu, Z., Hersch, S. M., et al. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddm078 · Cited by 210

Conditional Deletion of Smad1 and Smad5 in Somatic Cells of Male and Female Gonads Leads to Metastatic Tumor Development in Mice

Pangas, S. A., Li, X., Umans, L., Zwijsen, A., Huylebroeck, D., Gutiérrez, C., Wang, D., Martin, J. F., Jamin, S. P., Behringer, R. R., et al. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01404-07 · Cited by 216

Primary biliary cirrhosis is associated with altered hepatic microRNA expression

Padgett, K. A., Lan, R. Y., Leung, P. C., Lleò, A., Dawson, K., Pfeiff, J., Mao, T. K., Coppel, R. L., Ansari, A. A., & Gershwin, M. E. (2009) · Journal of Autoimmunity · doi:10.1016/j.jaut.2009.02.022 · Cited by 209

Age-related variations in the methylome associated with gene expression in human monocytes and T cells

Reynolds, L. M., Taylor, J. R., Ding, J., Lohman, K., Johnson, C. W., Siscovick, D. S., Burke, G. L., Post, W. S., Shea, S., Jacobs, D. R., et al. (2014) · Nature Communications · doi:10.1038/ncomms6366 · Cited by 204

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds

Gehring, M. A., Missirian, V., & Henikoff, S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023687 · Cited by 206

When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

Kresnowati, M. T. A. P., van Winden, W. A., Almering, M. J. H., ten Pierick, A., Ras, C., Knijnenburg, T., Daran-Lapujade, P. A. S., Pronk, J. T., Heijnen, J. J., & Daran, J.-M. G. (2006) · Molecular Systems Biology · doi:10.1038/msb4100083 · Cited by 209

A Method to Integrate Benchmark Dose Estimates with Genomic Data to Assess the Functional Effects of Chemical Exposure

Thomas, R. S., Allen, B. C., Nong, A., Yang, L., Bermudez, E., M.A., H. J. C. I., & Andersen, M. E. (2007) · Toxicological Sciences · doi:10.1093/toxsci/kfm092 · Cited by 208

Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function

Avrahami, D., Li, C., Zhang, J., Schug, J., Avrahami, R., Rao, S., Stadler, M. B., Burger, L., Schübeler, D., Glaser, B., et al. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2015.07.025 · Cited by 207

ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth

Markljung, E., Jiang, L., Jaffe, J. D., Mikkelsen, T. S., Wallerman, O., Larhammar, M., Zhang, X., Wang, L., Saenz-Vash, V., Gnirke, A., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000256 · Cited by 207

Chronic Endoplasmic Reticulum Stress Activates Unfolded Protein Response in Arterial Endothelium in Regions of Susceptibility to Atherosclerosis

Civelek, M., Manduchi, E., Riley, R., Stoeckert, C. J., & Davies, P. F. (2009) · Circulation Research · doi:10.1161/circresaha.109.203711 · Cited by 208

Transcriptome Analysis of the Planarian Eye Identifies ovo as a Specific Regulator of Eye Regeneration

Lapan, S. W., & Reddien, P. W. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.06.018 · Cited by 207

Rapid Onset of Intestinal Epithelial Barrier Dysfunction in Primary Human Immunodeficiency Virus Infection Is Driven by an Imbalance between Immune Response and Mucosal Repair and Regeneration

Sankaran, S., George, M. D., Reay, E., Guadalupe, M., Flamm, J., Prindiville, T. P., & Dandekar, S. (2007) · Journal of Virology · doi:10.1128/jvi.01449-07 · Cited by 208

Anticancer activity of biogenerated silver nanoparticles: an integrated proteomic investigation

Buttacavoli, M., Albanese, N. N., Cara, G. D., Alduina, R., Faleri, C., Gallo, M., Pizzolanti, G., Gallo, G., Feo, S., Baldi, F., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.23859 · Cited by 207

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data

Orange, D. E., Agius, P., DiCarlo, E. F., Robine, N., Geiger, H. M., Szymonifka, J. D., McNamara, M., Cummings, R. W., Andersen, K. M., Mirza, S. Z., et al. (2018) · Arthritis & Rheumatology · doi:10.1002/art.40428 · Cited by 209

Genomic analysis of the interaction between pesticide exposure and nutrition in honey bees (Apis mellifera)

Schmehl, D. R., Teal, P. E. A., Frazier, J. L., & Grozinger, C. M. (2014) · Journal of Insect Physiology · doi:10.1016/j.jinsphys.2014.10.002 · Cited by 206

Gender-Specific Gene Expression in Post-Mortem Human Brain: Localization to Sex Chromosomes

Vawter, M. P., Evans, S. J., Choudary, P. V., Tomita, H., Meador-Woodruff, J., Molnar, M., Li, J. Z., López, J. F., Myers, R. M., Cox, D. R., et al. (2003) · Neuropsychopharmacology · doi:10.1038/sj.npp.1300337 · Cited by 204

MicroRNA dysregulation in schizophrenia

Beveridge, N. J., & Cairns, M. J. (2011) · Neurobiology of Disease · doi:10.1016/j.nbd.2011.12.029 · Cited by 209

Genome‐wide tissue‐specific farnesoid X receptor binding in mouse liver and intestine†

Thomas, A., Hart, S. N., Kong, B., Fang, J., Zhong, X., & Guo, G. L. (2009) · Hepatology · doi:10.1002/hep.23450 · Cited by 205

Biological Profiling of Gene Groups utilizing Gene Ontology

Blüthgen, N., Brand, K., Čajavec, B., Swat, M., Herzel, H., & Beule, D. (2004) · PubMed · doi:10.48550/arxiv.q-bio/0407034 · Cited by 206

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

Saulière, J., Murigneux, V., Wang, Z., Marquenet, E., Barbosa, I., Tonquèze, O. L., Audic, Y., Paillard, L., Crollius, H. R., & Hir, H. L. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2420 · Cited by 216

Patterns of pain: Meta-analysis of microarray studies of pain

LaCroix‐Fralish, M. L., Austin, J., Zheng, F. Y., Levitin, D. J., & Mogil, J. S. (2011) · Pain · doi:10.1016/j.pain.2011.04.014 · Cited by 204

Down-regulation of NF-κB Transcriptional Activity in HIV-associated Kidney Disease by BRD4 Inhibition

Zhang, G., Liu, R., Zhong, Y., Plotnikov, A. N., Zhang, W., Zeng, L., Rusinova, E. V., Gerona-Nevarro, G., Moshkina, N., Joshua, J., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.359505 · Cited by 207

A High-Resolution Map of Segmental DNA Copy Number Variation in the Mouse Genome

Graubert, T. A., Cahan, P., Edwin, D., Selzer, R. R., Richmond, T., Eis, P. S., Shannon, W. D., Li, X., McLeod, H. L., Cheverud, J. M., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0030003 · Cited by 203

The Rat Epididymal Transcriptome: Comparison of Segmental Gene Expression in the Rat and Mouse Epididymides1

Jelinsky, S. A., Turner, T. T., Bang, H. J., Finger, J. N., Solarz, M. K., Wilson, E., Brown, E. L., Kopf, G. S., & Johnston, D. S. (2006) · Biology of Reproduction · doi:10.1095/biolreprod.106.057323 · Cited by 203

Characterization of cell lines derived from breast cancers and normal mammary tissues for the study of the intrinsic molecular subtypes

Prat, A., Karginova, O. A., Parker, J. S., Fan, C., He, X., Bixby, L. M., Harrell, J. C., Roman, E., Adamo, B., Troester, M. A., et al. (2013) · Breast Cancer Research and Treatment · doi:10.1007/s10549-013-2743-3 · Cited by 212

Genome-wide analysis reveals Sall4 to be a major regulator of pluripotency in murine-embryonic stem cells

Yang, J., Chai, L., Fowles, T. C., Alipio, Z., Xu, D., Fink, L. M., Ward, D. C., & Ma, Y. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809321105 · Cited by 209

Evolution and function of CAG/polyglutamine repeats in protein–protein interaction networks

Schaefer, M. H., Wanker, E. E., & Andrade-Navarro, M. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks011 · Cited by 208

The influence of surface microroughness and hydrophilicity of titanium on the up-regulation of TGFβ/BMP signalling in osteoblasts.

Vlacic-Zischke, J., Hamlet, S. M., Friis, T., Tonetti, M. S., & Ivanovski, S. (2010) · Biomaterials · doi:10.1016/j.biomaterials.2010.09.025 · Cited by 200

m 6 A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2

Chen, J., Zhang, Y.-C., Huang, C.-M., Shen, H., Sun, B., Cheng, X., Zhang, Y., Yang, Y., Shu, Q., Yang, Y., et al. (2019) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2018.12.007 · Cited by 199

An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer

Cui, J., Chen, Y., Chou, W., Sun, L., Chen, L., Suo, J., Ni, Z., Zhang, M., Kong, X., Hoffman, L. L., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq960 · Cited by 199

Circulating miRNA analysis for cancer diagnostics and therapy

Valihrach, L., Androvic, P., & Kubista, M. (2019) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2019.10.002 · Cited by 201

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Mahdessian, D., Cesnik, A. J., Gnann, C., Danielsson, F., Stenström, L., Arif, M., Zhang, C., Le, T. H., Johansson, F., Schutten, R., et al. (2021) · Nature · doi:10.1038/s41586-021-03232-9 · Cited by 204

Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development

Xiong, Z., Xu, K., Lin, Z., Kong, F., Wang, Q., Quan, Y., Sha, Q., Li, F., Zou, Z., Liu, L., et al. (2022) · Nature Cell Biology · doi:10.1038/s41556-022-00928-6 · Cited by 199

Hypoxia Modifies the Transcriptome of Primary Human Monocytes: Modulation of Novel Immune-Related Genes and Identification Of CC-Chemokine Ligand 20 as a New Hypoxia-Inducible Gene

Bosco, M. C., Puppo, M., Santangelo, C., Anfosso, L., Pfeffer, U., Fardin, P., Battaglia, F., & Varesio, L. (2006) · The Journal of Immunology · doi:10.4049/jimmunol.177.3.1941 · Cited by 202

Data integration: challenges for drug discovery

Searls, D. B. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1608 · Cited by 204

Genome-wide analyses of human perisylvian cerebral cortical patterning

Abrahams, B. S., Tentler, D., Perederiy, J. V., Oldham, M. C., Coppola, G., & Geschwind, D. H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706128104 · Cited by 202

'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus

Bundy, J. G., Sidhu, J. K., Rana, F., Spurgeon, D. J., Svendsen, C., Wren, J. F., Stürzenbaum, S. R., Morgan, A. J., & Kille, P. (2008) · BMC Biology · doi:10.1186/1741-7007-6-25 · Cited by 198

Disease-specific, neurosphere-derived cells as models for brain disorders

Matigian, N., Abrahamsen, G., Sutharsan, R., Cook, A. L., Vitale, A. M., Nouwens, A. S., Bellette, B., An, J., Anderson, M. J., Beckhouse, A. G., et al. (2010) · Disease Models & Mechanisms · doi:10.1242/dmm.005447 · Cited by 202

HDAC inhibitors induce tumor-cell-selective pro-apoptotic transcriptional responses

Bolden, J. E., Shi, W., Jankowski, K., Kan, C.-Y., Cluse, L. A., Martin, B. P., MacKenzie, K. L., Smyth, G. K., & Johnstone, R. W. (2013) · Cell Death and Disease · doi:10.1038/cddis.2013.9 · Cited by 197

Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians

Lehnert, E. M., Mouchka, M. E., Burriesci, M. S., Gallo, N. D., Schwarz, J. A., & Pringle, J. R. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.009084 · Cited by 197

Chromatin Immunoprecipitation on Microarray Analysis of Smad2/3 Binding Sites Reveals Roles of ETS1 and TFAP2A in Transforming Growth Factor β Signaling

Koinuma, D., Tsutsumi, S., Kamimura, N., Taniguchi, H., Miyazawa, K., Sunamura, M., Imamura, T., Miyazono, K., & Aburatani, H. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01038-08 · Cited by 205

Patterns of gene expression in the limbic system of suicides with and without major depression

Sequeira, A., Klempan, T. A., Canetti, L., ffrench-Mullen, J. M. H., Benkelfat, C., Rouleau, G. A., & Turecki, G. (2007) · Molecular Psychiatry · doi:10.1038/sj.mp.4001969 · Cited by 200

A novel inhibitor of glucose uptake sensitizes cells to FAS-induced cell death

Wood, T. E., Dalili, S., Simpson, C. D., Hurren, R., Mao, X., Suárez, F., Gronda, M., Eberhard, Y., Minden, M. D., Bilan, P. J., et al. (2008) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-08-0569 · Cited by 200

Endometrial gene expression in the window of implantation is altered in obese women especially in association with polycystic ovary syndrome

Bellver, J., Martínez-Conejero, J. A., Labarta, E., Alamá, P., de Melo, M. A. B., Remohi, J. A., Pellicer, A., & Horcajadas, J. A. (2011) · Fertility and Sterility · doi:10.1016/j.fertnstert.2011.03.021 · Cited by 203

Transcriptome-wide Analysis of Exosome Targets

Schneider, C., Kudla, G., Wlotzka, W., Tuck, A., & Tollervey, D. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.013 · Cited by 195

UV Radiation-Induced Immunosuppression Is Greater in Men and Prevented by Topical Nicotinamide

Damian, D. L., Patterson, C. R. S., Stapelberg, M., Park, J., Barnetson, R. S., & Halliday, G. M. (2007) · Journal of Investigative Dermatology · doi:10.1038/sj.jid.5701058 · Cited by 204

Comparing Statistical Methods for Constructing Large Scale Gene Networks

Allen, J. D., Xie, Y., Chen, M., Girard, L., & Xiao, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029348 · Cited by 186

A Molecular Function Map of Ewing's Sarcoma

Kauer, M. O., Ban, J., Kofler, R., Walker, R. L., Davis, S. R., Meltzer, P. S., & Kovar, H. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005415 · Cited by 195

Corticolimbic Transcriptome Changes are State-Dependent and Region-Specific in a Rodent Model of Depression and of Antidepressant Reversal

Surget, A., Wang, Y., Leman, S., Ibargüen-Vargas, Y., Edgar, N. M., Griebel, G., Belzung, C., & Sibille, E. L. (2008) · Neuropsychopharmacology · doi:10.1038/npp.2008.76 · Cited by 203

A Reconfigured Pattern of MLL Occupancy within Mitotic Chromatin Promotes Rapid Transcriptional Reactivation Following Mitotic Exit

Blobel, G. A., Kadauke, S., Wang, E., Lau, A. W., Zuber, J. A., Chou, M. M., & Vakoc, C. R. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.001 · Cited by 194

Genetic and genomic studies of Drosophila parkin mutants implicate oxidative stress and innate immune responses in pathogenesis

Greene, J. C., Whitworth, A. J., Andrews, L. A., Parker, T. J., & Pallanck, L. J. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi074 · Cited by 194

Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning

Marjani, S. L., Everts, R. E., Tian, X., Du, F., Sung, L., Rodriguez‐Zas, S. L., Jeong, B., Renard, J. P. J. P., Lewin, H. A., & Yang, X. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508952102 · Cited by 194

Up-Regulation of MicroRNAs in Brain of Human Alcoholics

Lewohl, J. M., Núnez, Y. O., Dodd, P. R., Tiwari, G. R., Harris, R. A., & Mayfield, R. D. (2011) · Alcoholism Clinical and Experimental Research · doi:10.1111/j.1530-0277.2011.01544.x · Cited by 196

The Escherichia coli Cpx Envelope Stress Response Regulates Genes of Diverse Function That Impact Antibiotic Resistance and Membrane Integrity

Raivio, T. L., Leblanc, S. K. D., & Price, N. L. (2013) · Journal of Bacteriology · doi:10.1128/jb.00105-13 · Cited by 193

Estrogen-related Receptor γ Is a Key Regulator of Muscle Mitochondrial Activity and Oxidative Capacity

Rangwala, S. M., Wang, X., Calvo, J. A., Lindsley, L., Zhang, Y., Deyneko, G., Beaulieu, V., Gao, J., Turner, G. M., & Markovits, J. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.125401 · Cited by 195

Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy

Li, J., Wang, W., Zhang, Y., Cieslik, M. P., Guo, J., Tan, M., Green, M. D., Wang, W., Lin, H., Li, W., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci134402 · Cited by 193

The histone variant macroH2A is an epigenetic regulator of key developmental genes

Buschbeck, M., Uribesalgo, I., Wibowo, I., Rué, P., Martin, D., Gutierrez, A., Morey, L., Guigó, R., López-Schier, H., & Di Croce, L. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1665 · Cited by 192

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

Tomczak, A., Mortensen, J., Winnenburg, R., Liu, C. Y., Alessi, D. T., Swamy, V., Vallania, F., Lofgren, S., Haynes, W. A., Shah, N. H., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-23395-2 · Cited by 207

MicroRNAs miR-30b, miR-30d, and miR-494 Regulate Human Endometrial Receptivity

Altmäe, S., Martínez-Conejero, J. A., Esteban, F. J., Ruíz-Alonso, M., Stavreus-Evers, A. C., Horcajadas, J. A., & Salumets, A. (2012) · Reproductive Sciences · doi:10.1177/1933719112453507 · Cited by 188

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Sherman, B. T., Huang, D. W., Tan, Q., Guo, Y., Bour, S. P., Liu, D., Stephens, R., Baseler, M., Lane, H. C., & Lempicki, R. A. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-426 · Cited by 559

Database for annotation, visualisation and integrated discovery

Sofi, M. Y., Shafi, A., & Masoodi, K. Z. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-91128-3.00015-x

The meaning of it all: web-based resources for large-scale functional annotation and visualization of DNA microarray data.

Guffanti, A., Reid, J. F., Alcalay, M., & Simon, G. (2004) · PubMed

DIG--a system for gene annotation and functional discovery

deLong, M. A., Yao, G., Wang, Q., Dobra, A., Black, E. P., Chang, J. T., Bild, A. H., West, M., Nevins, J. R., & Dressman, H. K. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti467 · Cited by 18

GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining

Masseroli, M., Martucci, D., & Pinciroli, F. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh432 · Cited by 80