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

An ESRP‐regulated splicing programme is abrogated during the epithelial–mesenchymal transition

Warzecha, C. C., Jiang, P., Amirikian, K., Dittmar, K. A., Lu, H., Shen, S., Guo, W., Xing, Y., & Carstens, R. P. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.195 · Cited by 383

Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics

Dennis, G., Holweg, C. T. J., Kummerfeld, S., Choy, D. F., Setiadi, A., Hackney, J. A., Haverty, P. M., Gilbert, H., Lin, W. Y., Diehl, L. J., et al. (2014) · Arthritis Research & Therapy · doi:10.1186/ar4555 · Cited by 382

A Drosophila Genetic Resource of Mutants to Study Mechanisms Underlying Human Genetic Diseases

Yamamoto, S., Jaiswal, M., Charng, W., Gambin, T., Karaca, E., Mirzaa, G., Wiszniewski, W. K., Sandoval, H., Haelterman, N. A. T., Xiong, B., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.002 · Cited by 383

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

Gao, N., White, P., & Kaestner, K. H. (2009) · Developmental Cell · doi:10.1016/j.devcel.2009.02.010 · Cited by 390

Development and validation of a TP53-associated immune prognostic model for hepatocellular carcinoma

Long, J., Wang, A., Bai, Y., Lin, J., Yang, X., Wang, D., Yang, X., Jiang, Y., & Zhao, H. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2019.03.022 · Cited by 381

The Transcription Factor Gata6 Links Tissue Macrophage Phenotype and Proliferative Renewal

Rosas, M., Davies, L. C., Giles, P. J., Liao, C., Kharfan, B., Stone, T., O’Donnell, V. B., Fraser, D. J., Jones, S. A., & Taylor, P. R. (2014) · Science · doi:10.1126/science.1251414 · Cited by 393

An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease

Pardo, M., Lang, B., Yu, L., Prosser, H., Bradley, A., Babu, M. M., & Choudhary, J. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.03.004 · Cited by 379

Macromolecule biosynthesis: a key function of sleep

Mackiewicz, M., Shockley, K. R., Romer, M. A., Galante, R. J., Zimmerman, J. E., Naidoo, N. N., Baldwin, D. A., Jensen, S. T., Churchill, G. A., & Pack, A. I. (2007) · Physiological Genomics · doi:10.1152/physiolgenomics.00275.2006 · Cited by 392

RAP2 mediates mechanoresponses of the Hippo pathway

Meng, Z., Qiu, Y., Lin, K. C., Kumar, A., Placone, J. K., Fang, C., Wang, K.-C., Lu, S., Pan, M., Hong, A. W., et al. (2018) · Nature · doi:10.1038/s41586-018-0444-0 · Cited by 377

Microrna-Dependent Regulation of Dna Methyltransferase-1 and Tumor Suppressor Gene Expression by Interleukin-6 in Human Malignant Cholangiocytes

Braconi, C., Huang, N., & Patel, T. C. (2009) · Hepatology · doi:10.1002/hep.23381 · Cited by 377

The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant gliomaPreprint

Bhat, K., Salazar, K. L., Balasubramaniyan, V., Wani, K., Heathcock, L. E., Hollingsworth, F., James, J. D., Gumin, J., Alfaro-Munoz, K. D., Kim, S. H., et al. (2011) · Genes & Development · doi:10.1101/gad.176800.111 · Cited by 385

DNA Methyltransferase 1 Is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells

Trowbridge, J. J., Snow, J. W., Kim, J., & Orkin, S. H. (2009) · Cell Stem Cell · doi:10.1016/j.stem.2009.08.016 · Cited by 373

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

Kaimal, V., Bardes, E. E., Tabar, S., Jegga, A. G., & Aronow, B. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq418 · Cited by 369

Weighted gene coexpression network analysis strategies applied to mouse weight

Fuller, T. F., Ghazalpour, A., Aten, J. E., Drake, T. A., Lusis, A. J., & Horvath, S. (2007) · Mammalian Genome · doi:10.1007/s00335-007-9043-3 · Cited by 372

Chromatin signature of embryonic pluripotency is established during genome activation

Vastenhouw, N. L., Zhang, Y., Woods, I. G., Imam, F. B., Regev, A., Liu, X. S., Rinn, J. L., & Schier, A. F. (2010) · Nature · doi:10.1038/nature08866 · Cited by 379

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism

Weyn-Vanhentenryck, S. M., Mele, A., Yan, Q., Sun, S., Farny, N., Zhang, Z., Xue, C., Herre, M., Silver, P. A., Zhang, M. Q., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.005 · Cited by 333

Principles and methods of integrative genomic analyses in cancer

Kristensen, V. N., Lingjærde, O. C., Russnes, H. G., Vollan, H. K. M., Frigessi, A., & Børresen‐Dale, A. (2014) · Nature reviews. Cancer · doi:10.1038/nrc3721 · Cited by 376

The proteome of the mouse photoreceptor sensory cilium complex

Liu, Q., Tan, G., Levenkova, N., Li, T., Pugh, E. N., Rux, J. J., Speicher, D. W., & Pierce, E. A. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700054-mcp200 · Cited by 359

The unfolded protein response transducer IRE1α prevents ER stress‐induced hepatic steatosis

Zhang, K., Wang, S., Malhotra, J. D., Hassler, J. R., Back, S. H., Wang, G., Chang, L., Xu, W., Miao, H. Z., Leonardi, R., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.52 · Cited by 368

WGCNA Application to Proteomic and Metabolomic Data Analysis

Pei, G., Chen, L., & Zhang, W. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.09.016 · Cited by 374

Depletion of FOXP3+ regulatory T cells promotes hypercholesterolemia and atherosclerosis

Klingenberg, R., Gerdes, N., Badeau, R. M., Gisterå, A., Strodthoff, D., Ketelhuth, D. F. J., Lundberg, A. M., Rudling, M., Nilsson, S. K., Olivecrona, G., et al. (2013) · Journal of Clinical Investigation · doi:10.1172/jci63891 · Cited by 380

DNA methylation signatures in development and aging of the human prefrontal cortex

Numata, S., Ye, T., Hyde, T. M., Guitart-Navarro, X., Tao, R., Wininger, M., Colantuoni, C., Weinberger, D. R., Kleinman, J. E., & Lipska, B. K. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.12.020 · Cited by 364

PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database

Altermann, E., & Klaenhammer, T. R. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-60 · Cited by 364

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

Choi, H., Fermin, D., & Nesvizhskii, A. I. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800203-mcp200 · Cited by 364

Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes

Xia, S., Feng, J. Q., Lei, L., Hu, J., Xia, L., Wang, J., Xiang, Y., Liu, L., Zhong, S., Han, L., et al. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw081 · Cited by 368

Using molecular classification to predict gains in maximal aerobic capacity following endurance exercise training in humans

Timmons, J. A., Knudsen, S., Rankinen, T., Koch, L. G., Sarzynski, M., Jensen, T., Keller, P., Scheele, C., Vollaard, N. B. J., Nielsen, S., et al. (2010) · Journal of Applied Physiology · doi:10.1152/japplphysiol.01295.2009 · Cited by 358

Presenting and exploring biological pathways with PathVisio

van Iersel, M., Kelder, T., Pico, A. R., Hanspers, K., Coort, S. L., Conklin, B. R., & Evelo, C. T. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-399 · Cited by 365

An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer

Teschendorff, A. E., Menon, U., Gentry‐Maharaj, A., Ramus, S. J., Gayther, S. A., Apostolidou, S., Jones, A., Lechner, M., Beck, S., Jacobs, I. J., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008274 · Cited by 364

Gene expression profiling of parkinsonian substantia nigra pars compacta; alterations in ubiquitin-proteasome, heat shock protein, iron and oxidative stress regulated proteins, cell adhesion/cellular matrix and vesicle trafficking genes

Grünblatt, E., Mandel, S. A., Jacob‐Hirsch, J., Zeligson, S., Amariglo, N., Rechavi, G., Li, J., Ravid, R., Roggendorf, W., Riederer, P. F., et al. (2004) · Journal of Neural Transmission · doi:10.1007/s00702-004-0212-1 · Cited by 355

Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation

Green, M. R., Kihira, S., Liu, C. L., Nair, R. V., Salari, R., Gentles, A. J., Irish, J. M., Stehr, H., Vicente‐Dueñas, C., Romero-Camarero, I., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1501199112 · Cited by 375

SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties

Han, K., Holder, J. L., Schaaf, C. P., Lu, H., Chen, H., Kang, H., Tang, J., Wu, Z., Hao, S., Cheung, S. W., et al. (2013) · Nature · doi:10.1038/nature12630 · Cited by 360

p53-independent upregulation of miR-34a during oncogene-induced senescence represses MYC

Christoffersen, N. R., Shalgi, R., Frankel, L. B., Leucci, E., Lees, M., Klausen, M., Pilpel, Y., Nielsen, F. C., Oren, M., & Lund, A. H. (2010) · Cell Death & Differentiation · doi:10.1038/cdd.2009.109 · Cited by 352

Endometrial receptivity is affected in women with high circulating progesterone levels at the end of the follicular phase: a functional genomics analysis

Labarta, E., Martinez-Conejero, J. A., Alama, P., Horcajadas, J. A., Pellicer, A., Simon, C., & Bosch, E. (2011) · Human Reproduction · doi:10.1093/humrep/der126 · Cited by 346

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

Siersbæk, R., Nielsen, R., John, S., Sung, M., Baek, S., Loft, A., Hager, G. L., & Mandrup, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.65 · Cited by 350

Cell Wall Hydrolases in Bacteria: Insight on the Diversity of Cell Wall Amidases, Glycosidases and Peptidases Toward Peptidoglycan

Vermassen, A., Léroy, S., Talòn, R., Provot, C., Popowska, M., & Desvaux, M. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00331 · Cited by 337

Condition‐adapted stress and longevity gene regulation by Caenorhabditis elegans SKN‐1/Nrf

Oliveira, R. D. P., Abate, J. P., Dilks, K., Landis, J. N., Ashraf, J. M., Murphy, C. T., & Blackwell, T. K. (2009) · Aging Cell · doi:10.1111/j.1474-9726.2009.00501.x · Cited by 359

Roles of CAMTA transcription factors and salicylic acid in configuring the low‐temperature transcriptome and freezing tolerance of A rabidopsis

Kim, Y., Park, S., Gilmour, S. J., & Thomashow, M. F. (2013) · The Plant Journal · doi:10.1111/tpj.12205 · Cited by 344

Cell- and gene-specific regulation of primary target genes by the androgen receptorPreprint

Bolton, E. C., So, A. Y., Chaivorapol, C., Haqq, C. M., Li, H., & Yamamoto, K. R. (2007) · Genes & Development · doi:10.1101/gad.1564207 · Cited by 348

Immunobiological Characterization of Cancer Stem Cells Isolated from Glioblastoma Patients

Tomaso, T. D., Mazzoleni, S., Wang, E., Sovena, G., Clavenna, D., Franzin, A., Mortini, P., Ferrone, S., Doglioni, C., Marincola, F. M., et al. (2010) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-09-2730 · Cited by 345

The Cytokines Interleukin 27 and Interferon-γ Promote Distinct Treg Cell Populations Required to Limit Infection-Induced Pathology

Hall, A. O., Beiting, D. P., Tato, C. M., John, B., Oldenhove, G., Lombana, C., Pritchard, G. H., Silver, J. S., Bouladoux, N. J., Stumhofer, J. S., et al. (2012) · Immunity · doi:10.1016/j.immuni.2012.06.014 · Cited by 354

Chromatin analysis in human early development reveals epigenetic transition during ZGA

Wu, J., Xu, J., Liu, B., Yao, G., Wang, P., Lin, Z., Huang, B., Wang, X., Li, T., Shi, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0080-8 · Cited by 351

Down syndrome acute lymphoblastic leukemia, a highly heterogeneous disease in which aberrant expression of CRLF2 is associated with mutated JAK2: a report from the International BFM Study Group

Hertzberg, L., Vendramini, E., Ganmore, I., Cazzaniga, G., Schmitz, M., Chalker, J., Shiloh, R., Iacobucci, I., Shochat, C., Zeligson, S., et al. (2009) · Blood · doi:10.1182/blood-2009-08-235408 · Cited by 342

Hedgehog signaling regulates epithelial-mesenchymal transition during biliary fibrosis in rodents and humans

Omenetti, A., Porrello, A., Jung, Y., Yang, L., Popov, Y. V., Choi, S. S., Witek, R. P., Alpini, G. D., Venter, J., VanDongen, H. M. A., et al. (2008) · Journal of Clinical Investigation · doi:10.1172/jci35875 · Cited by 346

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

Ouyang, Z., Zhou, Q., & Wong, W. H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904863106 · Cited by 334

Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity

Ewald, C. Y., Landis, J. N., Abate, J. P., Murphy, C. T., & Blackwell, T. K. (2014) · Nature · doi:10.1038/nature14021 · Cited by 331

TERT Promotes Epithelial Proliferation through Transcriptional Control of a Myc- and Wnt-Related Developmental Program

Choi, J., Southworth, L. K., Sarin, K. Y., Venteicher, A. S., Ma, W., Chang, W., Cheung, P., Jun, S., Artandi, M. K., Shah, N., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.0040010 · Cited by 336

Aspartate-glutamate-alanine-histidine box motif (DEAH)/RNA helicase A helicases sense microbial DNA in human plasmacytoid dendritic cells

Kim, T., Pazhoor, S., Bao, M., Zhang, Z., Hanabuchi, S., Facchinetti, V., Bover, L. C., Plumas, J., Chaperot, L., Qin, J., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006539107 · Cited by 332

Rational drug design

Mandal, S., Moudgil, M., & Mandal, S. K. (2009) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2009.06.065 · Cited by 337

Automated Network Analysis Identifies Core Pathways in Glioblastoma

Cerami, E. G., Demir, E., Schultz, N. D., Taylor, B. S., & Sander, C. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008918 · Cited by 331

Restriction of Receptor Movement Alters Cellular Response: Physical Force Sensing by EphA2

Salaita, K. S., Nair, P. M., Petit, R. S., Neve, R. M., Das, D., Gray, J. W., & Groves, J. T. (2010) · Science · doi:10.1126/science.1181729 · Cited by 331

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

Kutter, C., Watt, S., Stefflova, K., Wilson, M. D., Gonçalves, Â., Ponting, C. P., Odom, D. T., & Marques, A. C. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002841 · Cited by 335

Dysregulation of miRNA 181b in the temporal cortex in schizophrenia

Beveridge, N. J., Tooney, P. A., Carroll, A. P., Gardiner, E. J., Bowden, N. A., Scott, R. J., Tran, N., Dedova, I. V., & Cairns, M. J. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn005 · Cited by 337

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

Elango, N., Hunt, B. G., Goodisman, M. A. D., & Yi, S. V. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900301106 · Cited by 329

Correction of Sickle Cell Disease in Adult Mice by Interference with Fetal Hemoglobin Silencing

Xu, J., Peng, C., Sankaran, V. G., Shao, Z., Esrick, E. B., Chong, B. G., Ippolito, G. C., Fujiwara, Y., Ebert, B. L., Tucker, P. W., et al. (2011) · Science · doi:10.1126/science.1211053 · Cited by 326

Weighted Network Analysis

Horvath, S. (2011) · Springer eBooks · doi:10.1007/978-1-4419-8819-5 · Cited by 320

Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury

Scotton, C. J., Krupiczojc, M. A., Königshoff, M., Mercer, P. F., Lee, G., Kaminski, N., Morser, J., Post, J. M., Maher, T. M., Nicholson, A. G., et al. (2009) · Journal of Clinical Investigation · doi:10.1172/jci33288 · Cited by 318

Mesenchymal Stem Cells from Human Umbilical Cord Express Preferentially Secreted Factors Related to Neuroprotection, Neurogenesis, and Angiogenesis

Hsieh, J.-Y., Wang, H., Chang, S., Liao, K., Lee, I., Lin, W., Wu, C., Lin, W., & Cheng, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072604 · Cited by 324

An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis

Moore, M. J., Wang, Q., Kennedy, C. J., & Silver, P. A. (2010) · Cell · doi:10.1016/j.cell.2010.07.019 · Cited by 323

Suz12 binds to silenced regions of the genome in a cell-type-specific mannerPreprint

Squazzo, S. L., O’Geen, H., Komashko, V., Krig, S. R., Jin, V. X., Jang, S.-W., Margueron, R., Reinberg, D., Green, R., & Farnham, P. (2006) · Genome Research · doi:10.1101/gr.5306606 · Cited by 324

Genetic Control of Human Brain Transcript Expression in Alzheimer Disease

Webster, J. A., Gibbs, J. R., Clarke, J., Ray, M., Zhang, W., Holmans, P., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., et al. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.03.011 · Cited by 304

Histone deacetylase 3 is an epigenomic brake in macrophage alternative activation

Mullican, S. E., Gaddis, C. A., Alenghat, T., Nair, M. G., Giacomin, P. R., Everett, L. J., Feng, D., Steger, D. J., Schug, J., Artis, D., et al. (2011) · Genes & Development · doi:10.1101/gad.175950.111 · Cited by 314

Meta-Analysis and Meta-Review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers

Griffith, O. L., Melck, A. L., Jones, S. J. M., & Wiseman, S. M. (2006) · Journal of Clinical Oncology · doi:10.1200/jco.2006.06.7330 · Cited by 314

Sequentially acting Sox transcription factors in neural lineage developmentPreprint

Bergsland, M., Ramsköld, D., Zaouter, C., Klum, S., Sandberg, R., & Muhr, J. (2011) · Genes & Development · doi:10.1101/gad.176008.111 · Cited by 314

The Molecular Basis of Shoot Responses of Maize Seedlings to Trichoderma harzianum T22 Inoculation of the Root: A Proteomic Approach

Shoresh, M., & Harman, G. E. (2008) · PLANT PHYSIOLOGY · doi:10.1104/pp.108.123810 · Cited by 311

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

Clark, M. J., Homer, N., O’Connor, B. D., Chen, Z., Eskin, A., Lee, H., Merriman, B., & Nelson, S. F. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000832 · Cited by 321

Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency

Hurst, C. D., Alder, O., Platt, F. M., Droop, A., Stead, L. F., Burns, J. E., Burghel, G. J., Jain, S., Klimczak, L. J., Lindsay, H. A., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.08.005 · Cited by 307

The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expressionPreprint

Sadasivam, S., Duan, S., & DeCaprio, J. A. (2012) · Genes & Development · doi:10.1101/gad.181933.111 · Cited by 323

Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy

Muchir, A., Pavlidis, P., Decostre, V., Herron, A. J., Arimura, T., Bonne, G., & Worman, H. J. (2007) · Journal of Clinical Investigation · doi:10.1172/jci29042 · Cited by 310

Involvement of mast cells in eosinophilic esophagitis

Abonia, J. P., Blanchard, C., Buckmeier, B. K., Rainey, H. F., Collins, M. H., Stringer, K. F., Putnam, P. E., & Rothenberg, M. E. (2010) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2010.04.009 · Cited by 310

Next-generation tag sequencing for cancer gene expression profilingPreprint

Morrissy, A. S., Morin, R. D., Delaney, A. D., Zeng, T., McDonald, H., Jones, S. J. M., Zhao, Y., Hirst, M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.094482.109 · Cited by 309

Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration

Monaghan, J. R., EPP, L. G., Putta, S., Page, R. B., Walker, J. A., Beachy, C. K., Zhu, W. Z., Pao, G. M., Verma, I. M., Hunter, T. R., et al. (2009) · BMC Biology · doi:10.1186/1741-7007-7-1 · Cited by 309

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

Yu, M., Riva, L., Xie, H., Schindler, Y. L., Moran, T. B., Cheng, Y., Yu, D., Hardison, R. C., Weiss, M. J., Orkin, S. H., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.002 · Cited by 308

Cumulus and granulosa cell markers of oocyte and embryo quality

Uyar, A., Torrealday, S., & Seli, E. U. (2013) · Fertility and Sterility · doi:10.1016/j.fertnstert.2013.01.129 · Cited by 317

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

Young, M. D., Willson, T. A., Wakefield, M. J., Trounson, E., Hilton, D. J., Blewitt, M. E., Oshlack, A., & Majewski, I. J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr416 · Cited by 312

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

Iurlaro, M., Ficz, G., Oxley, D., Raiber, E., Bachman, M., Booth, M. J., Andrews, S., Balasubramanian, S., & Reik, W. (2013) · Genome biology · doi:10.1186/gb-2013-14-10-r119 · Cited by 321

EnrichNet: network-based gene set enrichment analysis

Glaab, E., Baudot, A., Krasnogor, N., Schneider, R., & Valencia, A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts389 · Cited by 311

Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer

Jazdzewski, K., Liyanarachchi, S., Swierniak, M., Pachucki, J., Ringel, M. D., Jarzab, B., & de la Chapelle, A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812591106 · Cited by 304

Identification of pediatric septic shock subclasses based on genome-wide expression profiling

Wong, H. R., Cvijanovich, N. Z., Lin, R., Allen, G. L., Thomas, N. J., Willson, D. F., Freishtat, R. J., ANAS, N. G., Meyer, K., Checchia, P. A., et al. (2009) · BMC Medicine · doi:10.1186/1741-7015-7-34 · Cited by 309

Human gene expression profiles of susceptibility and resistance in tuberculosis

Maertzdorf, J., Repsilber, D., Parida, S. K., Stanley, K., Roberts, T., Black, G. F., Walzl, G., & Kaufmann, S. H. E. (2010) · Genes and Immunity · doi:10.1038/gene.2010.51 · Cited by 304

A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogasteradults

Parisi, M. J., Nuttall, R., Edwards, P., Minor, J. M., Naiman, D. Q., Lü, J., Doctolero, M. H., Vainer, M., Cathy, C., Malley, J. D., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-6-r40 · Cited by 301

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R., & Zhang, M. Q. (2008) · Genes & Development · doi:10.1101/gad.1703108 · Cited by 300

Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development

Vassena, R., Boué, S., González‐Roca, E., Arán, B., Auer, H., Veiga, A., & Belmonte, J. C. I. (2011) · Development · doi:10.1242/dev.064741 · Cited by 312

Population-Based Resequencing of Experimentally Evolved Populations Reveals the Genetic Basis of Body Size Variation in Drosophila melanogaster

Turner, T. L., Stewart, A. D., Fields, A. T., Rice, W. R., & Tarone, A. M. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001336 · Cited by 297

A Comparison of Whole Genome Gene Expression Profiles of HepaRG Cells and HepG2 Cells to Primary Human Hepatocytes and Human Liver Tissues

Hart, S. N., Li, Y., Nakamoto, K., Subileau, E.-A., Steen, D., & Zhong, X.-B. (2010) · Drug Metabolism and Disposition · doi:10.1124/dmd.109.031831 · Cited by 298

Dysregulated gene expression networks in human acute myelogenous leukemia stem cells

Majeti, R., Becker, M. W., Tian, Q., Lee, T.-L. M., Yan, X., Liu, R., Chiang, J.-H., Hood, L., Clarke, M. F., & Weissman, I. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900089106 · Cited by 281

Coordinate Interaction between IL-13 and Epithelial Differentiation Cluster Genes in Eosinophilic Esophagitis

Blanchard, C., Stucke, E. M., Burwinkel, K., Caldwell, J. M., Collins, M. H., Ahrens, A., Buckmeier, B. K., Jameson, S. C., Greenberg, A. B., Kaul, A., et al. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.0903069 · Cited by 297

SNAIL Regulates Interleukin-8 Expression, Stem Cell–Like Activity, and Tumorigenicity of Human Colorectal Carcinoma Cells

Hwang, W., Yang, M., Tsai, M., Lan, H., Su, S., Chang, S., Teng, H., Yang, S., Lan, Y., Chiou, S., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.04.008 · Cited by 300

Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces

Mulder, I. E., Schmidt, B., Stokes, C., Lewis, M. C., Bailey, M., Aminov, R. I., Prosser, J. I., Gill, B. P., Pluske, J. R., Mayer, C., et al. (2009) · BMC Biology · doi:10.1186/1741-7007-7-79 · Cited by 311

The MYCN oncogene is a direct target of miR-34a

Wei, J. S., Song, Y., Durinck, S., Chen, Q.-R., Cheuk, A., Tsang, P., Zhang, Q., Thiele, C. J., Slack, A., Shohet, J. M., et al. (2008) · Oncogene · doi:10.1038/onc.2008.154 · Cited by 299

microRNAs in Early Diabetic Retinopathy in Streptozotocin-Induced Diabetic Rats

Kovacs, B., Lumayag, S., Cowan, C. E., & Xu, S. (2011) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.10-6879 · Cited by 293

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease

Twine, N. A., Janitz, K., Wilkins, M. R., & Janitz, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016266 · Cited by 309

Identification and Initial Functional Characterization of a Human Vascular Cell–Enriched Long Noncoding RNA

Bell, R. D., Long, X., Lin, M., Bergmann, J. H., Nanda, V., Cowan, S. L., Zhou, Q., Han, Y., Spector, D. L., Zheng, D., et al. (2014) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.114.303240 · Cited by 294

Genomic Profiling of MicroRNAs and Messenger RNAs Reveals Hormonal Regulation in MicroRNA Expression in Human Endometrium1

Kuokkanen, S., Chen, B., Ojalvo, L., Benard, L., Santoro, N., & Pollard, J. W. (2010) · Biology of Reproduction · doi:10.1095/biolreprod.109.081059 · Cited by 288

Proline: The Distribution, Frequency, Positioning, and Common Functional Roles of Proline and Polyproline Sequences in the Human Proteome

Morgan, A. A., & Rubenstein, E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053785 · Cited by 281

Gene expression profiling reveals novel biomarkers in nonsmall cell lung cancer

Sánchez‐Palencia, A., Gómez‐Morales, M., Gómez‐Capilla, J. A., Pedraza, V., Boyero, L., Rosell, R., & Fárez‐Vidal, M. E. (2010) · International Journal of Cancer · doi:10.1002/ijc.25704 · Cited by 287

Modified titanium surfaces promote accelerated osteogenic differentiation of mesenchymal stromal cells in vitro

Wall, I. B., Donos, N., Carlqvist, K., Jones, F. H., & Brett, P. (2009) · Bone · doi:10.1016/j.bone.2009.03.662 · Cited by 287

Target RNA motif and target mRNAs of the Quaking STAR protein

Galarneau, A., & Richard, S. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb963 · Cited by 285

TGF-β and Insulin Signaling Regulate Reproductive Aging via Oocyte and Germline Quality Maintenance

Luo, S., Kleemann, G. A., Ashraf, J. M., Shaw, W. M., & Murphy, C. T. (2010) · Cell · doi:10.1016/j.cell.2010.09.013 · Cited by 286

Identification of the Transcriptional Targets of FOXP2, a Gene Linked to Speech and Language, in Developing Human Brain

Spiteri, E., Konopka, G., Coppola, G., Bomar, J. M., Oldham, M. C., Ou, J., Vernes, S. C., Fisher, S. E., Ren, B., & Geschwind, D. H. (2007) · The American Journal of Human Genetics · doi:10.1086/522237 · Cited by 288

Reciprocal Regulation between the Circadian Clock and Hypoxia Signaling at the Genome Level in Mammals

Wu, Y., Tang, D., Liu, N., Xiong, W., Huang, H., Li, Y., Ma, Z., Zhao, H., Chen, P., Qi, X., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.09.009 · Cited by 284

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