Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,082

DAVID: Database for Annotation, Visualization, and Integrated Discovery

Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.-H., Pagès, F., Trajanoski, Z., & Galon, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp101 · Cited by 6,280

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

Maere, S., Heymans, K., & Kuiper, M. T. R. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti551 · Cited by 4,093

On the Interpretation of χ 2 from Contingency Tables, and the Calculation of P

Fisher, R. A. (1922) · Journal Of The Royal Statistical Society · doi:10.2307/2340521 · Cited by 2,975

Drosophila immune priming to Enterococcus faecalis relies on immune tolerance rather than resistance

Cabrera, K., Hoard, D. S., Gibson, O., Martinez, D. I., & Wunderlich, Z. (2023) · PLoS Pathogens · doi:10.1371/journal.ppat.1011567 · Cited by 27

Multiomics analyses reveal dynamic bioenergetic pathways and functional remodeling of the heart during intermittent fasting

Arumugam, T. V., Shaik, A. A., Liehn, E. A., Selvaraji, S., Poh, L., Rajeev, V., Cho, Y., Cho, Y. E., Kim, J.-H., Kim, J., et al. (2023) · eLife · doi:10.7554/elife.89214 · Cited by 27

Oxidized Low-Density Lipoprotein Accumulation Suppresses Glycolysis and Attenuates the Macrophage Inflammatory Response by Diverting Transcription from the HIF-1α to the Nrf2 Pathway

Ting, K. K. Y., Yu, P., Dow, R., Floro, E. J., Ibrahim, H. M., Scipione, C. A., Hyduk, S. J., Polenz, C. K., Zaslaver, O., Karmaus, P. W. F., et al. (2023) · The Journal of Immunology · doi:10.4049/jimmunol.2300293 · Cited by 27

Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis

Kamdar, S. N., Ho, L., Kron, K. J., Isserlin, R., van der Kwast, T., Zlotta, A. R., Fleshner, N. E., Bader, G. D., & Bapat, B. V. (2016) · Clinical Epigenetics · doi:10.1186/s13148-016-0195-4 · Cited by 27

miR-508 Defines the Stem-like/Mesenchymal Subtype in Colorectal Cancer

Yan, T., Ren, L., Shen, C., Wang, Z., Yu, Y., Liang, Q., Tang, J., Chen, Y., Sun, D., Zgodziński, W., et al. (2018) · Cancer Research · doi:10.1158/0008-5472.can-17-2101 · Cited by 27

Phototransduction and circadian entrainment are the key pathways in the signaling mechanism for the baculovirus induced tree-top disease in the lepidopteran larvae

Bhattarai, U. R., Li, F., Bhattarai, M. K., Masoudi, A., & Wang, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-35885-4 · Cited by 27

Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model

Liu, L. Y., Ma, X., Ouyang, B., Ings, D. P., Marwah, S., Liu, J., Chen, A. Y., Gupta, R., Manuel, J., Chen, X., et al. (2020) · ACS Nano · doi:10.1021/acsnano.0c00468 · Cited by 27

Transcriptional Analysis of Liver Tissue Identifies Distinct Phenotypes of Indeterminate Pediatric Acute Liver Failure

Chapin, C. A., Taylor, S. A., Malladi, P., Neighbors, K., Melín‐Aldana, H., Kreiger, P. A., Bowsher, N., Schipma, M. J., Loomes, K. M., Behrens, E. M., et al. (2021) · Hepatology Communications · doi:10.1002/hep4.1726 · Cited by 27

Examination of Epigenetic and other Molecular Factors Associated with mda-9/Syntenin Dysregulation in Cancer Through Integrated Analyses of Public Genomic Datasets

Bacolod, M. D., Das, S. K., Sokhi, U. K., Bradley, S., Fenstermacher, D., Pellecchia, M., Emdad, L., Sarkar, D., & Fisher, P. B. (2015) · Advances in cancer research · doi:10.1016/bs.acr.2015.04.006 · Cited by 27

GRK6 regulates ROS response and maintains hematopoietic stem cell self-renewal

Le, Q., Yao, W., Chen, Y., Yan, B., Cao, L., Yuan, M., Zhou, Y., & Ma, L. (2016) · Cell Death and Disease · doi:10.1038/cddis.2016.377 · Cited by 27

Age-associated microglial transcriptome leads to diminished immunogenicity and dysregulation of MCT4 and P2RY12/P2RY13 related functions

Škandík, M., Frieß, L., Vázquez-Cabrera, G., Keane, L., Grabert, K., Santos, M. C. D. L., Posada-Pérez, M., Balevičiūtė, A., Cheray, M., & Joseph, B. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02295-1 · Cited by 26

Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer’s disease

Cai, Y., Kanyo, J. E., Wilson, R. S., Bathla, S., Cardozo, P. L., Тонг, Л., Qin, S., Fuentes, L. A., Pinheiro‐de‐Sousa, I., Huynh, T., et al. (2025) · Nature Aging · doi:10.1038/s43587-025-00823-3 · Cited by 27

An eight-long non-coding RNA signature as a candidate prognostic biomarker for lung cancer

Tu, Z., He, D., Deng, X., Xiong, M., Huang, X., Li, X., Hao, L., Ding, Q., & Zhang, Q. (2016) · Oncology Reports · doi:10.3892/or.2016.4817 · Cited by 26

Identification of lncRNA functions in lung cancer based on associated protein-protein interaction modules

Wu, C.-H., Hsu, C., Lu, P.-C., Lin, W., Juan, H., & Huang, H. (2016) · Scientific Reports · doi:10.1038/srep35939 · Cited by 26

Combined Therapy Sensitivity Index Based on a 13-Gene Signature Predicts Prognosis for IDH Wild-type and MGMT Promoter Unmethylated Glioblastoma Patients

Ye, N., Jiang, N., Feng, C.-Y., Wang, F., Zhang, H., Bai, H. X., Yang, L., Su, Y., Huang, C., Wanggou, S., et al. (2019) · Journal of Cancer · doi:10.7150/jca.30614 · Cited by 26

EBF1 Gene mRNA Levels in Maternal Blood and Spontaneous Preterm Birth

Zhou, G., Holzman, C., Heng, Y. J., Kibschull, M., Lye, S. J., & Vazquez, A. I. (2020) · Reproductive Sciences · doi:10.1007/s43032-019-00027-2 · Cited by 27

Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities

Idicula‐Thomas, S., Gawde, U., Bhaye, S., Pokar, K., & Bader, G. D. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.06.023 · Cited by 27

The Role of Autophagy and lncRNAs in the Maintenance of Cancer Stem Cells

Jahangiri, L., Ishola, T., Pucci, P., Trigg, R. M., Pereira, J. D., Williams, J. A., Cavanagh, M. L., Gkoutos, G. V., Tsaprouni, L., & Turner, S. D. (2021) · Cancers · doi:10.3390/cancers13061239 · Cited by 26

FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers

Zhao, L., Xing, P., Polavarapu, V. K., Zhao, M., Valero-Martínez, B., Dang, Y., Maturi, N., Mathot, L., Neves, I., Yildirim, I., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab813 · Cited by 26

Regulated splicing of large exons is linked to phase‐separation of vertebrate transcription factors

Kawachi, T., Masuda, A., Yamashita, Y., Takeda, J., Ohkawara, B., Ito, M., & Ohno, K. (2021) · The EMBO Journal · doi:10.15252/embj.2020107485 · Cited by 28

Skeletal dysplasia-causing TRPV4 mutations suppress the hypertrophic differentiation of human iPSC-derived chondrocytes

Dicks, A. R., Maksaev, G. I., Harissa, Z., Savadipour, A., Tang, R., Steward, N. S., Liedtke, W., Nichols, C. G., Wu, C., & Guilak, F. (2023) · eLife · doi:10.7554/elife.71154 · Cited by 26

Selective inhibition of HDAC6 promotes bladder cancer radiosensitization and mitigates the radiation-induced CXCL1 signalling

Tsai, Y., Wang, T.-Y., Hsu, C., Lin, W., Chen, J.-Y., Li, J.-H., Pu, Y., Cheng, A., Cheng, J. C., & Su, S. (2023) · British Journal of Cancer · doi:10.1038/s41416-023-02195-0 · Cited by 26

Positive and Relaxed Selective Pressures Have Both Strongly Influenced the Evolution of Cryonotothenioid Fishes during Their Radiation in the Freezing Southern Ocean

Bilyk, K. T., Zhuang, X., & Papetti, C. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad049 · Cited by 26

Single-cell transcriptomic analysis of the identity and function of fibro/adipogenic progenitors in healthy and dystrophic muscle

Uapinyoying, P., Hogarth, M. W., Battacharya, S., Mázala, D. A. G., Panchapakesan, K., Bönnemann, C. G., & Jaiswal, J. K. (2023) · iScience · doi:10.1016/j.isci.2023.107479 · Cited by 26

Potential tumorigenic programs associated with TP53 mutation status reveal role of VEGF pathway

Joshi, H. N., Bhanot, G., Børresen-Dale, A.-L., & Kristensen, V. N. (2012) · British Journal of Cancer · doi:10.1038/bjc.2012.461 · Cited by 26

Metabolomic profiling in liver of adiponectin-knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action

Liu, Y., Sen, S. R., Wannaiampikul, S., Palanivel, R., Hoo, R. L. C., Isserlin, R., Bader, G. D., Tungtrongchitr, R., Deshaies, Y., Xu, A., et al. (2015) · Biochemical Journal · doi:10.1042/bj20141455 · Cited by 26

Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue’s extracellular milieu precede immune responses in Sjögren’s syndrome

Delaleu, N., Nguyen, C. Q., Tekle, K., Jonsson, R., & Peck, A. B. (2013) · Arthritis Research & Therapy · doi:10.1186/ar4362 · Cited by 26

Screening of potentially crucial genes and regulatory factors involved in epithelial ovarian cancer using microarray analysis

Shi, C., & Zhang, Z. (2017) · Oncology Letters · doi:10.3892/ol.2017.6183 · Cited by 26

Postnatal Tshz3 Deletion Drives Altered Corticostriatal Function and Autism Spectrum Disorder–like Behavior

Chabbert, D., Caubit, X., Roubertoux, P. L., Carlier, M., Habermann, B. H., Jacq, B., Salin, P., Metwaly, M., Frahm, C., Fatmi, A., et al. (2019) · Biological Psychiatry · doi:10.1016/j.biopsych.2019.03.974 · Cited by 27

Functionally significant metabolic differences between B and T lymphocyte lineages

Khalsa, J. K., Chawla, A. S., Prabhu, S. B., Vats, M., Dhar, A., Dev, G., Das, N., Mukherjee, S., Tanwar, S., Banerjee, H., et al. (2019) · Immunology · doi:10.1111/imm.13098 · Cited by 26

Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation

Schneider, K., Nelson, G. M., Watson, J. L., Morf, J., Dalglish, M. M., Luh, L. M., Weber, A., & Bertolotti, A. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108154 · Cited by 29

Maternal obesity persistently alters cardiac progenitor gene expression and programs adult-onset heart disease susceptibility

Ahmed, A., Liang, M., Chi, L., Zhou, Y., Sled, J. G., Wilson, M. D., & Delgado-Olguı́n, P. (2020) · Molecular Metabolism · doi:10.1016/j.molmet.2020.101116 · Cited by 26

Systems pharmacology dissection of Epimedium targeting tumor microenvironment to enhance cytotoxic T lymphocyte responses in lung cancer

Huang, C., Li, Z., Zhu, J., Chen, X., Hao, Y., Yang, R., Huang, R., Zhou, J., Wang, Z., Xiao, W., et al. (2021) · Aging · doi:10.18632/aging.202410 · Cited by 26

Distinct physiological, plasma amino acid, and liver transcriptome responses to purified dietary beef, chicken, fish, and pork proteins in young rats

Song, S., Hooiveld, G. J. E. J., Li, M., Zhao, F., Zhang, W., Xu, X., Müller, M. M., Li, C., & Zhou, G. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500789 · Cited by 26

Deep profiling of gene expression across 18 human cancers

Qiu, W., Dincer, A. B., Janizek, J. D., Çelik, S., Pittet, M. J., Naxerova, K., & Lee, S. (2024) · Nature Biomedical Engineering · doi:10.1038/s41551-024-01290-8 · Cited by 25

Dominant-negative Ikaros cooperates with BCR-ABL1 to induce human acute myeloid leukemia in xenografts

Theocharides, A. P. A., Dobson, S. M., Laurenti, E., Notta, F., Voisin, V., Cheng, P.-Y., Yuan, J. S., Guidos, C. J., Minden, M. D., Mullighan, C. G., et al. (2014) · Leukemia · doi:10.1038/leu.2014.150 · Cited by 25

Identification of long non-coding RNAs biomarkers for early diagnosis of myocardial infarction from the dysregulated coding-non-coding co-expression network

Sun, C., Jiang, H., Sun, Z., Gui, Y., & Xia, H. (2016) · Oncotarget · doi:10.18632/oncotarget.11999 · Cited by 25

Integrated analysis of miRNA and mRNA expression data identifies multiple miRNAs regulatory networks for the tumorigenesis of colorectal cancer

Xu, P., Wang, J., Sun, B., & Xiao, Z. (2018) · Gene · doi:10.1016/j.gene.2018.03.050 · Cited by 25

IGFBP7 Drives Resistance to Epidermal Growth Factor Receptor Tyrosine Kinase Inhibition in Lung Cancer

Wu, S., Chang, T., Tsai, M., Liu, Y., Hsu, C., Chang, Y., Yu, C., & Shih, J. (2019) · Cancers · doi:10.3390/cancers11010036 · Cited by 25

GeneSetCluster: a tool for summarizing and integrating gene-set analysis results

Ewing, E., Planell, N., Jagodic, M., & Gómez-Cabrero, D. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03784-z · Cited by 25

Peritoneal Dialysis Fluid Supplementation with Alanyl-Glutamine Attenuates Conventional Dialysis Fluid-Mediated Endothelial Cell Injury by Restoring Perturbed Cytoprotective Responses

Herzog, R., Bartosova, M., Tarantino, S., Wagner, A., Unterwurzacher, M., Sacnun, J. M., Lichtenauer, A. M., Kuster, L., Schaefer, B., Alper, S. L., et al. (2020) · Biomolecules · doi:10.3390/biom10121678 · Cited by 26

Revealing NOTCH-dependencies in synaptic targets associated with Alzheimer's disease

Perna, A., Marathe, S. V., Dreos, R., Falquet, L., Akarsu, H., & Auber, L. A. (2021) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2021.103657 · Cited by 25

The Spleen as a Target to Characterize Immunomodulatory Effects of Down-Stream Processed Cyberlindnera jadinii Yeasts in Atlantic Salmon Exposed to a Dietary Soybean Meal Challenge

Lange, B. M., Agboola, J. O., Hansen, J. Ø., Lagos, L. X., Øyås, O., Mercado, L. A., Mydland, L. T., & Øverland, M. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.708747 · Cited by 25

Aberrantly reduced expression of miR-342-5p contributes to CCND1-associated chronic myeloid leukemia progression and imatinib resistance

Wu, Y., Lai, H.-F., Huang, T., Chen, Y., Ye, R., Chang, P., Lai, S., Chen, Y., Lee, C., Liu, W.-N., et al. (2021) · Cell Death and Disease · doi:10.1038/s41419-021-04209-2 · Cited by 25

Prognostic Gene Expression-Based Signature in Clear-Cell Renal Cell Carcinoma

Roldán, F. L., Izquierdo, L., Ingelmo‐Torres, M., Lozano, J. J., Carrasco, R., Cuñado, A., Reig, Ò., Mengual, L., & Alcaraz, A. (2022) · Cancers · doi:10.3390/cancers14153754 · Cited by 25

Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells

Tsirigoti, C., Ali, M. M., Maturi, V., Heldin, C., & Moustakas, A. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-05280-z · Cited by 25

Human influenza virus infection elicits distinct patterns of monocyte and dendritic cell mobilization in blood and the nasopharynx

Vangeti, S., Falck‐Jones, S., Yu, M., Österberg, B., Liu, S., Asghar, M., Sondén, K., Paterson, C., Whitley, P., Albert, J., et al. (2023) · eLife · doi:10.7554/elife.77345 · Cited by 25

ANO6-mediated trogocytosis of cancer-associated fibroblasts promotes pancreatic cancer cell growth and immune suppression

Ogier, C., Mercy, C. S. A., Bondarenko, E., Wu, Z., Lu, Z., Bui, Q. T., Dhamdhere, M. R., Tang, Y., Recoules, L., Klochkova, A., et al. (2026) · Nature Cancer · doi:10.1101/2023.09.15.557802 · Cited by 25

Genes Required for Survival in Microgravity Revealed by Genome-Wide Yeast Deletion Collections Cultured during Spaceflight

Nislow, C., Lee, A. Y., Allen, P., Giaever, G. N., Smith, A., Gebbia, M., Stodieck, L., Hammond, J. S., Birdsall, H. H., & Hammond, T. G. (2015) · BioMed Research International · doi:10.1155/2015/976458 · Cited by 25

Antioxidant Treatment Promotes Prostate Epithelial Proliferation in Nkx3.1 Mutant Mice

Martinez, E. E., Anderson, P. D., Logan, M., & Abdulkadir, S. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046792 · Cited by 25

CTDP1 regulates breast cancer survival and DNA repair through BRCT-specific interactions with FANCI

Hu, W.-F., Krieger, K. L., Lagundžin, D., Li, X., Cheung, R. S., Taniguchi, T., Johnson, K. R., Bessho, T., Monteiro, Á. N. A., & Woods, N. T. (2019) · Cell Death Discovery · doi:10.1038/s41420-019-0185-3 · Cited by 26

Norrin mediates tumor-promoting and -suppressive effects in glioblastoma via Notch and Wnt

El‐Sehemy, A., Selvadurai, H. J., Ortín-Martínez, A., Pokrajac, N. T., Mamatjan, Y., Tachibana, N., Rowland, K., Lee, L., Park, N., Aldape, K., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci128994 · Cited by 25

Myeloid-specific IRE1alpha deletion reduces tumour development in a diabetic, non-alcoholic steatohepatitis-induced hepatocellular carcinoma mouse model.

Campenhout, S. V., Tilleman, L., Lefere, S., Vandierendonck, A., Raevens, S., Verhelst, X., Geerts, A., van Nieuwerburgh, F., van Vlierberghe, H., & Devisscher, L. (2020) · Metabolism: Clinical and Experimental · doi:10.1016/j.metabol.2020.154220 · Cited by 23

Digging deeper in the proteome of different regions from schizophrenia brains

Reis‐de‐Oliveira, G., Zuccoli, G. S., Fioramonte, M., Schimitt, A. C. B., Falkai, P., de Almeida, V., & Martins‐de‐Souza, D. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103814 · Cited by 25

Helveticoside is a biologically active component of the seed extract of Descurainia sophia and induces reciprocal gene regulation in A549 human lung cancer cells

Kim, B., Lee, J. H., & Kim, N. S. (2015) · BMC Genomics · doi:10.1186/s12864-015-1918-1 · Cited by 24

Gene Network and Proteomic Analyses of Cardiac Responses to Pathological and Physiological Stress

Drozdov, I. A., Didangelos, A., Yin, X., Zampetaki, A., Abonnenc, M., Murdoch, C. E., Zhang, M., Ouzounis, C., Mayr, M., Tsoka, S., et al. (2013) · Circulation Cardiovascular Genetics · doi:10.1161/circgenetics.113.000063 · Cited by 24

Characterization of inflammatory markers and transcriptome profiles of differentially activated embryonic stem cell‐derived microglia

Beins, E. C., Ulas, T., Ternes, S., Neumann, H., Schultze, J. L., & Zimmer, A. (2016) · Glia · doi:10.1002/glia.22979 · Cited by 25

Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules

Mosca, E., Bersanelli, M., Gnocchi, M., Moscatelli, M., Castellani, G., Milanesi, L., & Mezzelani, A. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00129 · Cited by 25

The retina/RPE proteome in chick myopia and hyperopia models: Commonalities with inherited and age-related ocular pathologies.

Riddell, N., Faou, P., Murphy, M., Giummarra, L., Downs, R. A., Rajapaksha, H., & Crewther, S. G. (2017) · PubMed Central · Cited by 24

Network-based modeling of drug effects on disease module in systemic sclerosis

Kim, K., Moon, S., Park, K., & Tagkopoulos, I. (2020) · Scientific Reports · doi:10.1038/s41598-020-70280-y · Cited by 24

Synergy between 15-lipoxygenase and secreted PLA 2 promotes inflammation by formation of TLR4 agonists from extracellular vesicles

Ha, V. T., Lainšček, D., Gesslbauer, B., Jovičić, E. J., Hyötyläinen, T., Ilc, N., Lakota, K., Tomšič, M., van de Loo, F. A. J., Bochkov, V. N., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2005111117 · Cited by 24

UBC9 coordinates inflammation affecting development of bladder cancer

Huang, X., Tao, Y., Gao, J., Zhou, X., Tang, S., Deng, C., Lai, Z., Lin, X., Wang, Q., & Li, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-77623-9 · Cited by 24

Fluvastatin mitigates SARS-CoV-2 infection in human lung cells

Belinchón, F. J. Z., Moeller, R. A., Laßwitz, L., van Ham, M., Becker, M., Brogden, G., Rosendal, E., Bi, W., Carriquí-Madroñal, B., Islam, K., et al. (2021) · iScience · doi:10.1016/j.isci.2021.103469 · Cited by 25

Phosphoproteomic profiling of influenza virus entry reveals infection-triggered filopodia induction counteracted by dynamic cortactin phosphorylation

Hunziker, A., Glas, I., Pohl, M. O., & Stertz, S. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110306 · Cited by 24

Proteomic and phosphoproteomic profiling in heart failure with preserved ejection fraction (HFpEF)

Valero‐Muñoz, M., Saw, E. L., Hekman, R. M., Blum, B. C., Hourani, Z., Granzier, H. L. M., Emili, A., & Sam, F. (2022) · Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.966968 · Cited by 27

The Rb/E2F axis is a key regulator of the molecular signatures instructing the quiescent and activated adult neural stem cell state

Fong, B. C., Chakroun, I., Iqbal, M. A., Paul, S., Bastasic, J., O’Neil, D., Yakubovich, E., Bejjani, A. T., Ahmadi, N., Carter, A., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111578 · Cited by 24

Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice

Wendorff, A. A., Quinn, S. A., Álvarez, S., Brown, J. A., Biswas, M., Gunning, T. S., Palomero, T., & Ferrando, A. A. (2022) · Nature Aging · doi:10.1038/s43587-022-00304-x · Cited by 24

Ectopic expression ofTAPETUM DETERMINANT1affects ovule development in Arabidopsis

Huang, J. Q., Wijeratne, A., Tang, C., Zhang, T., Fenelon, R. E., Owen, H. A., & Zhao, D. (2015) · Journal of Experimental Botany · doi:10.1093/jxb/erv523 · Cited by 24

Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress

Simoneau, A., Ricard, É., Weber, S., Hammond-Martel, I., Wong, L. H., Sellam, A., Giaever, G. N., Nislow, C., Raymond, M., & Würtele, H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1537 · Cited by 24

A short-term intervention with selenium affects expression of genes implicated in the epithelial-to-mesenchymal transition in the prostate

Kok, D. E. G., Kiemeney, L. A. L. M., Verhaegh, G. W. C. T., Schalken, J. A., van Lin, E. N. J. T., Sedelaar, J. P. M., Witjes, J. A., van de Kaa, C. A. H. ‐., Veer, P. V. ’., Kampman, E., et al. (2017) · Oncotarget · doi:10.18632/oncotarget.14551 · Cited by 24

Cholinergic neuron gene expression differences captured by translational profiling in a mouse model of Alzheimer's disease

McKeever, P. M., Kim, T. P., Hesketh, A. R., MacNair, L., Miletic, D., Favrin, G., Oliver, S. G., Zhang, Z., George‐Hyslop, P. S., & Robertson, J. (2017) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2017.05.014 · Cited by 27

Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription

Israel, J. W., Chappell, G. A., Simon, J. M., Pott, S., Safi, A., Lewis, L., Cotney, P. A., Boulos, H., Bodnar, W. M., Lieb, J. D., et al. (2018) · Mammalian Genome · doi:10.1007/s00335-018-9739-6 · Cited by 25

Deciphering the multicomponent synergy mechanism from a systems pharmacology perspective: Application to Gualou Xiebai Decoction for coronary heart disease

Yang, Y., Huang, C., Su, X., Zhu, J., Chen, X., Fu, Y., Wang, Z., Zhou, J., Xiao, W., Zheng, C., et al. (2018) · Journal of Functional Foods · doi:10.1016/j.jff.2018.02.030 · Cited by 24

AIF1L regulates actomyosin contractility and filopodial extensions in human podocytes

Yasuda‒Yamahara, M., Rogg, M., Yamahara, K., Maier, J. I., Huber, T. B., & Schell, C. (2018) · PLoS ONE · doi:10.1371/journal.pone.0200487 · Cited by 24

Integrated proteomic analysis of tumor necrosis factor α and interleukin 1β-induced endothelial inflammation

Béguin, E. P., van den Eshof, B. L., Hoogendijk, A. J., Nota, B., Mertens, K., Meijer, A. B., & van den Biggelaar, M. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.08.011 · Cited by 24

In vitro effects of boric acid on human liver hepatoma cell line (HepG2) at the half-maximal inhibitory concentration

Tombuloglu, A., Çöpoğlu, H., Son, Y. A., & Güray, T. (2020) · Journal of Trace Elements in Medicine and Biology · doi:10.1016/j.jtemb.2020.126573 · Cited by 24

Mechanistic insights on the mode of action of an antiproliferative thiosemicarbazone-nickel complex revealed by an integrated chemogenomic profiling study

Baruffini, E., Ruotolo, R., Bisceglie, F., Montalbano, S., Ottonello, S., Pelosi, G., Buschini, A., & Lodi, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-67439-y · Cited by 24

Motor neuron translatome reveals deregulation of SYNGR4 and PLEKHB1 in mutant TDP-43 amyotrophic lateral sclerosis models

Marques, R. F., Engler, J. B., Küchler, K., Jones, R. A., Lingner, T., Salinas, G., Gillingwater, T. H., Friese, M. A., & Duncan, K. E. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa140 · Cited by 24

The Na/K‐ATPase α1/Src interaction regulates metabolic reserve and Western diet intolerance

Kutz, L. C., Cui, X., Xie, J. X., Mukherji, S. T., Terrell, K. C., Huang, M., Wang, X., Wang, J., Martin, A. J., Pessoa, M. T., et al. (2021) · Acta Physiologica · doi:10.1111/apha.13652 · Cited by 24

Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation

Guo, H., Garcia‐Vedrenne, A. E., Isserlin, R., Lugowski, A., Morada, A. O., Sun, A., Miao, Y., Kuzmanov, U., Wan, C., Ma, H., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201500159 · Cited by 25

Therapeutic properties of Scutellaria baicalensis in db/db mice evaluated using Connectivity Map and network pharmacology

Kim, B., Song, K. H., Lim, C., & Cho, S. (2017) · Scientific Reports · doi:10.1038/srep41711 · Cited by 23

Optogenetic Stimulation of Prelimbic Pyramidal Neurons Maintains Fear Memories and Modulates Amygdala Pyramidal Neuron Transcriptome

Laricchiuta, D., Sciamanna, G., Gimenez, J., Termine, A., Fabrizio, C., Caioli, S., Balsamo, F., Panuccio, A., Bardi, M. D., Saba, L., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020810 · Cited by 20

Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance

Socodato, R., Almeida, T. O., Portugal, C. C., Santos, E. C. D. S., Tedim-Moreira, J., Galvão-Ferreira, J., Canedo, T., Baptista, F. I., Magalhães, A., Ambrósio, A. F., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113447 · Cited by 26

A large-scale proteomics resource of circulating extracellular vesicles for biomarker discovery in pancreatic cancer

Bockorny, B., Muthuswamy, L. B., Huang, L., Hadisurya, M., Lim, C. M., Tsai, L. L., Gill, R. R., Wei, J. L., Bullock, A. J., Grossman, J. E., et al. (2024) · eLife · doi:10.7554/elife.87369.3 · Cited by 23

Inbreeding Affects Gene Expression Differently in Two Self-IncompatibleArabidopsis lyrataPopulations with Similar Levels of Inbreeding Depression

Menzel, M., Sletvold, N., Ågren, J., & Hansson, B. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv086 · Cited by 23

Regulation of CD 4 T cells and their effects on immunopathological inflammation following viral infection

Bhattacharyya, M., Madden, P. J., Henning, N. F. C., Gregory, S., Aïd, M., Martinot, A. J., Barouch, D. H., & Penaloza‐MacMaster, P. (2017) · Immunology · doi:10.1111/imm.12771 · Cited by 23

In vivo effects of dexamethasone on blood gene expression in ataxia telangiectasia

Menotta, M., Biagiotti, S., Orazi, S., Rossi, L., Chessa, L., Leuzzi, V., D’Agnano, D., Plebani, A., Soresina, A., & Magnani, M. (2017) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-017-3122-x · Cited by 23

Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq

Krivoshiev, B. V., Beemster, G. T. S., Sprangers, K., Cuypers, B., Laukens, K., Blust, R., & Husson, S. J. (2017) · Toxicology in Vitro · doi:10.1016/j.tiv.2017.10.011 · Cited by 23

Antiproliferative Effects of the Natural Oxadiazine Nocuolin A Are Associated With Impairment of Mitochondrial Oxidative Phosphorylation

Sousa, M. L., Preto, M., Vasconcelos, V. M., Linder, S. T., & Urbatzka, R. (2019) · Frontiers in Oncology · doi:10.3389/fonc.2019.00224 · Cited by 23

Identification of key transcription factors associated with cerebral ischemia‑reperfusion injury based on gene‑set enrichment analysis

Zhang, Y., Wang, K., Liu, Y.-E., Wang, W., Liu, A., Zhou, J., Li, C., Zhang, Y., Zhang, A., Lv, J., et al. (2019) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2019.4159 · Cited by 23

Lichenoid dysplasia is not a distinct pathological entity

Farah, C. S., Fox, S. A., Shearston, K., Newman, L., Babic, S., & Vacher, M. A. (2021) · Oral Oncology · doi:10.1016/j.oraloncology.2021.105362 · Cited by 23

Isoflavones in soy flour diet have different effects on whole‐genome expression patterns than purified isoflavone mix in human MCF‐7 breast tumors in ovariectomized athymic nude mice

Liu, Y., Hilakivi‐Clarke, L., Zhang, Y., Wang, X., Pan, Y., Xuan, J., Fleck, S. C., Doerge, D. R., & Helferich, W. G. (2015) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500028 · Cited by 24

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer typesPreprint

PCAWG Transcriptome Core Group, Calabrese, C., Davidson, N. R., Fonseca, N. A., He, Y., Kahles, A., Lehmann, K.-V., Liu, F., Shiraishi, Y., Soulette, C. M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/183889 · Cited by 25

LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer

Murray, C. W., Brady, J. J., Han, M., Cai, H., Tsai, M. K., Pierce, S. E., Cheng, R., Demeter, J., Feldser, D. M., Jackson, P. K., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28619-8 · Cited by 22

The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation

Xiao-xi, X., Ma, Y., Xu, Y., Ogbuehi, A. C., Liu, X., Deng, Y., Xi, J., Pan, H., Qian, L., Li, B., et al. (2021) · Disease Markers · doi:10.1155/2021/8831948 · Cited by 22

Transcriptional programming drives Ibrutinib-resistance evolution in mantle cell lymphoma

Zhao, X., Wang, M. Y., Jiang, H., Lwin, T., Park, P. M. C., Gao, J., Meads, M. B., Ren, Y., Li, T., Sun, J., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108870 · Cited by 22

Hepsin regulates TGFβ signaling via fibronectin proteolysis

Belitškin, D., Pant, S. M., Munne, P., Suleymanova, I., Belitškina, K., Hongisto, H., Englund, J. I., Raatikainen, T., Klezovitch, O., Vasioukhin, V. I., et al. (2021) · EMBO Reports · doi:10.15252/embr.202152532 · Cited by 22

Electrospun Scaffold Micro-Architecture Induces an Activated Transcriptional Phenotype within Tendon Fibroblasts

Baldwin, M. J., Mimpen, J. Y., Cribbs, A. P., Stace, E. T., Philpott, M., Dakin, S. G., Carr, A. J., & Snelling, S. J. B. (2022) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.795748 · Cited by 22

Improvement in heat stress-induced multiple organ dysfunction and intestinal damage through protection of intestinal goblet cells from prostaglandin E1 analogue misoprostol

Hii, H., Lo, W.-Z., Fu, Y.-H., Chen, M., Shih, C.-C., Tsao, C., Ka, S., Chiu, Y., Wu, C.-C., & Shih, C. (2022) · Life Sciences · doi:10.1016/j.lfs.2022.121039 · Cited by 22

Subgingival host–microbiome metatranscriptomic changes following scaling and root planing in grade II / III periodontitis

Duran-Pinedo, A. E., Solbiati, J., Teles, F., & Frias‐Lopez, J. (2022) · Journal Of Clinical Periodontology · doi:10.1111/jcpe.13737 · Cited by 22

Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map

Merico, D., Isserlin, R., & Bader, G. D. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-276-2_12 · Cited by 76

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis

Geistlinger, L., Csaba, G., & Zimmer, R. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0884-1 · Cited by 93

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

Constellation Map: Downstream visualization and interpretation of gene set enrichment results

Tan, Y. Q., Wu, F., Tamayo, P., Haining, W. N., & Mesirov, J. P. (2015) · F1000Research · doi:10.12688/f1000research.6644.1 · Cited by 4

GSPlot: Visualizing gene set similarity in enrichment resultsPreprint

Le, T. C., Espinoza, C. G., Courtois, J., & Babur, Ö. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.11.731691