The Variation of Transcriptomic Perturbations is Associated with the Development and Progression of Various Diseases
Open accessAbstract
Background. Although transcriptomic data have been widely applied to explore various diseases, few studies have investigated the association between transcriptomic perturbations and disease development in a wide variety of diseases. Methods. Based on a previously developed algorithm for quantifying intratumor heterogeneity at the transcriptomic level, we defined the variation of transcriptomic perturbations (VTP) of a disease relative to the health status. Based on publicly available transcriptome datasets, we compared VTP values between the disease and health status and analyzed correlations between VTP values and disease progression or severity in various diseases, including neurological disorders, infectious diseases, cardiovascular diseases, respiratory diseases, liver diseases, kidney diseases, digestive diseases, and endocrine diseases. We also identified the genes and pathways whose expression perturbations correlated positively with VTP across diverse diseases. Results. VTP values were upregulated in various diseases relative to their normal controls. VTP values were significantly greater in define than in possible or probable Alzheimer’s disease. VTP values were significantly larger in intensive care unit (ICU) COVID-19 patients than in non-ICU patients, and in COVID-19 patients requiring mechanical ventilatory support (MVS) than in those not requiring MVS. VTP correlated positively with viral loads in acquired immune deficiency syndrome (AIDS) patients. Moreover, the AIDS patients treated with abacavir or zidovudine had lower VTP values than those without such therapies. In pulmonary tuberculosis (TB) patients, VTP values followed the pattern: active TB > latent TB > normal controls. VTP values were greater in clinically apparent than in presymptomatic malaria. VTP correlated negatively with the cardiac index of left ventricular ejection fraction (LVEF). In chronic obstructive pulmonary disease (COPD), VTP showed a negative correlation with forced expiratory volume in the first second (FEV1). VTP values increased with H. pylori infection and were upregulated in atrophic gastritis caused by H. pylori infection. The genes and pathways whose expression perturbations correlated positively with VTP scores across diseases were mainly involved in the regulation of immune, metabolic, and cellular activities. Conclusions. VTP is upregulated in the disease versus health status, and its upregulation is associated with disease progression and severity in various diseases. Thus, VTP has potential clinical implications for disease diagnosis and prognosis.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Increased heterogeneity in Ts21 parallels observations in Alzheimer's disease, where transcriptomic variability scores correlate with clinical severity and neurofibrillary tangle burden.
“This increased heterogeneity in Ts21 parallels observations in Alzheimer's disease (AD), where transcriptomic variability scores correlate with clinical severity and neurofibrillary tangle burden (16).”
From Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex (2026) · cites this paper as [16]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
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 · see citing works
KEGG: new perspectives on genomes, pathways, diseases and drugs
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1092 · Cited by 8,865 · see citing works
López, J. A., González, H. M., & Léger, G. C. (2019) · Handbook of clinical neurology · doi:10.1016/b978-0-12-804766-8.00013-3 · Cited by 834 · see citing works
Large-Scale Multi-omic Analysis of COVID-19 Severity
Overmyer, K. A., Shishkova, E., Miller, I. J., Balnis, J., Bernstein, M. N., Peters-Clarke, T. M., Meyer, J. G., Quan, Q., Muehlbauer, L. K., Trujillo, E. A., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2020.10.003 · Cited by 584 · see citing works
Wang, M., Roussos, P., McKenzie, A., Zhou, X., Kajiwara, Y., Brennand, K. J., De Luca, G. C., Crary, J. F., Casaccia, P., Buxbaum, J. D., et al. (2016) · Genome Medicine · doi:10.1186/s13073-016-0355-3 · Cited by 314 · see citing works
Arijs, I., Hertogh, G. D., Lemaire, K., Quintens, R., Lommel, L. V., Steen, K. V., Leemans, P., Cleynen, I., Assche, G. V., Vermeire, S., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007984 · Cited by 304 · see citing works
Mas, V. R., Maluf, D. G., Archer, K. J., Yanek, K. C., Kong, X., Kulik, L., Freise, C. E., Olthoff, K. M., Ghobrial, R. M., McIver, P., et al. (2009) · Molecular Medicine · doi:10.2119/molmed.2008.00110 · Cited by 293 · see citing works
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age
Lieberman, N. A. P., Peddu, V., Xie, H. J., Shrestha, L., Huang, M.-L. W., Mears, M. C., Cajimat, M. N. B., Bente, D. A., Shi, P., Bovier, F. T., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000849 · Cited by 260 · see citing works
Transcriptional Genomics Associates FOX Transcription Factors With Human Heart Failure
Hannenhalli, S. S., Putt, M., Gilmore, J. M., Wang, J., Parmacek, M. S., Epstein, J. A., Morrisey, E. E., Margulies, K. B., & Cappola, T. P. (2006) · Circulation · doi:10.1161/circulationaha.106.632430 · Cited by 257 · see citing works
A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status
Sood, S., Gallagher, I. J., Lunnon, K., Rullman, E., Keohane, A., Crossland, H., Phillips, B. E., Cederholm, T., Jensen, T., van Loon, L. J. C., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0750-x · Cited by 240 · see citing works
Garcia, L. S. (2010) · Clinics in Laboratory Medicine · doi:10.1016/j.cll.2009.10.001 · Cited by 226 · see citing works
Gene Expression in Peripheral Blood Mononuclear Cells from Children with Diabetes
Kaizer, E., Glaser, C., Chaussabel, D., Banchereau, J., Pascual, V., & White, P. C. (2007) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2007-0979 · Cited by 219 · see citing works
Wang, S. M., Ooi, L. L., & Hui, K. M. (2007) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-06-2236 · Cited by 198 · see citing works
Metabolic pathways and immunometabolism in rare kidney diseases
Grayson, P. C., Eddy, S. F., Taroni, J., Lightfoot, Y. L., Mariani, L., Parikh, H. M., Lindenmeyer, M. T., Ju, W., Greene, C. S., Godfrey, B. A., et al. (2018) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2017-212935 · Cited by 190 · see citing works
Rotger, M., Dang, K. K., Fellay, J., Heinzen, E., Feng, S., Descombes, P., Shianna, K., Ge, D., Günthard, H., Goldstein, D., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000781 · Cited by 187 · see citing works
Arion, D., Corradi, J. P., Tang, S., Datta, D., Boothe, F., He, A., Cacace, A. M., Zaczek, R., Albright, C. F., Tseng, G., et al. (2015) · Molecular Psychiatry · doi:10.1038/mp.2014.171 · Cited by 177 · see citing works
Functional Correlations of Pathogenesis-Driven Gene Expression Signatures in Tuberculosis
Maertzdorf, J., Ota, M. O. C., Repsilber, D., Mollenkopf, H., Weiner, J. M., Hill, P. C., & Kaufmann, S. H. E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026938 · Cited by 166 · see citing works
Hypertension Is a Risk Factor for Several Types of Heart Disease: Review of Prospective Studies
Kokubo, Y., & Matsumoto, C. (2016) · Advances in experimental medicine and biology · doi:10.1007/5584_2016_99 · Cited by 153 · see citing works
Ockenhouse, C. F., Hu, W., Kester, K. E., Cummings, J. F., Stewart, A., Heppner, D. G., Jedlicka, A., Scott, A. L., WOLFE, N. D., Vahey, M., et al. (2006) · Infection and Immunity · doi:10.1128/iai.00408-06 · Cited by 145 · see citing works
de Jong, S., Boks, M. P., Fuller, T. F., Strengman, E., Janson, E., de Kovel, C. G. F., Ori, A. P. S., Vi, N., Mulder, F., Blom, J. D., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039498 · Cited by 143 · see citing works
Peripheral Blood Mononuclear Cell Gene Expression in Chronic Obstructive Pulmonary Disease
Bahr, T. M., Hughes, G. J., Armstrong, M., Reisdorph, R., Coldren, C. D., Edwards, M. G., Schnell, C., Kedl, R. M., LaFlamme, D. J., Reisdorph, N. A., et al. (2013) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2012-0230oc · Cited by 132 · see citing works
Transcriptomic analysis of probable asymptomatic and symptomatic alzheimer brains
Patel, H., Hodges, A., Curtis, C. J. C., Lee, S. H., Troakes, C., Dobson, R., & Newhouse, S. (2019) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2019.05.009 · Cited by 123 · see citing works
Arion, D., Huo, Z., Enwright, J. F., Corradi, J., Tseng, G. C., & Lewis, D. A. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2017.03.018 · Cited by 122 · see citing works
A Whole Blood Molecular Signature for Acute Myocardial Infarction
Muse, E. D., Kramer, E. R., Wang, H., Barrett, P. M., Parviz, F., Novotny, M. A., Lasken, R. S., Jatkoe, T. A., Oliveira, G., Peng, H., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-12166-0 · Cited by 121 · see citing works
Mariani, L. H., Martini, S., Barisoni, L. M. C., Canetta, P. A., Troost, J. P., Hodgin, J. B., Palmer, M., Rosenberg, A. Z., Lemley, K. V., Chien, H., et al. (2016) · Nephrology Dialysis Transplantation · doi:10.1093/ndt/gfw443 · Cited by 118 · see citing works
Suresh, R., Li, X., Chiriac, A. E., Goel, K., Terzic, A., Pérez-Terzic, C. M., & Nelson, T. J. (2014) · Journal of Molecular and Cellular Cardiology · doi:10.1016/j.yjmcc.2014.04.017 · Cited by 114 · see citing works
Dysregulated transcriptional responses to SARS-CoV-2 in the periphery
McClain, M. T., Constantine, F. J., Henao, R., Liu, Y., Tsalik, E. L., Burke, T. W., Steinbrink, J. M., Petzold, E., Nicholson, B. P., Rolfe, R. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21289-y · Cited by 114 · see citing works
van Tienen, F. H. J., Praet, S. F. E., de Feyter, H. M., van den Broek, N. M., Lindsey, P. J., Schoonderwoerd, K. G. C., de Coo, I. F. M., Nicolay, K., Prompers, J. J., Smeets, H. J. M., et al. (2012) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2011-3454 · Cited by 111 · see citing works
Evidence for additive and interaction effects of host genotype and infection in malaria
Idaghdour, Y., Quinlan, J., Goulet, J.-P., Berghout, J., Gbeha, E., Bruat, V., de Malliard, T., Grenier, J., Gomez, S., Gros, P., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1204945109 · Cited by 104 · see citing works
An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles
Li, M., Zhang, Z., Li, L., & Wang, X. (2020) · Communications Biology · doi:10.1038/s42003-020-01230-7 · Cited by 101 · see citing works
Self-citationTranscriptomic analysis of the woodchuck model of chronic hepatitis B
Fletcher, S. P., Chin, D. J., Ji, Y., Iniguez, L. A., Taillon, B. E., Swinney, D. C., Ravindran, P., Cheng, D. T., Bitter, H., Lopatin, U. A., et al. (2012) · Hepatology · doi:10.1002/hep.25730 · Cited by 100 · see citing works
Kiliszek, M., Burzyńska, B., Michalak, M., Góra, M., Winkler, A., Maciejak, A., Leszczynska, A., Gajda, E., Kochanowski, J., & Opolski, G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050054 · Cited by 96 · see citing works
Shih, C., Yang, C.-C., Choijilsuren, G., Chang, C.-H., & Liou, A.-T. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2018.01.009 · Cited by 90 · see citing works
Zhou, W., Ma, Y., Zhang, J., Hu, J., Zhang, M., Wang, Y., Li, Y., Wu, L., Pan, Y., Zhang, Y., et al. (2017) · Liver International · doi:10.1111/liv.13427 · Cited by 87 · see citing works
Erythroid-Specific Transcriptional Changes in PBMCs from Pulmonary Hypertension Patients
Cheadle, C., Berger, A. E., Mathai, S. C., Grigoryev, D. N., Watkins, T. N., Sugawara, Y., Barkataki, S., Fan, J., Boorgula, M. P., Hummers, L. K., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034951 · Cited by 77 · see citing works
Ameling, S., Herda, L. R., Hammer, E., Steil, L., Teumer, A., Trimpert, C., Dörr, M., Kroemer, H. K., Klingel, K., Kandolf, R., et al. (2012) · European Heart Journal · doi:10.1093/eurheartj/ehs330 · Cited by 75 · see citing works
Nookaew, I., Thorell, K., Worah, K., Wang, S., Hibberd, M. L., Sjövall, H., Pettersson, S., Nielsen, J., & Lundin, S. B. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-41 · Cited by 68 · see citing works
van de Leemput, J., Hess, J., Glatt, S. J., & Tsuang, M. T. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.08.001 · Cited by 68 · see citing works
The blood transcriptome of childhood malaria
Boldt, A. B. W., Tong, H. V., Grobusch, M. P., Kalmbach, Y., Dzeing‐Ella, A., Kombila, M., Meyer, C. G., Kun, J. F. J., Kremsner, P. G., & Velavan, T. P. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2018.12.055 · Cited by 63 · see citing works
Alteration of human blood cell transcriptome in uremia
Scherer, A., Günther, O. P., Balshaw, R. F., Hollander, Z., Wilson-McManus, J., Ng, R. T., McMaster, W. R., McManus, B. M., & Keown, P. A. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-23 · Cited by 50 · see citing works
Faner, R., Gonzalez, N., Cruz, T., Kalko, S. G., & Agustí, A. G. N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097491 · Cited by 50 · see citing works
Diagnosis and differential diagnosis of diabetes insipidus: Update
Refardt, J. C. (2020) · Best Practice & Research Clinical Endocrinology & Metabolism · doi:10.1016/j.beem.2020.101398 · Cited by 49 · see citing works
Molecular insights into the progression of crystalline silica‐induced pulmonary toxicity in rats
Sellamuthu, R., Umbright, C., Roberts, J. R., Cumpston, A. M., McKinney, W., Chen, B. T., Frazer, D. G., Li, S., Kashon, M. L., & Joseph, P. (2012) · Journal of Applied Toxicology · doi:10.1002/jat.2733 · Cited by 49 · see citing works
Biomarcadores biológicos en las enfermedades respiratorias
Rio, F. G., Navarrete, B. A., Castillo, D., Cillóniz, C., García‐Ortega, A., Leiro‐Fernández, V., Lojo-Rodríguez, I., Galo, A. P., Quezada-Loaiza, C. A., Rodríguez-Portal, J. A., et al. (2022) · Archivos de Bronconeumología · doi:10.1016/j.arbres.2022.01.003 · Cited by 40 · see citing works
Schanoski, A. S., Sauerwald, N., Goforth, C. W., Periasamy, S., Weir, D. L., Lizewski, S. E., Lizewski, R. A., Ge, Y., Kuzmina, N. A., Nair, V. D., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.821730 · Cited by 39 · see citing works
Chowdhury, F. Z., Ouyang, Z., Buzón, M. J., Walker, B. D., Lichterfeld, M. D., & Yu, X. G. (2018) · AIDS · doi:10.1097/qad.0000000000002007 · Cited by 38 · see citing works
Sighting acute myocardial infarction through platelet gene expression
Gobbi, G., Carubbi, C., Tagliazucchi, G. M., Masselli, E., Mirandola, P., Pigazzani, F., Crocamo, A., Notarangelo, M. F., Suma, S., Paraboschi, E. M., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-56047-0 · Cited by 36 · see citing works
Office Spirometry: Indications and Interpretation.
Langan, R. C., & Goodbred, A. J. (2020) · PubMed · Cited by 36 · see citing works
Datta, D., Enwright, J. F., Arion, D., Paspalas, C. D., Morozov, Y. M., Lewis, D. A., & Arnsten, A. F. T. (2020) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2020.578483 · Cited by 31 · see citing works
Witt, E., Hammer, E., Dörr, M., Weitmann, K., Beug, D., Lehnert, K., Nauck, M. A., Völker, U., Felix, S. B., & Ameling, S. (2019) · Physiological Genomics · doi:10.1152/physiolgenomics.00111.2018 · Cited by 30 · see citing works
Burel, J. G., Singhania, A., Dubelko, P., Müller, J., Tanner, R., Parizotto, E. A., Dedicoat, M. J., Fletcher, T. E., Dunbar, J., Cunningham, A. F., et al. (2021) · Tuberculosis · doi:10.1016/j.tube.2021.102127 · Cited by 24 · see citing works
Lu, Y.-Y., Fang, Z., Li, M., Chen, Q., Zeng, T., Lu, L., Chen, Q., Zhang, H., Zhou, Q., Sun, Y., et al. (2019) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjz025 · Cited by 20 · see citing works
Broderick, C. M., Cliff, J. M., Lee, J., Kaforou, M., & Moore, D. (2020) · Tuberculosis · doi:10.1016/j.tube.2020.102033 · Cited by 18 · see citing works
Schlossberg, D. (2010) · Infectious Disease Clinics of North America · doi:10.1016/j.idc.2009.10.009 · Cited by 16 · see citing works
Barthelson, K., Pederson, S., Newman, M., Jiang, H., & Lardelli, M. T. (2021) · Journal of Alzheimer s Disease Reports · doi:10.3233/adr-200279 · Cited by 11 · see citing works
Acquired Immune Deficiency Syndrome
Collier, A. C., & Handsfield, H. H. (1984) · Urologic Clinics of North America · doi:10.1016/s0094-0143(21)00757-6 · Cited by 11 · see citing works
Gao, S., Wolanyk, N., Chen, Y., Jia, S., Hessner, M. J., & Wang, X. (2017) · BMC Medical Genomics · doi:10.1186/s12920-017-0243-8 · Cited by 9 · see citing works
Self-citationQuach, A., Horvath, S., Nemanim, N. M., Vatakis, D. N., Witt, M. D., Miller, E. N., Detels, R., Langfelder, P., Shapshak, P., Singer, E. J., et al. (2018) · Journal of NeuroVirology · doi:10.1007/s13365-018-0625-5 · Cited by 6 · see citing works
Shahmanesh, M., Phillips, K. L., Boothby, M., & Tomlinson, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0117164 · Cited by 5 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex
Risgaard, R. D., Hanthanan Arachchilage, K., Knaack, S. A., Hosseini, M., Chen, R. J., Kumarage, P., Schmidt, D. K., Huang, X., Sheng, J., Wang, C. J., et al. (2026) · Science · doi:10.1126/science.aea1549 · Cited by 12 · see citing works
- Authors
- Dong, Z., Yan, Q., & Wang, X.
- Affiliations
- China Pharmaceutical University (CN)
- Corresponding author
- Wang, Xiaosheng
- ORCID
- Wang, Xiaosheng
- Venue
- Disease Markers
- Publisher
- Wiley
- Published
- 2022-09-26
- Volume
- 2022
- Pages
- 1-19
- ISSN
- 0278-0240 (ISSN-L)
- 1875-8630
- PMC
- PMC9530920
- OpenAlex
- W4297103613
- Cited by
- 1
- References
- 60
- Citations by year
- 2026: 1
- FWCI
- 0.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Disease Markers (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- China Pharmaceutical University (3150120001)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- intratumoral heterogeneity, disease progression, disease severity, transcriptome, Alzheimer's disease, COVID-19 pandemic, AIDS, pulmonary tuberculosis, malaria, chronic obstructive pulmonary disease, Helicobacter pylori infection, atrophic gastritis, left ventricular ejection fraction, gene expression perturbation, disease diagnosis and prognosis
- MeSH terms
- COVID-19, Acquired Immunodeficiency Syndrome, Humans, Stroke Volume, Zidovudine, Ventricular Function, Left, Disease Progression, Pulmonary Disease, Chronic Obstructive, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
