A Human "eFP" Browser for Generating Gene Expression Anatograms

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 Mar 9

PMID 26954504

Citations 8

Authors

Rohan V Patel

Erin T Hamanishi

Nicholas J Provart

Affiliations

Soon will be listed here.

Abstract

Transcriptomic studies help to further our understanding of gene function. Human transcriptomic studies tend to focus on a particular subset of tissue types or a particular disease state; however, it is possible to collate into a compendium multiple studies that have been profiled using the same expression analysis platform to provide an overview of gene expression levels in many different tissues or under different conditions. In order to increase the knowledge and understanding we gain from such studies, intuitive visualization of gene expression data in such a compendium can be useful. The Human eFP ("electronic Fluorescent Pictograph") Browser presented here is a tool for intuitive visualization of large human gene expression data sets on pictographic representations of the human body as gene expression "anatograms". Pictographic representations for new data sets may be generated easily. The Human eFP Browser can also serve as a portal to other gene-specific information through link-outs to various online resources.

Citing Articles

Developing libraries of semantically-augmented graphics as visual standards for biomedical information systems.

Clarkson M, Roggenkamp S, Detwiler L J Biomed Inform. 2025; 163:104804.

PMID: 39961540 PMC: 11899390. DOI: 10.1016/j.jbi.2025.104804.

Elucidating the molecular mechanisms underlying anti-inflammatory effects of Morchella esculenta in the arachidonic acid metabolic pathway by network pharmacology and molecular docking.

Xiaoying M, Zhiming H, Tao Y, Jun X, Ying Z, Na G Sci Rep. 2023; 13(1):15881.

PMID: 37741847 PMC: 10517965. DOI: 10.1038/s41598-023-42658-1.

Integration of network pharmacology and molecular docking to explore the molecular mechanism of Cordycepin in the treatment of Alzheimer's disease.

Ma X, Zhao Y, Yang T, Gong N, Chen X, Liu G Front Aging Neurosci. 2023; 14:1058780.

PMID: 36620771 PMC: 9817107. DOI: 10.3389/fnagi.2022.1058780.

The Pharmacological Mechanism of Xiyanping Injection for the Treatment of Novel Coronavirus Pneumonia (COVID-19): Based on Network Pharmacology Strategy.

Xia L, Zhang L, Yang K, Chen T, Ye X, Yan Z Evid Based Complement Alternat Med. 2022; 2022:9152201.

PMID: 35818408 PMC: 9271007. DOI: 10.1155/2022/9152201.

Network Pharmacology-Based Strategy to Investigate the Pharmacologic Mechanisms of Coptidis Rhizoma for the Treatment of Alzheimer's Disease.

Ye X, Wang H, Cheng S, Xia L, Xu X, Li X Front Aging Neurosci. 2022; 14:890046.

PMID: 35795239 PMC: 9252849. DOI: 10.3389/fnagi.2022.890046.

References

Liu X, Yu X, Zack D, Zhu H, Qian J . TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics. 2008; 9:271. PMC: 2438328. DOI: 10.1186/1471-2105-9-271. View

Roe O, Anderssen E, Helge E, Pettersen C, Olsen K, Sandeck H . Genome-wide profile of pleural mesothelioma versus parietal and visceral pleura: the emerging gene portrait of the mesothelioma phenotype. PLoS One. 2009; 4(8):e6554. PMC: 2717215. DOI: 10.1371/journal.pone.0006554. View

Petryszak R, Burdett T, Fiorelli B, Fonseca N, Gonzalez-Porta M, Hastings E . Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res. 2013; 42(Database issue):D926-32. PMC: 3964963. DOI: 10.1093/nar/gkt1270. View

Ge X, Yamamoto S, Tsutsumi S, Midorikawa Y, Ihara S, Wang S . Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics. 2005; 86(2):127-41. DOI: 10.1016/j.ygeno.2005.04.008. View

Wu C, MacLeod I, Su A . BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res. 2012; 41(Database issue):D561-5. PMC: 3531157. DOI: 10.1093/nar/gks1114. View

Mutskov V, Felsenfeld G . The human insulin gene is part of a large open chromatin domain specific for human islets. Proc Natl Acad Sci U S A. 2009; 106(41):17419-24. PMC: 2765094. DOI: 10.1073/pnas.0909288106. View

Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M . Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. 2010; 28(12):1248-50. DOI: 10.1038/nbt1210-1248. View

Miller J, Ding S, Sunkin S, Smith K, Ng L, Szafer A . Transcriptional landscape of the prenatal human brain. Nature. 2014; 508(7495):199-206. PMC: 4105188. DOI: 10.1038/nature13185. View

Bao X, Sinha M, Liu T, Hong C, Luxon B, Garofalo R . Identification of human metapneumovirus-induced gene networks in airway epithelial cells by microarray analysis. Virology. 2008; 374(1):114-27. PMC: 2777699. DOI: 10.1016/j.virol.2007.12.024. View

10.

Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M . GeneCards Version 3: the human gene integrator. Database (Oxford). 2010; 2010:baq020. PMC: 2938269. DOI: 10.1093/database/baq020. View

11.

Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L . Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics. 2009; 2008:420747. PMC: 2777001. DOI: 10.1155/2008/420747. View

12.

Toufighi K, Brady S, Austin R, Ly E, Provart N . The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J. 2005; 43(1):153-63. DOI: 10.1111/j.1365-313X.2005.02437.x. View

13.

Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin M . Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A. 2007; 104(49):19428-33. PMC: 2148306. DOI: 10.1073/pnas.0709013104. View

14.

Karoly E, Li Z, Dailey L, Hyseni X, Huang Y . Up-regulation of tissue factor in human pulmonary artery endothelial cells after ultrafine particle exposure. Environ Health Perspect. 2007; 115(4):535-40. PMC: 1852686. DOI: 10.1289/ehp.9556. View

15.

Johnson L, Clasper S, Holt A, Lalor P, Baban D, Jackson D . An inflammation-induced mechanism for leukocyte transmigration across lymphatic vessel endothelium. J Exp Med. 2006; 203(12):2763-77. PMC: 2118156. DOI: 10.1084/jem.20051759. View

16.

Flicek P, Ahmed I, Amode M, Barrell D, Beal K, Brent S . Ensembl 2013. Nucleic Acids Res. 2012; 41(Database issue):D48-55. PMC: 3531136. DOI: 10.1093/nar/gks1236. View

17.

Roth R, Hevezi P, Lee J, Willhite D, Lechner S, Foster A . Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics. 2006; 7(2):67-80. DOI: 10.1007/s10048-006-0032-6. View

18.

Okamoto K, Bosch M, Hayashi Y . The roles of CaMKII and F-actin in the structural plasticity of dendritic spines: a potential molecular identity of a synaptic tag?. Physiology (Bethesda). 2009; 24:357-66. DOI: 10.1152/physiol.00029.2009. View

19.

Maglott D, Ostell J, Pruitt K, Tatusova T . Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2010; 39(Database issue):D52-7. PMC: 3013746. DOI: 10.1093/nar/gkq1237. View

20.

Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L . The human proteome project: current state and future direction. Mol Cell Proteomics. 2011; 10(7):M111.009993. PMC: 3134076. DOI: 10.1074/mcp.M111.009993. View