Comprehensive comparison of large-scale tissue expression datasets

PeerJ

Volumn 2015, Issue 6, 2015, Pages

  Santos, Alberto ^a   Tsafou, Kalliopi ^a   Stolte, Christian ^b   Pletscher Frankild, Sune ^a,d   O'Donoghue, Seán I ^b,c   Jensen, Lars Juhl ^a  

^a University of Copenhagen   (Denmark)

^b CSIRO   (Australia)

^c GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^d Ferring Pharmaceuticals AS   (Denmark)

Author keywords

Databases; Immunohistochemistry; Mass spectrometry; Microarrays; RNA sequencing; Tissue expression; Tissue specificity

Indexed keywords

PROTEOME; TRANSCRIPTOME;

ARTICLE; COMPUTER ANALYSIS; CORRELATION ANALYSIS; DATA PROCESSING; EXON; GENE EXPRESSION; GENE LIBRARY; GENE MAPPING; GENETIC DATABASE; HIGH DENSITY MICROARRAY; HUMAN; IMMUNOHISTOCHEMISTRY; MASS SPECTROMETRY; MATHEMATICAL MODEL; MOLECULAR GENETICS; PROTEIN EXPRESSION; PROTEOMICS; RNA SEQUENCE; TEXT MINING; TISSUE EXPRESSION; TISSUE MICROARRAY; UNIGENE; UNIPROTKB; WEB OF SCIENCE;

EID: 84941717906     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.1054     Document Type: Article

References (62)

1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651-1656 DOI 10.1126/science.2047873.
2. Adkins JN. 2002. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Molecular & Cellular Proteomics 1:947-955 DOI 10.1074/mcp. M200066-MCP200.
3. Aerts S, Haeussler M, Van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Consortium TORA. 2008. Text-mining assisted regulatory annotation. Genome Biology 9:R31 DOI 10.1186/gb-2008-9-2-r31.
4. Aretz S, Krohne TU, Kammerer K, Warnken U, Hotz-Wagenblatt A, Bergmann M, Stanzel BV, Kempf T, Holz FG, Schnölzer M, Kopitz J. 2013. In-depth mass spectrometric mapping of the human vitreous proteome. Proteome Science 11:Article 22 DOI 10.1186/1477-5956-11-22.
5. Bailey L, Searls D, Overton G. 1998. Analysis of EST-driven gene annotation in human genomic sequence. Genome Research 8:362-376 DOI 10.1101/gr.8.3.234.
6. Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A. 2011. NCBI GEO: archive for functional genomics data sets-10 years on. Nucleic Acids Research 39:D1005-D1010 DOI 10.1093/nar/gkq1184.
7. Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. 2014. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database 2014:bau012-bau012 DOI 10.1093/database/bau012.
8. Bitton DA, Okoniewski MJ, Connolly Y, Miller CJ. 2008. Exon level integration of proteomics and microarray data. BMC Bioinformatics 9:118 DOI 10.1186/1471-2105-9-118.
9. Börnigen D, Pers TH, Thorrez L, Huttenhower C, Moreau Y, Brunak S. 2013. Concordance of gene expression in human protein complexes reveals tissue specificity and pathology. Nucleic Acids Research 41:e171 DOI 10.1093/nar/gkt661.
10. Bossi A, Lehner B. 2009. Tissue specificity and the human protein interaction network. Molecular Systems Biology 5:Article 260 DOI 10.1038/msb.2009.17.
11. Buchwalow I, Samoilova V, Boecker W, Tiemann M. 2011. Non-specific binding of antibodies in immunohistochemistry: fallacies and facts. Scientific Reports 1:Article 28 DOI 10.1038/srep00028.
12. Chang C-W, ChengW-C, Chen C-R, ShuW-Y, Tsai M-L, Huang C-L, Hsu IC. 2011. Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis. PLoS ONE 6:e22859 DOI 10.1371/journal.pone.0022859.
13. Churchill GA. 2002. Fundamentals of experimental design for cDNA microarrays. Nature (32):490-495 DOI 10.1038/ng1031.
14. Clark TA, Schweitzer AC, Chen TX, Staples MK, Lu G, Wang H, Williams A, Blume JE. 2007. Discovery of tissue-specific exons using comprehensive human exon microarrays. Genome Biology 8:R64 DOI 10.1186/gb-2007-8-4-r64.
15. Dezso Z, Nikolsky Y, Sviridov E, Shi W, Serebriyskaya T, Dosymbekov D, Bugrim A, Rakhmatulin E, Brennan RJ, Guryanov A, Li K, Blake J, Samaha RR, Nikolskaya T. 2008. A comprehensive functional analysis of tissue specificity of human gene expression. BMC Biology 6:49 DOI 10.1186/1741-7007-6-49.
16. Eisenberg E, Levanon EY. 2013. Human housekeeping genes, revisited. Trends in Genetics 29:569-574 DOI 10.1016/j.tig.2013.05.010.
17. Emig D, Albrecht M. 2011. Tissue-specific proteins and functional implications. Journal of Proteome Research 10:1893-1903 DOI 10.1021/pr101132h.
18. Ezkurdia I, Vázquez J, Valencia A, Tress M. 2014. Analyzing the first drafts of the human proteome. Journal of Proteome Research 13:3854-3855 DOI 10.1021/pr500572z.
19. Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CA-K, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, Von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M. 2014. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular & Cellular Proteomics 13:397-406 DOI 10.1074/mcp. M113.035600.
20. Franceschini A, Szklarczyk D. 2013. STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research 41:D808-D815 DOI 10.1093/nar/gks1094.
21. Harrington CA, Rosenow C, Retief J. 2000. Monitoring gene expression using DNA microarrays. Current Opinion in Microbiology 3:285-291 DOI 10.1016/S1369-5274(00)00091-6.
22. Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng Z, Mutter GL, Frosch MP, MacDonald ME, Milford EL, Crum CP, Bueno R, Pratt RE, Mahadevappa M, Warrington JA, Stephanopoulos G, Gullans SR. 2001. A compendium of gene expression in normal human tissues. Physiological Genomics 7:97-104 DOI 10.1152/physiolgenomics.00040.2001.
23. Kampf C, Olsson I, Ryberg U, Sjöstedt E, Pontén F. 2012. Production of tissue microarrays, immunohistochemistry staining and digitalization within the human protein atlas. Journal of Visualized Experiments 63:3620 DOI 10.3791/3620.
24. Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A. 2010. Gene expression atlas at the European Bioinformatics Institute. Nucleic Acids Research 38:D690-D698 DOI 10.1093/nar/gkp936.
25. Kim M-S, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LDN, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang T-C, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TSK, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A. 2014. A draft map of the human proteome. Nature 509:575-581 DOI 10.1038/nature13302.
26. Kogenaru S, Val C, Hotz-Wagenblatt A, Glatting K-H. 2009. Tissue Distribution DBs: a repository of organism-specific tissue-distribution profiles. Theoretical Chemistry Accounts 125:651-658 DOI 10.1007/s00214-009-0670-5.
27. Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. 2012. RNA-Seq Atlas-a reference database for gene expression profiling in normal tissue by next-generation sequencing. Bioinformatics 28:1184-1185 DOI 10.1093/bioinformatics/bts084.
28. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S. 2008. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proceedings of the National Academy of Sciences of the United States of America 105:20870-20875 DOI 10.1073/pnas.0810772105.
29. Lercher MJ, Urrutia AO, Hurst LD. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genetics 31:180-183 DOI 10.1038/ng887.
30. Li JJ, Bickel PJ, Biggin MD. 2014. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ 2:e270 DOI 10.7717/peerj.270.
31. Liang S, Li Y, Be X, Howes S, Liu W. 2006. Detecting and profiling tissue-selective genes. Physiological Genomics 26:158-162 DOI 10.1152/physiolgenomics.00313.2005.
32. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ. 1999. High density synthetic oligonucleotide arrays. Nature Genetics 21:20-24 DOI 10.1038/4447.
33. Liu X, Yu X, Zack DJ, Zhu H, Qian J. 2008. TiG ER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics 9:271 DOI 10.1186/1471-2105-9-271.
34. Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N, Foster B, Moser M, Karasik E, Gillard B, Ramsey K, Sullivan S, Bridge J, Magazine H, Syron J, Fleming J, SiminoffL, Traino H, Mosavel M, Barker L, Jewell S, Rohrer D, Maxim D, Filkins D, Harbach P, Cortadillo E, Berghuis B, Turner L, Hudson E, Feenstra K, Sobin L, Robb J, Branton P, Korzeniewski G, Shive C, Tabor D, Qi L, Groch K, Nampally S, Buia S, Zimmerman A, Smith A, Burges R, Robinson K, Valentino K, Bradbury D, Cosentino M, Diaz-Mayoral N, Kennedy M, Engel T, Williams P, Erickson K, Ardlie K, Winckler W, Getz G, DeLuca D, MacArthur D, Kellis M, Thomson A, Young T, Gelfand E, Donovan M, Meng Y, Grant G, Mash D, Marcus Y, Basile M, Liu J, Zhu J, Tu Z, Cox NJ, Nicolae DL, Gamazon ER, Im HK, Konkashbaev A, Pritchard J, Stevens M, Flutre T, Wen X, Dermitzakis ET, Lappalainen T, Guigo R, Monlong J, Sammeth M, Koller D, Battle A, Mostafavi S, McCarthy M, Rivas M, Maller J, Rusyn I, Nobel A, Wright F, Shabalin A, Feolo M, Sharopova N, Sturcke A, Paschal J, Anderson JM, Wilder EL, Derr LK, Green ED, Struewing JP, Temple G, Volpi S, Boyer JT, Thomson EJ, Guyer MS, Ng C, Abdallah A, Colantuoni D, Insel TR, Koester SE, Little AR, Bender PK, Lehner T, Yao Y, Compton CC, Vaught JB, Sawyer S, Lockhart NC, Demchok J, Moore HF. 2013. The Genotype-Tissue Expression (GTEx) project. Nature Genetics 45:580-585 DOI 10.1038/ng.2653.
35. Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV. 2012. Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. Nature Communications 3:Article 876 DOI 10.1038/ncomms1871.
36. Magger O, Waldman YY, Ruppin E, Sharan R. 2012. Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks. PLoS Computational Biology 8:e1002690 DOI 10.1371/journal.pcbi.1002690.
37. Nagalakshmi U, Waern K, Snyder M. 2010. RNA-Seq: a method for comprehensive transcriptome analysis. Current Protocols in Molecular Biology 89:Unit 4.11 DOI 10.1002/0471142727.mb0411s89.
38. Nagaraj SH, Gasser RB, Ranganathan S. 2007. A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics 8:6-21 DOI 10.1093/bib/bbl015.
39. Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, Vasileiadou A, Arvanitidis C, Jensen LJ. 2013. The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text. PLoS ONE 8:e65390 DOI 10.1371/journal.pone.0065390.
40. Paul D, Kumar A, Gajbhiye A, Santra MK, Srikanth R. 2013. Mass spectrometry-based proteomics in molecular diagnostics: discovery of cancer biomarkers using tissue culture. BioMed Research International 2013:783131 DOI 10.1155/2013/783131.
41. Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ. 2014. DISEASES: text mining and data integration of disease-gene associations. Methods 74:83-89 DOI 10.1016/j.ymeth.2014.11.020.
42. Pontén F, Gry M, Fagerberg L, Lundberg E, Asplund A, Berglund L, Oksvold P, Björling E, Hober S, Kampf C, Navani S, Nilsson P, Ottosson J, Persson A, Wernérus H, Wester K, Uhlén M. 2009. A global view of protein expression in human cells, tissues, and organs. Molecular Systems Biology 5:Article 337 DOI 10.1038/msb.2009.93.
43. Pontius JU, Wagner L, Schuler GD. 2002. UniGene: a unified view of the transcriptome. Technical Report, National Center for Biotechnology Information. National Center for Biotechnology Information, Bethesda. Available at http://www.ncbi.nlm.nih.gov/books/NBK21083/?report=reader.
44. Schaefer MH, Lopes TJS, Mah N, Shoemaker JE, Matsuoka Y, Fontaine J-F, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro MA. 2013. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions. PLoS Computational Biology 9:e1002860 DOI 10.1371/journal.pcbi.1002860.
45. Schmidt A, Aebersold R. 2006. High-accuracy proteome maps of human body fluids. Genome Biology 7:Article 242 DOI 10.1186/gb-2006-7-11-242.
46. Schomburg I, Chang A, Placzek S, Söhngen C, Rother M, Lang M, Munaretto C, Ulas S, Stelzer M, Grote A, Scheer M, Schomburg D. 2013. BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Research 41:D764-D772 DOI 10.1093/nar/gks1049.
47. Schwartz SA. 2004. Protein profiling in brain tumors using mass spectrometry: feasibility of a new technique for the analysis of protein expression. Clinical Cancer Research 10:981-987 DOI 10.1158/1078-0432.CCR-0927-3.
48. Seeley EH, Caprioli RM. 2008. Molecular imaging of proteins in tissues by mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 105:18126-18131 DOI 10.1073/pnas.0801374105.
49. Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR. 2005. A DNA microarray survey of gene expression in normal human tissues. Genome Biology 6:R22 DOI 10.1186/gb-2005-6-3-r22.
50. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America 101:6062-6067 DOI 10.1073/pnas.0400782101.
51. The UniProt Consortium. 2014. Activities at the universal protein resource (UniProt). Nucleic Acids Research 42:D191-D198 DOI 10.1093/nar/gkt1140.
52. Uhlen M, Fagerberg L, Hallstrom BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson A, Kampf C, Sjostedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA-K, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist P-H, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, Von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, Von Heijne G, Nielsen J, Ponten F. 2015. Tissue-based map of the human proteome. Science 347:1260419-1260419 DOI 10.1126/science.1260419.
53. Van Auken K, Fey P, Berardini TZ, Dodson R, Cooper L, Li D, Chan J, Li Y, Basu S, Muller H-M, Chisholm R, Huala E, Sternberg PW. 2012. Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database: The Journal of Biological Databases and Curation 2012:bas040 DOI 10.1093/database/bas040.
54. Vasmatzis G, Klee EW, Kube DM, Therneau TM, Kosari F. 2007. Quantitating tissue specificity of human genes to facilitate biomarker discovery. Bioinformatics 23:1348-1355 DOI 10.1093/bioinformatics/btm102.
55. Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews. Genetics 10:57-63 DOI 10.1038/nrg2484.
56. Waters KM, Pounds JG, Thrall BD. 2006. Data merging for integrated microarray and proteomic analysis. Briefings in Functional Genomics & Proteomics 5:261-272 DOI 10.1093/bfgp/ell019.
57. Wheeler DL. 2003. Database resources of the National Center for Biotechnology. Nucleic Acids Research 31:28-33 DOI 10.1093/nar/gkg033.
58. Wilhelm M, Schlegl J, Hahne H. 2014. Mass-spectrometry-based draft of the human proteome. Nature 509:582-587 DOI 10.1038/nature13319.
59. Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW, Su AI. 2009. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. Genome Biology 10:R130 DOI 10.1186/gb-2009-10-11-r130.
60. Yang X, Ye Y, Wang G, Huang H, Yu D, Liang S. 2011. VeryGene: linking tissue-specific genes to diseases, drugs, and beyond for knowledge discovery. Physiological Genomics 43:457-460 DOI 10.1152/physiolgenomics.00178.2010.
61. Zhu J, He F, Hu S, Yu J. 2008b. On the nature of human housekeeping genes. Trends in Genetics 24:481-484 DOI 10.1016/j.tig.2008.08.004.
62. Zhu J, He F, Song S, Wang J, Yu J. 2008a. How many human genes can be defined as housekeeping with current expression data? BMC Genomics 9:172 DOI 10.1186/1471-2164-9-172.