Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

Nature Biotechnology

Volumn 26, Issue 3, 2008, Pages 305-312

  Deutsch, Eric W ^a   Ball, Catherine A ^b   Berman, Jules J ^c   Bova, G Steven ^d   Brazma, Alvis ^e   Bumgarner, Roger E ^f   Campbell, David ^a   Causton, Helen C ^g   Christiansen, Jeffrey H ^h   Daian, Fabrice ⁱ   Dauga, Delphine ⁱ   Davidson, Duncan R ^h   Gimenez, Gregory ⁱ   Goo, Young Ah ^a,j   Grimmond, Sean ^k   Henrich, Thorsten ^l   Herrmann, Bernhard G ^m   Johnson, Michael H ^a   Korb, Martin ^a   Mills, Jason C ⁿ   Oudes, Asa J ^a,j   Parkinson, Helen E ^e   Pascal, Laura E ^a,j   Pollet, Nicolas ^o   Quackenbush, John ^p   Ramialison, Mirana ^l   Ringwald, Martin ^q   Salgado, David ⁱ   Sansone, Susanna Assunta ^e   Sherlock, Gavin ^b   Stoeckert, Christian J ^r   Swedlow, Jason ^s   Taylor, Ronald C ^t   Walashek, Laura ^a,j   Warford, Anthony ^u   Wilkinson, David G ^v   Zhou, Yi ^w   Zon, Leonard I ^w   Liu, Alvin Y ^a,j   True, Lawrence D ^f   more..

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c Association for Molecular Pathology   (United States)

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f UNIVERSITY OF WASHINGTON   (United States)

^g IMPERIAL COLLEGE SCHOOL OF MEDICINE   (United Kingdom)

^h WESTERN GENERAL HOSPITAL   (United Kingdom)

ⁱ AIX MARSEILLE UNIVERSITÉ   (France)

^j UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^k UNIVERSITY OF QUEENSLAND   (Australia)

^l EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^m MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

ⁿ WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^o CNRS   (France)

^p DANA FARBER CANCER INSTITUTE   (United States)

^q JACKSON LABORATORY   (United States)

^r UNIVERSITY OF PENNSYLVANIA   (United States)

^s UNIVERSITY OF DUNDEE   (United Kingdom)

^t PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^u WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^v NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

^w BOSTON CHILDREN S HOSPITAL   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BIOMATERIALS; BIOMEDICAL ENGINEERING; BIOTECHNOLOGY; DATA ACQUISITION; DATA REDUCTION; GENE EXPRESSION;

IMAGE CHARACTERIZATIONS; IMAGING DATA; IMMUNOHISTOCHEMISTRY EXPERIMENTS (MISFISHIE); IN SITU HYBRIDIZATION;

IMMUNOLOGY;

BIOMATERIAL;

BIBLIOGRAPHIC DATABASE; EXPERIMENTAL DESIGN; GENE EXPRESSION; IMAGING; INFORMATION DISSEMINATION; MINIMUM INFORMATION SPECIFICATION FOR IN SITU HYBRIDIZATION AND IMMUNOHISTOCHEMISTRY EXPERIMENT; PRACTICE GUIDELINE; PRIORITY JOURNAL; RESEARCH; REVIEW; STAINING;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; IMMUNOHISTOCHEMISTRY; IN SITU HYBRIDIZATION;

EID: 40449117669     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1391     Document Type: Review

References (70)

1. True, L.D. Quantitative immunohistochemistry: a new tool for surgical pathology? Am. J. Clin. Pathol. 90, 324-325 (1988).
2. Brazma, A. et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat. Genet. 29, 365-371 (2001).
3. Spellman, P.T. et al. Design and implementation of Microarray Gene Expression Markup Language (MAGE-ML). Genome Biol. 3, RESEARCH0046 (2002).
4. Stoeckert, C.J. & Parkinson, H. The MGED ontology: a framework for describing functional genomics experiments. Comp. Funct. Genomics 4, 127-132 (2003).
5. Taylor, C.F. et al. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat. Biotechnol. 21, 247-254 (2003).
6. Garwood, K. et al. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics 5, 68 (2004).
7. Jones, A., Hunt, E., Wastling, J.M., Pizarro, A. & Stoeckert, C.J. Jr. An object model and database for functional genomics. Bioinformatics 20, 1583-1590 (2004).
8. Xirasagar, S. et al. CEBS object model for systems biology data, SysBio-OM. Bioinformatics 20, 2004-2015 (2004).
9. Jenkins, H. et al. A proposed framework for the description of plant metabolomics experiments and their results. Nat. Biotechnol. 22, 1601-1606 (2004).
10. Lindon, J.C. et al. Summary recommendations for standardization and reporting of metabolic analyses. Nat. Biotechnol. 23, 833-838 (2005).
11. Berman, J.J., Edgerton, M.E. & Friedman, B.A. The tissue microarray data exchange specification: a community-based, open source tool for sharing tissue microarray data. BMC Med. Inform. Decis. Mak. 3, 5 (2003).
12. Stoeckert, C.J., Quackenbush, J., Brazma, A. & Ball, C.A. Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies. Drug Discov. Today Targets 3, 159-164 (2004).
13. Jones, A.R. et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat. Biotechnol. 25, 1127-1133 (2007).
14. Rayner, T.F. et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7, 489 (2006).
15. Brazma, A., Krestyaninova, M. & Sarkans, U. Standards for systems biology. Nat. Rev. Genet. 7, 593-605 (2006).
16. Taylor, C.F. et al. HUPO - Proteomics Standards Initiative (PSI). OMICS 10, 145-151 (2006).
17. Ball, C.A. & Brazma, A. MGED standards. OMICS 10, 138-144 (2006).
18. Sansone, S.-A. et al. A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. OMICS 10, 164-171 (2006).
19. Taylor, C.F. et al. Promoting coherent minimum reporting requirements for biological and biomedical investigations: the MIBBI Project. Nat. Biotechnol. (in the press).
20. Salgado, D., Gimenez, G., Coulier, F. & Marcelle, C. COMPARE, a multi-organism system for cross-species data comparison and transfer of information. Bioinformatics, published online 1 December 2007 (doi:10.1093/bioinformatics/btm599).
21. Haudry, Y. et al. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res. 36 (database issue), D847-D853 (2007).
22. Swanson, P.E. Methodologic standardization in immunohistochemistry: a doorway opens. Appl. Immunohistochem. 1, 229-231 (1993).
23. Taylor, C.R. An exaltation of experts: concerted efforts in the standardization of immunohistochemistry. Hum. Pathol. 25, 2-11 (1994).
24. McShane, L.M. et al. Reporting recommendations for tumor marker prognostic studies (REMARK). J. Natl. Cancer Inst. 97, 1180-1184 (2005).
25. Smith, C.M. et al. The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res. 35 (database issue), D618-D623 (2007).
26. Baldock, R.A. et al. EMAP and EMAGE: a framework for understanding spatially organized data. Neuroinformatics 1, 309-325 (2003).
27. Whetzel, P.L. et al. Development of FuGO - an ontology for functional genomics experiments. OMICS 10, 199-204 (2006).
28. Dobashi, Y. et al. Active cyclin A-CDK2 complex, a possible critical factor for cell proliferation in human primary lung carcinomas. Am. J. Pathol. 153, 963-972 (1998).
29. De Marzo, A.M., Fedor, H.H., Gage, W.R. & Rubin, M.A. Inadequate formalin fixation decreases reliability of p27 immunohistochemical staining: probing optimal fixation time using high-density tissue microarrays. Hum. Pathol. 33, 756-760 (2002).
30. Sprague, J. et al. The Zebrafish Information Network (ZFIN): the zebrafish model organism database. Nucleic Acids Res. 31, 241-243 (2003).
31. Carazo, J.M. & Stelzer, E.H. The BioImage Database Project: organizing multidimensional biological images in an object-relational database. J. Struct. Biol. 125, 97-102 (1999).
32. Rosse, C. & Mejino, J.L. Jr. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J. Biomed. Inform. 36, 478-500 (2003).
33. Bard, J., Rhee, S.Y. & Ashburner, M. An ontology for cell types. Genome Biol. 6, R21 (2005).
34. Bard, J.L. et al. An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech. Dev. 74, 111-120 (1998).
35. Hayamizu, T.F., Mangan, M., Corradi, J.P., Kadin, J.A. & Ringwald, M. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 6, R29 (2005).
36. Berman, J.J. A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies. BMC Med. Inform. Decis. Mak. 3, 6 (2003).
37. Abd El-Rehim, D.M. et al. Expression of luminal and basal cytokeratins in human breast carcinoma. J. Pathol. 203, 661-671 (2004).
38. Bova, G.S. et al. Web-based tissue microarray image data analysis: initial validation testing through prostate cancer Gleason grading. Hum. Pathol. 32, 417-427 (2001).
39. Liu, A.Y. & True, L.D. Characterization of prostate cell types by CD cell surface molecules. Am. J. Pathol. 160, 37-43 (2002).
40. Kernek, K.M. et al. Fluorescence in situ hybridization analysis of chromosome 12p in paraffin-embedded tissue is useful for establishing germ cell origin of metastatic tumors. Mod. Pathol. 17, 1309-1313 (2004).
41. McKenney, J.K. et al. Basal cell proliferations of the prostate other than usual basal cell hyperplasia: a clinicopathologic study of 23 cases, including four carcinomas, with a proposed classification. Am. J. Surg. Pathol. 28, 1289-1298 (2004).
42. Amara, N. et al. Prostate stem cell antigen is overexpressed in human transitional cell carcinoma. Cancer Res. 61, 4660-4665 (2001).
43. Ayala, G. et al. High levels of phosphorylated form of Akt-1 in prostate cancer and non-neoplastic prostate tissues are strong predictors of biochemical recurrence. Clin. Cancer Res. 10, 6572-6578 (2004).
44. Bart, J. et al. The distribution of drug-efflux pumps, P-gp, BCRP, MRP1 and MRP2, in the normal blood-testis barrier and in primary testicular tumours. Eur. J. Cancer 40, 2064-2070 (2004).
45. Browne, T.J. et al. Prospective evaluation of AMACR (P504S) and basal cell markers in the assessment of routine prostate needle biopsy specimens. Hum. Pathol. 35, 1462-1468 (2004).
46. Chen, D. et al. Syndecan-1 expression in locally invasive and metastatic prostate cancer. Urology 63, 402-407 (2004).
47. Clayton, H., Titley, I. & Vivanco, M. Growth and differentiation of progenitor/stem cells derived from the human mammary gland. Exp. Cell Res. 297, 444-460 (2004).
48. Cooray, H.C., Blackmore, C.G., Maskell, L. & Barrand, M.A. Localisation of breast cancer resistance protein in microvessel endothelium of human brain. Neuroreport 13, 2059-2063 (2002).
49. Giangreco, A., Shen, H., Reynolds, S.D. & Stripp, B.R. Molecular phenotype of airway side population cells. Am. J. Physiol. Lung Cell. Mol. Physiol. 286, L624-L630 (2004).
50. Gmyrek, G.A. et al. Normal and malignant prostate epithelial cells differ in their response to hepatocyte growth factor/scatter factor. Am. J. Pathol. 159, 579-590 (2001).
51. Hwang, J.H. et al. Isolation of muscle derived stem cells from rat and its smooth muscle differentiation. Mol. Cells 17, 57-61 (2004); erratum 17, 381 (2004).
52. Jonker, J.W. et al. The breast cancer resistance protein BCRP (ABCG2) concentrates drugs and carcinogenic xenotoxins into milk. Nat. Med. 11, 127-129 (2005).
53. Knudsen, B.S. et al. High expression of the Met receptor in prostate cancer metastasis to bone. Urology 60, 1113-1117 (2002).
54. Larkin, A. et al. Investigation of MRP-1 protein and MDR-1 P-glycoprotein expression in invasive breast cancer: a prognostic study. Int. J. Cancer 112, 286-294 (2004).
55. Lee, K., Klein-Szanto, A.J. & Kruh, G.D. Analysis of the MRP4 drug resistance profile in transfected NIH3T3 cells. J. Natl. Cancer Inst. 92, 1934-1940 (2000).
56. Li, R. et al. High level of androgen receptor is associated with aggressive clinicopathologic features and decreased biochemical recurrence-free survival in prostate: cancer patients treated with radical prostatectomy. Am. J. Surg. Pathol. 28, 928-934 (2004).
57. Martin, C.M. et al. Persistent expression of the ATP-binding cassette transporter, Abcg2, identifies cardiac SP cells in the developing and adult heart. Dev. Biol. 265, 262-275 (2004).
58. Martin, M.J., Muotri, A., Gage, F. & Varki, A. Human embryonic stem cells express an immunogenic nonhuman sialic acid. Nat. Med. 11, 228-232 (2005).
59. Master, V.A., Wei, G., Liu, W. & Baskin, L.S. Urothlelium facilitates the recruitment and trans-differentiation of fibroblasts into smooth muscle in acellular matrix. J. Urol. 170, 1628-1632 (2003).
60. Piotrowska, A.P. et al. Alterations in smooth muscle contractile and cytoskeleton proteins and interstitial cells of Cajal in megacystis microcolon intestinal hypoperistalsis syndrome. J. Pediatr. Surg. 38, 749-755 (2003).
61. Ricciardelli, C. et al. Androgen receptor levels in prostate cancer epithelial and peritumoral stromal cells identify non-organ confined disease. Prostate 63, 19-28 (2005).
62. Roudier, M.P. et al. Phenotypic heterogeneity of end-stage prostate carcinoma metastatic to bone. Hum. Pathol. 34, 646-653 (2003).
63. Rubin, M.A. et al. Quantitative determination of expression of the prostate cancer protein alpha-methylacyl-CoA racemase using automated quantitative analysis (AQUA): a novel paradigm for automated and continuous biomarker measurements. Am. J. Pathol. 164, 831-840 (2004).
64. Santagata, S. et al. JAGGED1 expression is associated with prostate cancer metastasis and recurrence. Cancer Res. 64, 6854-6857 (2004).
65. Scotlandi, K. et al. C-kit receptor expression in Ewing's sarcoma: lack of prognostic value but therapeutic targeting opportunities in appropriate conditions. J. Clin. Oncol. 21, 1952-1960 (2003).
66. Shah, R.B. et al. Androgen-independent prostate cancer is a heterogeneous group of diseases: lessons from a rapid autopsy program. Cancer Res. 64, 9209-9216 (2004).
67. St Croix, B. et al. Genes expressed in human tumor endothelium. Science 289, 1197-1202 (2000).
68. Wang, Z. et al. Expression of the human cachexia-associated protein (HCAP) in prostate cancer and in a prostate cancer animal model of cachexia. Int. J. Cancer 105, 123-129 (2003).
69. Zhigang, Z. & Wenlv, S. Prostate stem cell antigen (PSCA) expression in human prostate cancer tissues: implications for prostate carcinogenesis and progression of prostate cancer. Jpn. J. Clin. Oncol. 34, 414-419 (2004).
70. Deutsch, E.W. et al. Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS 10, 205-208 (2006).