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

One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.

[1]  L. True,et al.  Quantitative immunohistochemistry: a new tool for surgical pathology? , 1988, American journal of clinical pathology.

[2]  C. Taylor,et al.  An exaltation of experts: concerted efforts in the standardization of immunohistochemistry. , 1994, Human pathology.

[3]  J. Bard,et al.  An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature , 1998, Mechanisms of Development.

[4]  S. Jiang,et al.  Active cyclin A-CDK2 complex, a possible critical factor for cell proliferation in human primary lung carcinomas. , 1998, The American journal of pathology.

[5]  J M Carazo,et al.  The BioImage Database Project: organizing multidimensional biological images in an object-relational database. , 1999, Journal of structural biology.

[6]  K. Kinzler,et al.  Genes expressed in human tumor endothelium. , 2000, Science.

[7]  A. Klein-Szanto,et al.  Analysis of the MRP4 drug resistance profile in transfected NIH3T3 cells. , 2000, Journal of the National Cancer Institute.

[8]  Janan T. Eppig,et al.  The Mouse Gene Expression Database (GXD) , 2001, Nucleic Acids Res..

[9]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[10]  G. Parmigiani,et al.  Web-based tissue microarray image data analysis: initial validation testing through prostate cancer Gleason grading. , 2001, Human pathology.

[11]  Zhennan Gu,et al.  Prostate stem cell antigen is overexpressed in human transitional cell carcinoma. , 2001, Cancer research.

[12]  G. V. Vande Woude,et al.  Normal and malignant prostate epithelial cells differ in their response to hepatocyte growth factor/scatter factor. , 2001, The American journal of pathology.

[13]  Lawrence D True,et al.  Characterization of prostate cell types by CD cell surface molecules. , 2002, The American journal of pathology.

[14]  M. Rubin,et al.  Inadequate formalin fixation decreases reliability of p27 immunohistochemical staining: probing optimal fixation time using high-density tissue microarrays. , 2002, Human pathology.

[15]  Douglas S Scherr,et al.  High expression of the Met receptor in prostate cancer metastasis to bone. , 2002, Urology.

[16]  M. Barrand,et al.  Localisation of breast cancer resistance protein in microvessel endothelium of human brain , 2002, Neuroreport.

[17]  Jason E. Stewart,et al.  Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.

[18]  V. Master,et al.  Urothlelium facilitates the recruitment and trans-differentiation of fibroblasts into smooth muscle in acellular matrix. , 2003, The Journal of urology.

[19]  Chris F. Taylor,et al.  A systematic approach to modeling, capturing, and disseminating proteomics experimental data , 2003, Nature Biotechnology.

[20]  J. Moake,et al.  This article has been cited by other articles , 2003 .

[21]  Jules J. Berman.  A tool for sharing annotated research data: the "Category 0" UMLS (Unified Medical Language System) vocabularies , 2003, BMC Medical Informatics Decis. Mak..

[22]  Hubert Vesselle,et al.  Phenotypic heterogeneity of end-stage prostate carcinoma metastatic to bone. , 2003, Human pathology.

[23]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[24]  A Bianchi,et al.  Alterations in smooth muscle contractile and cytoskeleton proteins and interstitial cells of Cajal in megacystis microcolon intestinal hypoperistalsis syndrome. , 2003, Journal of pediatric surgery.

[25]  Jules J. Berman,et al.  The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data , 2003, BMC Medical Informatics Decis. Mak..

[26]  P. Lollini,et al.  C-kit receptor expression in Ewing's sarcoma: lack of prognostic value but therapeutic targeting opportunities in appropriate conditions. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[27]  R. Vessella,et al.  Expression of the human cachexia‐associated protein (HCAP) in prostate cancer and in a prostate cancer animal model of cachexia , 2003, International journal of cancer.

[28]  Monte Westerfield,et al.  The Zebrafish Information Network (ZFIN): the zebrafish model organism database , 2003, Nucleic Acids Res..

[29]  Helen Parkinson,et al.  The MGED Ontology: A Framework for Describing Functional Genomics Experiments , 2003, Comparative and functional genomics.

[30]  Matteo Brunelli,et al.  Fluorescence in situ hybridization analysis of chromosome 12p in paraffin-embedded tissue is useful for establishing germ cell origin of metastatic tumors , 2004, Modern Pathology.

[31]  Alistair J. P. Brown,et al.  PEDRo: A database for storing, searching and disseminating experimental proteomics data , 2004, BMC Genomics.

[32]  Christian J. Stoeckert,et al.  Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies , 2004 .

[33]  P. Scardino,et al.  High Levels of Phosphorylated Form of Akt-1 in Prostate Cancer and Non-Neoplastic Prostate Tissues Are Strong Predictors of Biochemical Recurrence , 2004, Clinical Cancer Research.

[34]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[35]  Nigel W. Hardy,et al.  A proposed framework for the description of plant metabolomics experiments and their results , 2004, Nature Biotechnology.

[36]  H. Groen,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. , 2004, European journal of cancer.

[37]  L. O’Driscoll,et al.  Investigation of MRP‐1 protein and MDR‐1 P‐glycoprotein expression in invasive breast cancer: A prognostic study , 2004, International journal of cancer.

[38]  B. Stripp,et al.  Molecular phenotype of airway side population cells. , 2004, American journal of physiology. Lung cellular and molecular physiology.

[39]  Zhao Zhigang,et al.  Prostate stem cell antigen (PSCA) expression in human prostate cancer tissues: implications for prostate carcinogenesis and progression of prostate cancer. , 2004, Japanese journal of clinical oncology.

[40]  Thomas Wheeler,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 , 2004, The American journal of surgical pathology.

[41]  S. Varambally,et al.  JAGGED1 Expression Is Associated with Prostate Cancer Metastasis and Recurrence , 2004, Cancer Research.

[42]  David L Rimm,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. , 2004, The American journal of pathology.

[43]  Mary E. Mangan,et al.  The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data , 2005, Genome Biology.

[44]  I. Ellis,et al.  Expression of luminal and basal cytokeratins in human breast carcinoma , 2004, The Journal of pathology.

[45]  Mark A Rubin,et al.  Prospective evaluation of AMACR (P504S) and basal cell markers in the assessment of routine prostate needle biopsy specimens. , 2004, Human pathology.

[46]  D. Ghosh,et al.  Androgen-Independent Prostate Cancer Is a Heterogeneous Group of Diseases , 2004, Cancer Research.

[47]  D. Grignon,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 , 2004, The American journal of surgical pathology.

[48]  Daniel J Garry,et al.  Persistent expression of the ATP-binding cassette transporter, Abcg2, identifies cardiac SP cells in the developing and adult heart. , 2004, Developmental biology.

[49]  Ziding Feng,et al.  Syndecan-1 expression in locally invasive and metastatic prostate cancer. , 2004, Urology.

[50]  Ji Hye Hwang,et al.  624 Isolation of muscle derived stem cells from rat and its smooth muscle differentiation , 2004 .

[51]  M. Vivanco,et al.  Growth and differentiation of progenitor/stem cells derived from the human mammary gland. , 2004, Experimental cell research.

[52]  John R. Yates,et al.  CEBS object model for systems biology data, SysBio-OM , 2004, Bioinform..

[53]  Judith A. Blake,et al.  The mouse Gene Expression Database (GXD): updates and enhancements , 2004, Nucleic Acids Res..

[54]  Ela Hunt,et al.  An object model and database for functional genomics , 2004, Bioinform..

[55]  D. Horsfall,et al.  Androgen receptor levels in prostate cancer epithelial and peritumoral stromal cells identify non‐organ confined disease , 2005, The Prostate.

[56]  T. Dale,et al.  The breast cancer resistance protein BCRP (ABCG2) concentrates drugs and carcinogenic xenotoxins into milk , 2005, Nature Medicine.

[57]  Nigel W. Hardy,et al.  Summary recommendations for standardization and reporting of metabolic analyses , 2005, Nature Biotechnology.

[58]  W. Sauerbrei,et al.  Reporting recommendations for tumor marker prognostic studies (REMARK). , 2005, Journal of the National Cancer Institute.

[59]  F. Gage,et al.  Human embryonic stem cells express an immunogenic nonhuman sialic acid , 2005, Nature Medicine.

[60]  Alvis Brazma,et al.  MGED standards: work in progress. , 2006, Omics : a journal of integrative biology.

[61]  EMAGE: a spatial database of gene expression patterns during mouse embryo development , 2005, Nucleic Acids Res..

[62]  A. Brazma,et al.  Standards for systems biology , 2006, Nature Reviews Genetics.

[63]  Chris F. Taylor,et al.  Development of FuGO: an ontology for functional genomics investigations. , 2006, Omics : a journal of integrative biology.

[64]  Andrew R Jones,et al.  FuGE: Functional Genomics Experiment Object Model. , 2006, Omics : a journal of integrative biology.

[65]  Paul T. Spellman,et al.  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.

[66]  Andrew R Jones,et al.  A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group. , 2006, Omics : a journal of integrative biology.

[67]  Ronald C. Taylor,et al.  Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). , 2006, Omics : a journal of integrative biology.

[68]  Chris F. Taylor,et al.  The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). , 2006, Omics : a journal of integrative biology.

[69]  C. Mason,et al.  Proposal for a universal minimum information convention for the reporting on the derivation of human embryonic stem cell lines. , 2006, Regenerative medicine.

[70]  Monte Westerfield,et al.  The Zebrafish Information Network: the zebrafish model organism database , 2005, Nucleic Acids Res..

[71]  Janan T. Eppig,et al.  The mouse Gene Expression Database (GXD): 2017 update , 2016, Nucleic Acids Res..

[72]  Nicholas Burton,et al.  EMAP and EMAGE - A framework for understanding spatially organized data , 2003, Neuroinformatics.

[73]  Nigel W. Hardy,et al.  The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics , 2007, Nature Biotechnology.

[74]  David Salgado,et al.  COMPARE, a multi-organism system for cross-species data comparison and transfer of information , 2008, Bioinform..

[75]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[76]  Thorsten Henrich,et al.  4DXpress: a database for cross-species expression pattern comparisons , 2007, Nucleic Acids Res..

[77]  J. Picard.  Centre National de la Recherche Scientifique (CNRS) , 2008 .

[78]  Shannon McWeeney,et al.  MIFlowCyt: The minimum information about a flow cytometry experiment , 2008, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[79]  David M. Shotton,et al.  FlyTED: the Drosophila Testis Gene Expression Database , 2009, Nucleic Acids Res..