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

Deutsch, Eric W.; Ball, Catherine A.; Berman, Jules J.; Bova, G. Steven; Brāzma, Alvis; Bumgarner, Roger E.; Campbell, D. S.; Causton, Helen C.; Christiansen, Jeffrey H.; Daian, Fabrice; Dauga, Delphine; Davidson, Duncan; Gimenez, Grégory; Goo, Young Ah; Grimmond, Sean M.; Henrich, Thorsten; Herrmann, Bernhard G.; Johnson, Michael H.; Korb, Martin; Mills, Jason C.; Oudes, Asa; Parkinson, Helen; Pascal, Laura E.; Pollet, Nicolas; Quackenbush, John; Ramialison, Mirana; Ringwald, Martin; Salgado, David; Sansone, Susanna-Assunta; Sherlock, Gavin; Stoeckert, Christian J.; Swedlow, Jason R.; Taylor, Ron; Walashek, Laura S; Warford, Anthony; Wilkinson, David G.; Zhou, Yi; Zon, Leonard I.; Liu, Alvin Y.; True, Lawrence D.

doi:10.1038/nbt1391

Cited by 116 publications

(84 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Anatomical data include anatomical ontologies in OBO format (Smith et al 2007), the collection of available reconstructed embryos, each with its biometry data and the 3DVE installation package. Expression data include all in situ hybridization data in a MISFISHIE-compliant XML format (Deutsch et al 2008), including images, and modified to associate expression patterns in experimentally manipulated and control situations (example available at http://aniseed-ibdm.univ-mrs.fr/exchange_format. php).…”

Section: System Administration Curation and Data Downloadmentioning

confidence: 99%

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

Tassy¹,

Dauga²,

Daian³

et al. 2010

Genome Res.

Self Cite

114

View full text Add to dashboard Cite

Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions.

show abstract

Section: System Administration Curation and Data Downloadmentioning

confidence: 99%

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

Tassy¹,

Dauga²,

Daian³

et al. 2010

Genome Res.

Self Cite

114

View full text Add to dashboard Cite

show abstract

“…To address these variations and to allow meta-analyses, many interest groups have established minimum information requirements for publishing data based on specific assays (mRNA expression profiling, 5 quantitative polymerase chain reaction (PCR), 6 immunohistochemistry and in situ hybridization 12 ) or technical disciplines (proteomics 50 and genomics 15,49 ). The human medical community has developed similar standards for prognostic biomarker reporting 29 and for the conduct of clinical trials.…”

Section: Introductionmentioning

confidence: 99%

Recommended Guidelines for the Conduct and Evaluation of Prognostic Studies in Veterinary Oncology

et al. 2010

View full text Add to dashboard Cite

There is an increasing need for more accurate prognostic and predictive markers in veterinary oncology because of an increasing number of treatment options, the increased financial costs associated with treatment, and the emotional stress experienced by owners in association with the disease and its treatment. Numerous studies have evaluated potential prognostic and predictive markers for veterinary neoplastic diseases, but there are no established guidelines or standards for the conduct and reporting of prognostic studies in veterinary medicine. This lack of standardization has made the evaluation and comparison of studies difficult. Most important, translating these results to clinical applications is problematic. To address this issue, the American College of Veterinary Pathologists' Oncology Committee organized an initiative to establish guidelines for the conduct and reporting of prognostic studies in veterinary oncology. The goal of this initiative is to increase the quality and standardization of veterinary prognostic studies to facilitate independent evaluation, validation, comparison, and implementation of study results. This article represents a consensus statement on the conduct and reporting of prognostic studies in veterinary oncology from veterinary pathologists and oncologists from around the world. These guidelines should be considered a recommendation based on the current state of knowledge in the field, and they will need to be continually reevaluated and revised as the field of veterinary oncology continues to progress. As mentioned, these guidelines were developed through an initiative of the American College of Veterinary Pathologists' Oncology Committee, and they have been reviewed and endorsed by the World Small Animal Veterinary Association.

show abstract

“…For instance, data coming from transcriptome, proteome and other "omic" technologies applied to biofilm populations should be documented as suggested by MIAME [14], MIAPE [15], and similar guidelines. This would also be the case for specific techniques, such as fluorescence in situ hybridisation or flow cytometry, for which minimum information guidelines have also been reported [16]. While existing XML-based laboratory standards, such as the AnIML (the Analytical Instrumentation Markup Language) [17], support the documentation of laboratory workflows, high-throughput and statistical methods are not conveniently linked.…”

Section: Bml Data Representationmentioning

confidence: 99%

Enabling systematic, harmonised and large-scale biofilms data computation: The Biofilms Experiment Workbench

Pérez-Rodríguez¹,

Glez-Peña²,

Azevedo

et al. 2015

Computer Methods and Programs in Biomedicine

View full text Add to dashboard Cite

show abstract

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

Cited by 116 publications

References 68 publications

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

Recommended Guidelines for the Conduct and Evaluation of Prognostic Studies in Veterinary Oncology

Enabling systematic, harmonised and large-scale biofilms data computation: The Biofilms Experiment Workbench

Contact Info

Product

Resources

About