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msDiff : comparison of two data files, for validation of conversion and preprocessing.
Many models in the Physiome Repository (most of which are JSim-based) have experimental data in the project files for validation testing.
As well, it is necessary to obtain permission from the Danish Health and Medicines Authority and the chief physician from relevant hospital departments to retrieve medical record files for validation of DNPR data.
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Therefore, we can use the gene-publication association in this file for validation purpose.
More general details about ontologies used in proteomics, the use of CV terms in connection with mapping files for semantic validation and MIAPE compliance checking and the OBO format and related tools for working with OBO files are presented in an overview article by Mayer et al. (in preparation).
Eleven genes were randomly selected from seven functional categories (Fig. 2a and Additional file 4) for validation by quantitative real-time PCR (qRT-PCR).
We selected three additional genes, PRDM16, ROBO3, and CXCL14, that displayed promoter hypermethylation already in the preleukemic or early leukemic stage (Additional file 4) for validation in human AML samples.
The primers and expected amplicon size are listed in Additional file 4. For validation, RNA was extracted from the spleen tissue of both the male and female bats using Trizol LS (Invitrogen, Carlsbad, CA).
For the Colorectal DSA 13 genes (Additional file 2) were selected for validation; all validations were carried out in three independent experiments (Additional file 3).
The experimental MS/MS spectra of 5-OAHSA, 9-OAHSA and 12-OAHSA (Additional file 1) were used for validation of the in silico library as they had not been employed in the library generation.
(XLSX 14 kb) Additional file 6: Primer sequences for validation of bi-allelic variant calls.
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