DHB and WSA performed sample annotation and gathered follow-up of the patients.
These databases are, however, heterogeneous in format, sample annotation, and statistical post-processing of experimental results.
Thresholding improves sample clustering (see below), provides a read-out for sample annotation, and simplifies quantification of sample relationships.
TVG looked up patient records in the database and tissue samples in the tumour bank, performed sample annotation and gathered follow-up of patients.
ADe, JPM, and KH provided clinical input, looked up patient records in the database, performed sample annotation, and gathered follow-up of patients.
To determine how Literature Lab compares with existing, publicly available sample annotation and literature mining technologies, we imported the AKT mouse and metastatic prostate cancer gene lists into GOMiner [ 21], MeSHer [ 20], and GeneCite [ 38].
Template generation is implemented using a MySQL database to store semantic relationships between standard experiment types from the MGED Ontology (Whetzel et al., 2006) and the sample annotation and experimental variables expected for each experiment type.
First, a formative study that examines the utility of PACT for expert curriculum designers and curriculum research groups, using a sample annotation process – and reflection on the outcomes of that process – to demonstrate that my approach is feasible and useful for those groups.
Primers for RT-qPCR are listed in Supplementary Data 7, and for ChIP-PCR in Supplementary Data 8. Normalized gene expression data were obtained from the Cancer Genome Atlas lower-grade glioma publication page (https://tcga-data.nci.nih.gov/docs/publications/lgg_2015/ //tcga-data.nci.nih.gov/docs/publications/lgg_2015/and appendix 2 of the lower-grade glioma publication2.
Microarray data and sample annotations have been deposited in the caArray database.
