Data files

Mean values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.

The ...

Incorporate research data

This table validation code is about simplifying validation of templates for end users. The main use case is an experimental scientist Elie sharing data with a Bioinformatician Bob. Elie and Bob agree to use a common template. This code enables Bob to provide Elie with a validator that checks if Elie's data conforms to the template. Making such a template check should be simple, using the checker should be simple, too. We seek to fill both requirements.

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling. The publication for the introduction and analysis of the benchmark problem collection is available at https://academic.oup.com/bioinformatics/article/35/17/3073/5280731.

1222 patients

NMN formation by NamPT was measured using LC-MS as described in supplementary information

Data used for training or testing of the model

For each module, GSEA analysis was conducted by using web-tool g:profiler and only biological process (BP) were retained. Parameters for GSEA are default.

Calculated by using R package GOSemSim.

Modules were identified by WGCNA. hub genes of each modules were identified based on intramodular degree.

Including 91 genes and 1222 Breast cancer patient This is an input data for WGCNA

Including 289 genes and 1222 Breast cancer patient This is an input data for WGCNA

Including 277 genes and 1222 Breast cancer patients. This is an input data for WGCNA.

Including 294 genes and 1222 Breast cancer Patient. This is an input data for WGCNA

Consensus between selected mapping methods.

Additional file 2

Additional File 1

Hallmark gene sets belong to different mapping schemes.

derived from Ulhen's research published in 2017.

The excel presents the mapping from GO terms to individual cancer hallmarks retrieved from selected papers.

It includes annotation number data at June 2012, June 2016 and Jan 2021.

related to Figure 6 and additional file 6

it can be used to construct the GO network

It can be used to construct the GO network

columns are ' id' , 'ncbi_taxa_id' , 'common_names' , 'lineage_string' , 'genus' , 'species' , 'parent_id' , 'left_value' , 'right_value' , 'taxonomic_rank'.