Major features

New workflows

• A new set of workflows is summarized under the start page button Metabolism
• Flux balance analysis to identify enzymes, reactions and metabolites including clustering and mapping of flux data
• Enriched upstream analysis (TRANSFAC® and TRANSPATH®)
• Focused upstream analysis (TRANSFAC® and TRANSPATH®)
• Upstream analysis with feedback loop (TRANSFAC® and TRANSPATH®) indicates master regulators with expression values (fold changes) from the input set
• Identify enriched motifs in tissue specific tracks (TRANSFAC®)
• Cross-species identification of enriched motifs in promoters
• Cross-species mapping to ontologies

New and updated databases

• Human Metabolic Reaction (HMR): HMR2 contains 3.765 genes associated with over 8.000 reactions and over 3.000 unique metabolites.
• Human metabolism global reconstruction (Recon 2): The most comprehensive representation of human metabolism that is applicable to computational modeling
• Integration of the latest TRANSFAC® and TRANSPATH® versions (releases 2019.3)
• HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO): This database provides transcription factor (TF) binding models for 601 human and 396 mouse TFs, partially based on TRANSFAC.
• Reactome database has been updated to version 63.
• Integration of new Ensembl versions (Release 96), Ensembl Homo sapiens (hg38), Ensembl Mus musculus (mm10), Ensembl Rattus norvegicus (rn6)

Subread – aligns DNA- and RNA-seq reads

Subjunc – exon–exon junctions

featureCounts – counting of reads

exactSNP – SNPs for individual samples

Limma voom – Differential expression analysis

Guided limma – Linear model analysis

HISAT2 – Fast and sensitive alignment tool

HTseq Count – reads mapping for each feature

HTseq QA – Quality report for reads

EdgeR – Empirical Analysis of Digital Gene Expression Data in R

Plotting – Pie and bar charts

Tree map – Reduce functional classification terms

Get miRNA targets

miRNA feed forward loops

Analyze miRNA target enrichment