What biological relationships are extracted in EmBiology?

Expression

Changes protein abundance by affecting levels of transcript or protein stability

MDM2 has a negative "Expression" relationship with TP53

miRNA Effect

Inhibitory effect of an miRNA on its mRNA target

miR-30 has a negative "miRNAEffect" relationship with TP53

Promoter Binding

Binds to the promoter of a gene

FOXC1 has a positive "PromoterBinding" relationship with MMP7

Regulation

Changes activity by an unknown mechanism (may be direct or indirect)

SOCS3 has a positive "Regulation" relationship with diabetes mellitus

Direct Regulation

Influences activity by direct physical interaction

BRCA1 has a "DirectRegulation" relationship with BARD1

Binding

Direct physical interaction between two molecules

FANCD2 has a "Binding" relationship with BRCA1

Protein Modification

Changes the modification of the target molecule, usually by direct interaction

SRC has a "ProtModification" relationship with GRB2

Biomarker

Identification of proteins/complexes/functional classes/metabolites that are prognostic or diagnostic biomarkers for a disease

Lung cancer has a "Biomarker" relationship with IL6

Genetic Change

Genetic changes such as gene deletions, amplifications, mutations or epigenetic changes

Lung cancer has a "GeneticChange" relationship with ALK

Quantitative Change

Changes in abundance/activity/expression of a gene/protein/small molecule in a disease state

Breast cancer has a positive "QuantitativeChange" relationship with AGK

State Change

Changes in a protein’s post-translational modification status or alternative splicing events

Breast cancer has a "StateChange" relationship with estrogen receptor

Functional Assoc.

Between a disease and a cellular process or another disease

Chronic pancreatitis has a "FunctionalAssociation" relationship with pancreatic cancer

Chemical Reaction

Either enzyme catalysed or spontaneous chemical reaction

CYP3A has a "ChemicalReaction" relationship with ticagrelor

Molecular Synthesis

Changes the concentration of the target

CYP3A has a "MolSynthesis" relationship with midazolam

Molecular Transport

Changes the localization of the target

Tamoxifen has a positive "MolTransport" relationship with MAPK3

Clinical Trial

Clinical trials conducted for a drug against a disease (from CT.gov)

Tamoxifen has a positive “Clinical Trial" relationship with breast cancer

Cell Expression

Expression of proteins within or on the surface of a cell

Hepatocyte has a "CellExpression" relationship with EGFR