Table 1 Interaction evidence types supported by myGRN

Mined from Literature

Inference of an interaction from in silico textual analysis of a published paper by a natural language processing (NLP) algorithm.

Transient transfection

Perturbation of expression of a reporter under control of the downstream gene promoter on disruption of upstream gene expression

Stable transgenic line

Perturbation of expression of a reporter under control of the downstream gene promoter on disruption of upstream gene expression

Protein synthesis inhibition

Demonstration of a direct interaction by inhibition of intermediate protein production using cyclohexamide or other inhibitors.

In silico prediction

Prediction of a binding site for the upstream gene product in the downstream gene promoter using in silico methods.

Elecrophoretic Mobility Shift Assay (EMSA)

EMSA showing direct binding between the upstream gene product and a fragment of the downstream gene promoter in vitro.

DNase Footprinting

Protection of a putative binding site in radiolabelled DNA containing the downstream gene promoter by the upstream gene product.

ChIP-on-chip

Chromatin Immunoprecipitation using antibody for the upstream gene, and analysis of the binding site locations on a microarray.

Stable transgenic reporter

Transgenic organism carrying a reporter gene under the control of the promoter of the gene of interest.

Transient transgenic reporter

Transient transfection of a construct carrying a reporter gene under the control of the promoter of the gene of interest.

SAGE

Detection of a sequence tag from an mRNA in a Serial Analysis of Gene Expression experiment.

RT-PCR

Measurement of mRNA by Reverse-Transcription Polymerase Chain Reaction.

Primer extension

Extension of a gene-specific primer using an mRNA template.

Nuclease protection

Measurement of mRNA by hybridization with an antisense probe followed by ribonuclease digestion of unbound RNA.

Northern Blot

Measurement of mRNA by northern blot.

In situ hybridisation

Measurement of mRNA by in-situ hybridization.

cDNA Library

Isolation of a gene from a cDNA library.

Array

Measurement of mRNA on an expression DNA microarray.

Western blot

Measurement of protein by western blot.

Mass Spectrometry

Detection of protein from cell or tissue extract using mass spectrometry.

Immunohistochemistry/immunocytochemistry

Measurement of protein by antibody staining in tissue slices or cultured cells.

Mutation of binding site

Site-directed mutagenesis of a known binding site of the upstream gene in the downstream gene's promoter leads to a decrease in activity of a reporter gene

In silico inference

Inference of an interaction from mathematical modelling of experimental data such as microarray time course.

Transient transgenic

Transient transfection of a DNA construct containing the upstream gene, controlled by a constitutive or inducible promoter.

Stable transgenic

Stable transgenic cell or organism line containing the upstream gene controlled by a constitutive or inducible promoter.

RNA-based overexpression

Introduction of synthetic or purified mRNA of upstream gene into target cells or tissues.

Protein-based overexpression

Introduction of synthetic or purified protein product of upstream gene to target cells or tissues.

Transgenic knock-out

Stable transgenic cell or organism line with the upstream gene knocked-out either functionally or by expression.

RNAi

RNA interference-based knock-down or silencing of the upstream gene.

Morpholino

Morpholino-based inhibition of translation of the upstream gene mRNA.

Molecular Inhibitor

Use of an inhibitor molecule to reduce or eliminate the function of the upstream gene product.

Dominant-negative protein expression

Insertion of a dominant-negative version of an upstream regulator into a system reduces or eliminates expression of the target gene.