TETRAMER | Download


A direct access to the TETRAMER app (Cytoscape environment), as well as to the required gene regulatory networks collected from major publicly available efforts.

TETRAMER version 1.1.3

TETRAMER is also available at the Cytoscape app repository.

Download Tutorial

A rather intuitive overview of how to use TETRAMER for reconstructing GRNs, as well as to predict master TF regulators.

Download PDF

A web version of this document is also available here.

Available networks

 TETRAMER integrates user-provided temporal/stage differential expression information with TF-TG relationships from previously reconstructed GRNs in a variety of cell/tissue systems, and from different methods for data acquisition (microarray transcriptomes (CellNet); Cap Analysis of Gene Expression (CAGE) (Regulatory circuits); qualified transcription factors ChIP-sequencing assays (NGS-QC Generator). Herein a reference to the original publications concerning these various generic GRNs are provided, as well as the possibility to their download for its use with TETRAMER. Its use as part of the Cytoscape app is described in the TETRAMER tutorial.

CellNet: Gene regulatory Networks reconstituted by the integration of ~100 mouse or ~60 human microarray transcriptomes covering 20 mouse or 16 human cell/tissue types. These network provide information on the type of transcriptional regulation (active or repressive as defined by the correlation edge attribute).

Website | Publication

qcGenomics: Gene regulatory networks reconstituted by the integration of 2332 mouse or 3913 human TF ChIP-sequencing datasets. These networks have been reconstructed by (i) applying global/local quality-scores datasets classification (see NGS-QC Generator approach); (ii) promoter-enhancer distance criterion; as well as (iii) binding sites enrichment confidence. As part of this download networks established for different promoter-enhancer distances (2.5, 10 or 20 kb) are available; each of them computed for a minimal binding sites enrichment confidence (MACS2 peak calling; p-value=1x10-50) and a minimal quality score of CCC (quality range from A to D; see NGS-QC Generator approach). It is worth to mention that under TETRAMER is possible to increase the analytical stringency by excluding events on the basis of the binding site intensity or its enrichment confidence (p-value).

Website | Publication

RegulatoryCircuits: Gene regulatory Networks reconstituted by the integration of human CAGE readouts assessed by the FANTOM consortium covering more than 300 human cell/tissue types. For its use with TETRAMER, all cell/tissue type networks were summarized into a single GRN. These network provide an score for the relevance of the TF-TG relationship that can be used for enhancing the analytical stringency (score edge attribute from 0 to 1; where 0 corresponds to the more confident edges).

Website | Publication