METANet

This project stores the data, scripts, citation and links which describe the source and transformations on externally produced data which is added to the Human TF Network project

Data

FANTOM5 CAGE

see data/FANTOM5

https://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/

The FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature 507, 462–470 (2014). https://doi.org/10.1038/nature13182

Andersson, R., Gebhard, C., Miguel-Escalada, I. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455–461 (2014). https://doi.org/10.1038/nature12787

Erik Arner et al., Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.Science347,1010-1014(2015).DOI:10.1126/science.1259418

Marbach TF networks

see data/Marbach

Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, Bergmann S: Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. Nat Methods 2016, 13(4):366-370. https://doi.org/10.1038/nmeth.3799

PANDA TF networks

see data/PANDA

Sonawane AR, Platig J, Fagny M, Chen C-Y, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML: Understanding Tissue-Specific Gene Regulation. Cell Reports 2017, 21(4):1077-1088. https://doi.org/10.1016/j.celrep.2017.10.001

Scripts

Processing REMAP 2020 TF ChIP-seq binding scores

see scripts/remap_labels

Expression filtering

see scripts/expression_filtering

LASSO expression feature construction

see scripts/lasso

BART expression feature construction

see scripts/bart

METANet XGBoost modeling

Scripts for preprocessing, modeling, and predictions using XGBoost. see metanet_modeling

Subsetting of PANDA networks

see scripts/PANDA_subsetting

Network quality evaluation scripts

see scripts/evaluation/network_quality/ for network quality evaluation scripts.

GO and GO-directness evaluation were done using BrentLab/NET-evaluation.

eQTL evaluation script

see scripts/evaluation/tissue_specificity

Interpreting evaluation results

see scripts/notebooks for jupyter notebooks of interpreting evaluation results.

FISHNET application

see scripts/fishnet