miRNA transcription factor loop webserver

Description

This webserver makes it possible to look up predicted 3-element regulatory loops containing a gene of interest. Mutually regulating transcription factors (TFs) and microRNAs (miRNAs) can regulate a third target gene utilising the regulatory benefits of feedforward and feedback to regulate target gene transcription.

Citing this work

Multiple independent analyses reveal transcription factors are an enriched functional class associated with microRNAs (submission in progress)
Larry Croft, Damian Szklarczyk, Lars Juhl Jensen, Jan Gorodkin

Searching for 3-element loops

To search 3-element loop motifs click the search link top right. To download 1-element and 2-element loops for human and mouse click the links below.

Additional data for manuscript

additional_1_supplementary_tables.xlsx
This file contains source data, additional graphs, and calculated values for this work in 15 Excel sheets: textmining data, textmining by eggNOG categories, textmining by GO categories, TarBase scoring system, TarBase data scored, TarBase score vs. TF enrichment, TarBase by eggNOG categories, TarBase by GO categories, predicted miRNA targets by eggNOG categories, predicted miRNA targets by GO categories, transcription factor binding site density distributions, human network 3-element motifs, mouse network 3-element motifs, human enriched loops, mouse enriched loops.

additional_2_human_miRNA_TF_net_ensg.tdf.gz
Tab delimited text file containing all links in the human predicted miRNA:TF network. First column is start node, second column is end node, last column is 1 or 2 depending whether the link is activating (1 transcription factor binding site) or suppressing (2 miRNA binding site). Gene identifiers are ENSEMBL IDs and miRBase IDs.

additional_3_mouse_miRNA_TF_net_ensg.tdf.gz
Tab delimited text file containing all links in the mouse predicted miRNA:TF network. First column is start node, second column is end node, last column is 1 or 2 depending whether the link is activating (1 transcription factor binding site) or suppressing (2 miRNA binding site). Gene identifiers are ENSEMBL IDs and miRBase IDs.

Additional data

Textmining dictionaries
miRbase15_dictionary.gz
A tab delimited text file containing a synonym dictionary used for text-mining miRNA co-occurrences.
String_protein_dictionary.gz
A tab delimited text file derived from String containing a synonym dictionary used for text-mining miRNA co-occurrences.

1 and 2 element loops as tab delimited files
list of human 1-element positive feedback loops (auto loops)
list of mouse 1-element positive feedback loops (auto loops)
list of human 2-element positive feedback loops
list of human 2-element negative feedback loops
list of mouse 2-element positive feedback loops
list of mouse 2-element negative feedback loops


Contacting us

Email croft[symbol]rth.dk for more information, or if you are having difficulties with the webserver.