database of ligand->receptor->TF(or transcriptional target)

Is there an online database or package-based tool to find interactions where each record has at least:

ligand gene
receptor gene
transcriptional target
direction of regulation [is (4) up or down in response to (1,2)]*

* (4) can just be omitted if (3) is always up in a certain database

Any species is fine (I have fish data), since I can just map the orthologs with biomart.

database signaling

• 1,002 views • link

updated 5.7 years ago by Biostar

• written 5.9 years ago by mk

0 answers

No answers yet.

More posts like this

OMA use case
written 1.4 years ago by nmalexan •

Hello, I have been using oma standalone to assign orthologs between vertebrate genomes like so: I essentially have one mammal and three birds and am …
Gene listed as "uncharacterized" even if I found it through another search term
written 3.5 years ago by 100dustedclays •

I was looking if a certain species had a particular gene, 1)so I went to NCBI and searched typed the "lipase" into the search bar. …
how to get rid of redundancies in an RNA-seq experiment but preserving genes changing in opposite d…
written 7.5 years ago by Mozart

Hello there, it ha been a while since my last post. I spent a lot of time with my music stuff (please, see my nickname …
Binding affinity DB out there?
written 7.6 years ago by phosphodiester_bond •

I know this is a long shot, but... Say you have a compound (could be a drug, but not necessarily), and a particular protein of …
Tool: UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D struc…
written 8.3 years ago by francois.bonnardel •

Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in …
biomaRt getSequence() connection time-out
written 9.2 years ago by flaviuvadan •

I am using biomaRt to pull some sequences from EnsEMBL using getSequence() from the biomaRt library in R. Here is a relevant piece of code: …
Tool: PlantTFDB and PlantRegMap: Plant Transcription Factor Database and Plant Regulation Data and …
written 9.8 years ago by jin •

Plant Transcription Factor Database ([PlantTFDB][1]) provides a comprehensive, high-quality resource of plant transcription factors (TFs), regulatory elements and interactions between them. In the latest version, …
Job: Computational postdoc in Cambridge UK: transcriptional regulation in 3D genome
written 12.1 years ago by a11msp

### [Transcriptional Regulation in 3D Genome Computational Postdoctoral Research Scientist][1] Closing Date: 1st September 2014 We are looking for a highly motivated computational postdoctoral scientist …
Using ensembl biomart retrieving orthologous codin sequence
written 12.3 years ago by ishengomae

<p>I have list of transcript IDs for the cow coding sequences and I want to use these IDs to retrieve orthologous sequences from other ensembl …
Problem Querying Archived Ensembl 73 With Biomart
written 12.6 years ago by neelroop •

<p>I regularly use biomaRt, the R package, to query archived versions of Ensembl. I had been querying Ensembl 65 for over a year with no …