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Rothamsted / knetminer

KnetMiner - webapp to search and visualize genome-scale knowledge graphs
https://knetminer.com
MIT License
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Add gene regulation data to knowledge networks #31

Open KeywanHP opened 8 years ago

KeywanHP commented 8 years ago

Integrate Arabidopsis transcription factor database into the knowledge network. Visualize the information as part of the gene-evidence networks (see email trail below).

From: Richard Barker Sent: 31 August 2015 14:30 To: Keywan Hassani-Pak Subject: Promoter analysis

I think that's a great idea. After i was finished with QTL-netminer i went straight over to the AGRIS data base, thus the intergration of these data into the QTL-netminer visualization web would be awesome!

On 31 August 2015 at 14:17, Keywan Hassani-Pak keywan.hassani-pak@rothamsted.ac.uk wrote: Hi Richard

We wouldn’t want to do de novo promoter analysis in QTLNetMiner but I could imagine to integrate an existing Arabidopsis transcription factor database and visualise gene-TF-TFBS relations as part of the gene-evidence networks. I know of these two:

http://planttfdb.cbi.pku.edu.cn/index.php?sp=Ath http://arabidopsis.med.ohio-state.edu/AtTFDB/

How useful would this be? Is there a way you could evaluate which one is better on your use case?

Cheers Keywan

From: Richard Barker Sent: 31 August 2015 13:19 To: Keywan Hassani-Pak Subject: Promoter analysis

Hi Keywan I've recently just tried to analyse the promoters of my target genes. I've used the Toronto BAR promomer tool to identify some patterns and has provided many links to literature / publications. But the way these links is rubbish compared to QTLnetminer. Is there any way QTLnetminer could also mine the promoter regions of the candidate genes and pull down any literature or patterns that can be identified? Best wishes, Richard

KeywanHP commented 6 years ago

Consider integrating ATRM in one of the next releases. Contains high-confidence manually curated Arabidopsis TF-Target regulation data:

http://atrm.cbi.pku.edu.cn/download.php

jparsons2222 commented 1 year ago

atrm.cbi.pku.edu.cn took too long to respond. http://atrm.gao-lab.org/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476157/ http://atrm.gao-lab.org/for_download/Regulations_in_ATRM.xlsx

Arnedeklerk commented 1 year ago

@jparsons2222 is this still something to work on, or? @KeywanHP