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READ_ME.txt
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OVERVIEW OF THE MATERIAL
CSV Files
The list of Green and Amber genes in Structural Eye disease has been downloaded from https://panelapp.genomicsengland.co.uk/panels/509/
version 1.3
Files contain human-mouse syntenic Long Range Interactions(hmsLRI) in which a green or amber gene is involved:
hmsLRI list files
"hmsLRI's_Promoter_within_Green_Genes.csv": List of hmsLRI in which the promoter anchor overlaps the promoter
of a Green Gene (defined as ± 2.5kb of TSS)
"hmsLRI's_Enhancer_within_Green_Genes.csv": List of hmsLRI in which the enhancer anchor is within a Green Gene region
"hmsLRI's_Promoter_within_Amber_Genes.csv": List of hmsLRI in which the promoter anchor overlaps the promoter
of an Amber Gene (defined as ± 2.5kb of TSS)
"hmsLRI's_Enhancer_within_Amber_Genes.csv": List of hmsLRI in which the enhancer anchor is within a Amber Gene region
"hmsLRI's_Promoter_within_Fitzpatrick_Genes.csv": List of hmsLRI in which the promoter anchor overlaps the promoter
of a Fitzpatrick Gene (defined as ± 2.5kb of TSS)
"hmsLRI's_Enhancer_within_Fitzpatrick_Genes.csv": List of hmsLRI in which the enhancer anchor is within a Fitzpatrick Gene region
"hmsLRI's_Promoter_within_Eye_development_Genes.csv": List of hmsLRI in which the promoter anchor overlaps the promoter
of an Eye development Gene (defined as ± 2.5kb of TSS)
"hmsLRI's_Enhancer_within_Eye_development_Genes.csv": List of hmsLRI in which the enhancer anchor is within a Eye development Gene region
Enhancer nodes files
"Enhancer_Nodes_Connected_to_Green_Genes.csv": List of Enhancer nodes in which the promoter anchor is the promoter of a Green Gene
(defined as ± 2.5kb of TSS)
"Enhancer_Nodes_within_Green_Genes.csv": List of Enhancer nodes in which the enhancer anchor is within a Green Gene region
"Enhancer_Nodes_Connected_to_Amber_Genes.csv": List of Enhancer nodes in which the promoter anchor is the promoter of an Amber Gene
(defined as ± 2.5kb of TSS)
"Enhancer_Nodes_within_Amber_Genes.csv": List of Enhancer nodes in which the enhancer anchor is within a Amber Gene region
"Enhancer_Nodes_Connected_to_Fitzpatrick_Genes.csv": List of Enhancer nodes in which the promoter anchor is the promoter of a Fitzpatrick Gene
(defined as ± 2.5kb of TSS)
"Enhancer_Nodes_within_Fitzpatrick_Genes.csv": List of Enhancer nodes in which the enhancer anchor is within a Fitzpatrick Gene region
"Enhancer_Nodes_Connected_to_Eye_development_Genes.csv": List of Enhancer nodes in which the promoter anchor is the promoter of an
Eye development Gene (defined as ± 2.5kb of TSS)
"Enhancer_Nodes_within_Eye_development_Genes.csv": List of Enhancer nodes in which the enhancer anchor is within a Eye development Gene region
Genome Browser track hub
UCSC Genome Browser
The hmsLRI are available as a remote track hub for UCSC Genome Browser, the interactions are represented using
different colors based on if the involved gene is a Green gene or an Amber gene and in a separate track there
are the interactions involving a gene identified by Fitzpatrick (Red) and the list of eye development genes (blue);
Below each interactions track there is a track with the enhancer node regions
You can browse them at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?redirect=manual&source=genome.ucsc.edu
Under the section "My Hubs" you can insert the following URL and add the Hub: https://github.com/ctglab/UCSC_Track_hub_hmsLRI_Eye_diseases/raw/main/UCSC_Genome_Browser_hub/hubDirectory/hub.txt