Module name: lba-enrichment

Localize preys using the localization by association (LBA) technique

parameters	definition	default
database	fasta database for mapping gene names to IDs
fdr	FDR threshold for defining significant preys	0.01
minBaits	minimum baits a prey must be seen with to be included in the analysis	1
minFC	minimum fold change to include a prey in an association list (exclusive)	1
namespace	GO namespace to use, one of BP, CC, MF	CC
outFile	output file name for prey localization data	lba-enrichment.txt
preyLimit	the maximum number of associated preys to use for defining prey profile	100
saintFile	SAINT txt file

Example file formats

database

>NP_001263222.1|gn|NISCH:11188| nischarin isoform 2 [Homo sapiens]
MATARTFGPEREAEPAKEARVVGSELVDTYTVYIIQVTDGSHEWTVKHRYSDFHDLHEKLVAERKIDKNL
LPPKKIIGKNSRSLVEKREKDLEVYLQKLLAAFPGVTPRVLAHFLHFHFYEINGITAALAEELFEKGEQL
LGAGEVFAIGPLQLYAVTEQLQQGKPTCASGDAKTDLGHILDFTCRLKYLKVSGTEGPFGTSNIQEQLLP
FDLSIFKSLHQVEISHCDAKHIRGLVASKPTLATLSVRFSATSMKEVLVPEASEFDEWEPEGTTLEGPVT
AVIPTWQALTTLDLSHNSISEIDESVKLIPKIEFLDLSHNGLLVVDNLQHLYNLVHLDLSYNKLSSLEGL
HTKLGNIKTLNLAGNLLESLSGLHKLYSLVNLDLRDNRIEQMEEVRSIGSLPCLEHVSLLNNPLSIIPDY
RTKVLAQFGERASEVCLDDTVTTEKELDTVEVLKAIQKAKEVKSKLSNPEKKGGEDSRLSAAPCIRPSSS
PPTVAPASASLPQPILSNQGNRVCILLLVEPHSPAWAPWLGWGWGRGASTCFQQGQTQGGQCLLQAGPRG
GTHGRGAWPDASCCLLGEDSQLL
>NP_001263218.1|gn|PRKAR1A:5573| cAMP-dependent protein kinase type I-alpha regulatory subunit isoform a [Homo sapiens]
MESGSTAASEEARSLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFERLEKEEAKQIQNLQK
AGTRTDSREDEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDYKTMAALAKAIEKNVLFSH
LDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGEGGSFGELALIYGTP
RAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQ
KIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKL
DRPRFERVLGPCSDILKRNIQQYNSFVSLSV

Output

• lba-enrichment.txt: table with enriched terms for each prey gene