Insights Into The Mechanisms Of AML Del9q Progression

Analysis of hnRNP K interacting RNAs in myeloid KG-1a cellsn

HNRNPK is part of the minimally deleted region (MDR) in AML del(9q). To understand the function of hnRNP K in pathogenesis of this AML subtype, we analyzed the function of hnRNP K as an RNA binding protein in myeloid cells. Co-immunoprecipitated RNAs from hnRNP K and non-related control immunoprecipitation as well as input RNA were subjected to next generation sequencing. This analysis revealed an specific interaction of hnRNP K with 1076 RNAs, among them many mRNAs encoding transcription factors involved in myeloid differentiation and AML pathogenesis.

Installing / Getting started

Software requirements:

1. Java
Java 8

2. R
To run the R markdowns you need, besides the core installation of R 4.0, the following R-Libraries:

biomaRt
DT
genefilter
tidyverse
ggplot2
ggseqlogo
cowplot
DESeq2
RColorBrewer
svglite

Usage instructions

1. Running Downstream analysis

2. Running MotifSearcher

The first step is to take the 1076 transcripts and perform Motif matching using our MotifSearcher program. In the following,
we print the help section of the program, describing its usage.

            ===========  __  __       _   _  __ _____                     _               
              =====  	|  \/  |     | | (_)/ _/ ____|                   | |              
               =====	| \  / | ___ | |_ _| || (___   ___  __ _ _ __ ___| |__   ___ _ __ 
 	        =====	| |\/| |/ _ \| __| |  _\___ \ / _ \/ _` | '__/ __| '_ \ / _ \ '__|
                 =====	| |  | | (_) | |_| | | ____) |  __/ (_| | | | (__| | | |  __/ |   
 	          ===== |_|  |_|\___/ \__|_|_||_____/ \___|\__,_|_|  \___|_| |_|\___|_|   
            ===========
              v 0.1.0

MotifMatching (0.1.0) 
Copyright (c) 2020 Ali T. Abdallah, All rights reserved.
-------------------------------------------------------------------------------

'MotifMatching' detects and counts all matches of one or multiple motifs in one
or multiple regions of one or multiple gene products.

The commands below should be preceded by 'java -jar':

Usage:
MotifMatching.jar
-i  INPUT_FILE_PATHS
	  [-n names]
-o  OUTFILE
	  -m MOTIFS_DEFINITION
    [options]
MotifMatching -h | --help | --version

Arguments:
i   a list of comma separated absolute paths of fasta files each of which
    containing one or multiple sequences from the same genomic region.\n"+
    The header is expected to follow the fasta format guidelines, " + 
n   a list of comma separated names of these files/regions [optional]
	  otherwise the names of the files are taken as standard names.
o   the absolute path of the output file.
m   A list of regular expressions defining the motifs to search for.
	  Optionally it is possible to add to each motif a size limitation
	  by adding {size} to each motif definition in the list. For example:
	  [CT]CCC*[CT]CCC*{19},[CT]CCC*[CT]CCC*[CT]CCC*[CT]CCC{38}.
	  In this example the algorithm will look for all instances of the first
	  motif having a size less than 19 and all instances having a size less
	  than 38.";

3. Running SequenceLogoGenerator script

Here you should say what actually happens when you execute the code above.

Licensing

"The code in this project is licensed under MIT license."

Zhaoxu-Gao / MotifSearcher