Download vap: a versatile aggregate profiler for efficient genome

VAP: A VERSATILE AGGREGATE
PROFILER FOR EFFICIENT GENOMEWIDE DATA REPRESENTATION AND
DISCOVERY
COULOMBE C, POITRAS C, NORDELL-MARKOVITS A, BRUNELLE M,
LAVOIE MA, ROBERT F, JACQUES PÉ. (2014)
Christian Poitras
IRCM
WHAT IS CHIP-SEQUENCING
¢  Combination
of chromatin immunoprecipitation
(ChIP) with ultra high-throughput massively
parallel sequencing
¢  Allows
mapping of protein-DNA interactions in
vivo on genome scale
CHIP-SEQ
* Jkwchui - Cell diagram adapted from LadyOfHats' Animal Cell diagram. Information based on Illumina data
sheet, as well as ChIP and immunoprecipitation articles & references.
WHAT IS VAP
¢  Stands
for “versatile aggregate profiler”
¢  Generates aggregate profiles of genomic datasets
over groups of regions of interest
¢  Uses absolute or relative method
¢  Customizable number of windows over a specified
number of reference points
— 
Reference points delimit the genes of interest as well
as their flanking genes, or even exons
¢  Accessible
through both a user-friendly platformindependent Java interface or via command line
¢  3 modes: Annotations, Exons and Coordinates
¢  Can run on laptops
CHIP-SEQ ANALYSIS WORKFLOW
VAP
VAP WORKFLOW
Input
• BedGraph,
WIG,
BigWig
• Annotations
(optional)
• Annotation
groups
• Filters
(optional)
VAP
• Version
1.1.0 (2015)
Data does not need to be ChIP-Seq or ChIP-chip
although this is the most common use
Output
• Aggregate
profiles
(Text, PNG)
• Heatmaps
(Text, PNG)
ANNOTATION GROUPS
¢  For
annotation and exon mode, the annotation
groups files contain gene names present in the
annotations file
¢  For coordinates mode, the annotation groups files
contain coordinates for 2 reference points
— 
For more than 2 reference points, a special format is
required
¢  VAP
can create aggregate profiles of any data
that have coordinates
WHAT IS ABSOLUTE METHOD AND WHY
SHOULD I CARE?
¢  Relative
— 
method:
Windows are larger for long genes
All genes are divided into the same number of windows
¢  Consequently, a signal appearing at the same distance from
the TSS (e.g. 200 bp) for a long and a short gene will be
placed in different windows (e.g. first window of a 4 kb gene
compared to the 20th window of a 400 bp gene divided into
40 windows)
¢ 
— 
Easier to program
¢  Absolute
— 
— 
method:
Windows are the same size for all genes
Some windows will not exist for small genes
RELATIVE VS ABSOLUTE
* Pokholok D, Harbison C, Levine S, Zeitlinger J, Lewitter F, Gifford DK,
Young RA. (2005)
RELATIVE VS ABSOLUTE
¢  Erroneous
conclusion “Long genes depend on the
Set2/Rpd3S pathway for accurate transcription”
due to relative method
* Li B, Gogol M, Carey M, Pattenden SG, Seidel C,
Workman JL. (2007)
VAP OUTPUT
VAP RAW AGGREGATE PROFILE (BASED ON
TEST DATA)
* Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe
PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, Young RA. (2005)
* Guillemette B, Bataille AR, Gévry N, Adam M, Blanchette M, Robert F, Gaudreau L. (2005)
VAP RAW HEATMAP (BASED ON TEST DATA
- UNSORTED)
* Guillemette B, Bataille AR, Gévry N, Adam M, Blanchette M, Robert F,
Gaudreau L. (2005)
VAP INTERFACE
VAP INTERFACE
VAP INTERFACE
THANKS
¢  Pierre-Étienne
Sherbrooke
Jacques
¢  Charles
Coulombe – Sherbrooke
¢  François Robert – IRCM
¢  And all other authors!
¢  Benoit
Coulombe Lab - IRCM