xQTLUserReview – Trac

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Version 22 (modified by Morris Swertz, 13 years ago) (diff)
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Feedback 2011_01_16

a) Meerdere QTL's in 1 plotje stoppen in de QTLFinder plugin, ipv alles los van elkaar. Dit is essentieel voor het vergelijken van de resultaten in de verschillende datasets. b) Afmaken en uploaden van de eerste dataset, iig zover mogelijk. Dus cureren en nalopen van de annotaties. BLASTen van de Wageningen probes komt dan later wel. c) WormQTL op de nieuwe server draaiend krijgen zodat we vanaf dan in de final productieomgeving opereren. d) Integratie van jBrowse visualisatie onderzoeken en als mogelijk uitwerken

Feedback QTL finder

1) De find tab zou goed het openings scherm kunnen zijn, dan kunnen de gebruikers gelijk iets typen

DONE 2) Dat er meerder probes zijn is nu niet handig, als daar ook een default voor kan komen, want het is nu niet duidelijk wat het betekend.

DONE 3) Als je op een common gen naam zoekt dan krijg je ook hits als “target of gen xxx “ omdat dat in de beschrijving staat dit is niet handig aan gezien je dan wel een hele lange lijst met probes krijgt en je niet weet welke nu van het gen is dat je zoekt.

DONE 4) Het QTL plaatje in nu veel te klein, dat zou op zijn minst leesbaar moeten zijn, dat je kan clicken om het te vergroten is wel goed.

LASTIG - plots zijn nu 'generiek' 5) Een overview functie zou ook handig zijn dus meerder QTL profiles op een figuur. Dat creëert meer waarde.

LASTIG - plots zijn nu 'generiek' 6) De QTL plaatjes zouden niet op de markers geplot moeten worden maar de bp, dan kunnenw e alle experimenten en verschillende populaties goed vergelijken.

LASTIG - plots zijn nu 'generiek' 7) De positie van het gen zo in het plaatje aangegeven kunnen worden op de x-as dan kan men gelijk zien of er een cis of trans qtl is.

DONE 8) De bp van de hoogste piek (per chromosoom) zou ook handig zijn.

Dataset tagging

We want a way to apply multiple 'tags' to datasets (matrices), e.g. "genotypes", "eQTL results", "Rockman_et_al_2010", "LOD_scores", "raw_data", etc. A suitable field would be the OntologyReference?, but this is only an XREF. It is inherited from InvestigationElement through ProtocolApplication to Data. If this would be an MREF, it would work. But this a quite a big change because it affects all InvestigationElements. An alternative is to add a new field to just Data.

Stories Yang

Story	How to demo
1. as a researcher I want to see all QTLs from a specific experiment	(1) user can choose the experiment name, e.g. GxT study, Gld-1 RNAi expression. (2) user can choose mapping method e.g. single marker mapping or full model mapping (3) user can view QTL dot plots: X axis: QTL position; Y axis: gene position; each dot represent QTL
2. as a researcher I want to see QTLs of some selected genes from a specific experiment	(1) user can paste a list of gene names into text field. (2) user can choose the experiment name, e.g. GxT study, Gld-1 RNAi expression. (3) user can choose mapping method e.g. single marker mapping or full model mapping (4) user can view QTL plots: X axis: marker position; Y axis: QTL;
3. as a researcher I want to see QTLs of some selected genes from the selected experiments data sets	(1) user can paste a list of gene names into text field. (2) user can choose the experiment names, e.g. GxT study, Gld-1 RNAi expression. (3) user can choose mapping method e.g. single marker mapping or full model mapping (4) user can view QTL plots: X axis: marker position; Y axis: QTL;
4. as a researcher I want to run "Regenotyper" to detect potential wrongly labeled samples in a selected experiments data set	(1) user can choose the experiment names, e.g. GxT study, Gld-1 RNAi expression. (2) user can view WLS score plots: X axis: samples; Y axis: WLS score
5. as a researcher I want to input genes from one pathway and show correlations in a graph	(1) user can paste a list of gene names into text field. (2) user can choose a correlation matrix. (3) user can view genes in circular graph with each edge showing the correlation strenght by thickness
6. as a researcher I want to input genes from one pathway and show QTL profiles in a graph	(1) user can paste a list of gene names into text field. (2) user can choose a specific experiemnt data set. (3) user can view genes in circular graph with QTL profiles next to gene
7. as a researcher I want to input genes from one pathway and compare correaltions between two conditions in a graph	(1) user can paste a list of gene names into text field. (2) user can choose two or more experiemnt data sets. (3) user can view genes from each conditions in circular graph with correlation strength by thickness (4) user can view genes between conditions in circular graph with correlation strength changes by thickness
8. as a researcher I want to input genes and visualize differential expression in a graph	(1) user can paste a list of gene names into text field. (2) user can choose a experiemnt data set with multiple conditions. (3) user can choose method to compute DE genes (4) view genes in ditrected circular graph with gradien color showing DE significance/fold changes
9. Similar story as 5-9, with input being "key word" from a biological process or gene fucntion etc.	same as story 5-9
10. as a researcher I want to input genes, infer causal realtionship, and visualize it in a graph	(1) user can paste a list of gene names into text field. (2) user can choose a experiemnt data set. (3) user can view genes in ditrected circular graph with inferred causal probability displayed on the arrows

Datamodel enhancements for Panacea

Genes [List] -> xQTL entity: Gene
Contains all the identified genes in a certain Wormbase release. It is a list with the main identifier the Wormbase ID (WBgene00000001). Furthermore it will contain the sequence name, common name, splice variants, start position, end position and (in a later version) can include information like intron, exon and promotor position.

Needed field	Example value	xQTL field
Wormbase ID	WBgene00000912	name
Common name	daf-16	Use: 'Alternative identifiers', MREF to 'AlternateId?' table (NEW)
Sequence name	R13H8.1	Use: 'Alternative identifiers', MREF to 'AlternateId?' table (NEW)
Splice variant	R13H8.1a	Use: XREF in 'Transcript' table pointing to 'Gene' (NEW)
Chromosome	I	chromosome_name
Start Position	10750332	bpstart
End Position	10776689	bpend

Platforms [List] -> xQTL entity: OntologyTerm
List with a micro-array platform identifier and a description about the micro-array platform

Needed field	Example value	xQTL field
PlatformID	WUR_Agilent	name
Info	4*44K array	description

Platform info [List] -> xQTL entity: Probe
This is a list per micro-array platform that contains all the info about the spots on the micro array. Spot ID, Gene ID, splice variant, probe sequence, probe position on the genome, etc.

Needed field	Example value	xQTL field
Spot ID	WUR_AGI_00001	name
Wormbase ID	WBgene00000912	Use: 'ReportsFor?' XREF pointing to a 'Gene' (NEW)
Splice variant	R13H8.1a	Use: the existing 'Transcript' to 'Gene' XREF
Probe sequence		seq
Probe Chromosome	I	chromosome_name
Probe position		bpstart
Unambiguous		mismatch

Samples [List] -> xQTL entity: Sample
List of samples. Sample ID, genotype, experiment. Sample properties == genotype matrix OR phenotype matrix

Needed field	Example value	xQTL field
Sample ID	Sample000001	name
Genotype	WN001	Use: a 'Data' matrix of Sample x DerivedTrait? instead. For example: Measurement(name=Genotype), ObservedValue?(value=WN001, feature=Genotype, target=Sample000001))
Experiment	TEMP16_EXP	Use: a 'Data' matrix, this is the name of the matrix.
Remarks		description

Experiments [List] -> xQTL entity: OntologyTerm?
List of experiments, Experiment ID, what was measured, conditions, etc… Experiments = ProtocolApplications? (== Data) Repeat per sample!

Needed field	Example value	xQTL field
Experiment ID	TEMP16_EXP	Use: Name of a 'Data' matrix (= 'ProtocolApplication?')
Measured	Gene expression	Use: Tags of a 'Data' matrix (= 'ProtocolApplication?')
Platform	WSU	Use: matrix data, phenotype of each sample in the set
Growing temperature	16	Use: matrix data, phenotype of each sample in the set
Stage	L4	Use: matrix data, phenotype of each sample in the set
Hours		Use: matrix data, phenotype of each sample in the set
Treatment	No	Use: matrix data, phenotype of each sample in the set
Remarks		Use: Description of a 'Data' matrix (= 'ProtocolApplication?')

Projects [List] -> xQTL entity: OntologyTerm?
List to link experiments together, because multiple experiments under different conditions can belong to one project. Might also be a way to give access to the different groups of data.

Report builder feedback 18 nov 2011

Yang:

Use but does not help you to 'get to know' the data in the first place.
Wanted:
- Quantative data: boxplot of measurements for each sample/individual, to inspect and detect/remove outliers -> Use e.g. boxplot(log(metaboliteexpression, exp(2.71828))) -> Or boxplot(log(t(metaboliteexpression), exp(2.71828))) for the (transposed) 'other view'
- Qualitative data: heatmap like view of e.g. genotypes -> Use e.g. image(matrix(as.numeric(as.factor(genotypes)),nrow(genotypes),ncol(genotypes))) -> Or heatmap(matrix(as.numeric(as.factor(genotypes)),nrow(genotypes),ncol(genotypes)),scale="none",Colv=NA, Rowv=NA)

Basten:

Enter gene -> get all eQTL information! Simple as can be.
Cis/trans information
Find genes in a region and get their QTLS (sounds like gBrowse)
Ofcourse everything in document 'concept map'

Matthias:

Need a bit more than just 'gene -> QTL' info, so like the Advanced button in the simple screen
Select a matrix with QTL results, then grab a row or column (e.g. select a trait)
Filter within that list using e.g. a threshold to get a smaller list of e.g. significant markers
Using this trait and marker, build a nice table with a report
Even more advanced: cross-datamatrix filtering. Select an individual and get from all matrices values which adhere to a certain filter.
Relation between promotor-gene-transcript-protein-enzyme-pathways should be used preferably to create a biological valuable report
gBrowse as an exploration tool would be super to have, and is reusable for many organisms

Panacea xQTL review Wed 9 nov 2011

Data curation and annotation of the Panacea Database (joint effort)
Host project analyses:
- Phase 1: Just add the R scripts as files for basic provenance
- Phase 2: Being able to rerun important scripts such as sample mislabeling and QTL x Env
- Phase 3: Make it easy to add and run any R script that was used
Data matrix:
- Download or visualize with CytoScape
- Need new view with more organization/hierarchy: group by experiment or annotation
- Need to couple this hierarchy with the ability to quickly run scripts for visualization or statistics on a piece of the data
Need 'supersearch' which produces reports on concepts (ie. everything related to a marker or individual)
- This should include a special 'QTL finder' tool to quickly create reports on findings using a matrix and/or traits as inputs
Focus on pathways:
- Want to query pathway information for an organism from 1..N sources (GO, WormBase, KEGG.. ?)
- Want to couple existing gene annotations to these pathways, semi-automatically (?)
- Want to use this information to run analysis/visualizations on these batches of genes
- Want to create pathway plots (biology!) with the gathered information (e.g. QTL profiles)
- Want to create CytoScape graphs of e.g. correlation of the genes

EURATRANS xQTL review Wed 9 nov 2011

Integrate with genome browser (gBrowse, formats WGL and GFF)
Need to save any filter as a URL
Need to clarify how a tool like gBrowse can specify a 'range' in filter URL syntax and link it
Also need the 'range' to work on matrices with locus data (e.g. markers) via URL
Need to add scripts as visualizers of data: e.g. let them appear in a list of possible plot types in matrix
Search box bugs: no '_name' searches possible
Use real column names instead of labels eventually, this is still very confusing
Need for advanced matrix views:
- On similar rows & columns, create 'subheaders' with multivalue display
- Alternatively, matrix merge operation to concatenate them
- Want to have a report on a value that appears in multiple matrices
- And/or reports with plots for e.g. a marker or probe with all related information from all sources

xQTL LL user workshop Fri 28 Oct 2011 general comments

Need more download formats: STATA, SAS, CSV (not TSV)
SNP data should somehow include metadata such as: imputed (yes/no), genome build, reliability, dosage, etc.
There should be a way to merge (part of a / a filtered) phenotype set with a genotype set, and retrieve the result
The application can be slow, need more speed
There are too many tabs, GUI is unclear
Need an hourglass (or something) to indicate the application is busy (blackout screen with progress bar when busy, GeneNetwork style?)
Making selections is too complex
Column paging is confusing
Filtering works 'half' (Joris please explain)
Data viewer should be able to create selections using your own file
Id's should be unrecognizable
Search filter should work on all measurements by default
Filters are lost when a user pages, this is annoying
Like other waiting times, applying a filter should cause the app to refresh with a 'wait please' status
Merging pheno- and geno sets is a special case of using a shopping cart (batches) to save selections for re-use elsewhere, this should be implemented. So you make a selection of participants based on phenotypic criteria, and then you view SNPs of interest for only those selected, and vice versa.

Download in other formats:

Plain Text

Needed field	Example value	xQTL field
Dataset ID	DATA_TEMP16	Use: Name field
Type	Gene expression	Use: Tags field
Unit	Log 2 intensities	Use: Tags field
Processed	Normalized	Use: Tags field
Experiment ID	TEMP16_EXP	Use: Tags field
Remarks		Use: Description field

Needed field	Example value	xQTL field
SNP ID	SNP_a000001	Use: Name field
Chromosome	I	Use: Chromosome_name field
Status	Confirmed	Use: Status field
Position	2312245	bpstart
Reference	A	Use: MREF of 'SNP' to 'Polymorphism' (NEW)
A	N2	Use: MREF of 'SNP' to 'Polymorphism' (NEW)
T		Use: MREF of 'SNP' to 'Polymorphism' (NEW)
C	CB4856	Use: MREF of 'SNP' to 'Polymorphism' (NEW)
G		Use: MREF of 'SNP' to 'Polymorphism' (NEW)
Remarks		Use: Description field

Needed field	Example value	xQTL field
Marker ID	Marker_00001	name
Other Name	pkI067	symbol
Type	PCR	ontologyreference_name
Chromosome	I	chromosome_name
Position	2312245	bpstart
SNP ID	SNP_a000001	Use: 'ReportsFor?' field (NEW)
Remarks		description

Needed field	Example value	xQTL field
Population ID	Pop_001	name
Parental strains	N2, CB4856	strain_name
Type	RIL	ontologyreference_name
Number of Genotypes	200	in Data
Publication		???
Remarks		description

Needed field	Example value	xQTL field
Strain_ID	N2	name
Isolation site	Bristol	phenotype of the panel
Description		description
Sequenced		phenotype of the panel