Transcription profiling by high throughput sequencing of five different organs of wheat (leaf, shoot, root, spike, and grain) at three developmental stages each

RNA-Seq mRNA baseline
Organism: Triticum aestivum
Reference(s): 25853487 (Filter by genes in paper)    
No change to top banner, tabs, or other tab content proposed
We get to this page after a search that matches one gene.
Proposal: after clicking on the heatmap rows in multiexperiment results, you go to this view too instead of the gene page
TODO: Should we do something if a search is for something that isn't a gene identifier, and matches one gene in this experiment?

Genes

TRIAE_CS42_2BS_TGACv1_146768_AA0472460
Keep the current semantics - if you want to see gene specific results for a different gene, you have to add the new one and remove the previous one
(most specific does nothing if there's one gene)
Expression value

Data units


Experimental variables

Selected: 15 / 15

There might be very many assay groups and the UI still has to work well. Possibly: flip the charts so that different experimental variables are on x axis?
Switch to heatmap view Alternative proposal: just show the heatmap on top instead of switching to it
See results for this gene in other experiments Unnecessary but proposed - links to the gene page

Gene annotations

+Attributes -> annotations Include also Reactome pathways Do not include "protein coding" Maybe not on top - now it looks like you will filter results you already have Similar: on the front page for an experiment have ready made categories that are enriched, facilitate searching for them Unnecessary but proposed. When you click on these, the gene query box gets populated, and you see the gene you are looking at plus some context e.g. the rest of the pathway the gene is on. It's meant to reinforce that the user is looking at results for one gene, and might be useful - inspired by "filter by genes in paper". Cons: competes with the same information on the gene page.
serine-type endopeptidase inhibitor activity
integral component of membrane
Biotype: protein coding

Expression values

Switch this to the log scale! Users are used to it, the boxplots getting squashed are fine, etc. We already have this, when you "switch to boxplot view"
Created with Highcharts 5.0.11-modifiedExpression (TPM)2.03 main shootand axillaryshoots visible atthree nodesstage, leaf2.03 main shoot and axillary shoots visible at three nodes stage, leafcotyledonemergencestage, leafcotyledon emergence stage, leafcotyledonemergencestage, rootcotyledon emergence stage, rootwhole plant fruitformation stage30 to 50%, fruitwhole plant fruit formation stage 30 to 50%, fruitwhole plant fruitformation stage30 to 50%, leafwhole plant fruit formation stage 30 to 50%, leafwhole plant fruitformation stage70% to final size,fruitwhole plant fruit formation stage 70% to final size, fruitFL.02 1/2 offlowers openstage,inflorescenceFL.02 1/2 of flowers open stage, inflorescencewhole plant fruitripening stage,fruitwhole plant fruit ripening stage, fruitFL.02 1/2 offlowers openstage, stemFL.02 1/2 of flowers open stage, stemLP.03 threeleaves visiblestage, rootLP.03 three leaves visible stage, rootSE.00 stemelongationbegins stage,stemSE.00 stem elongation begins stage, stemSE.02 two nodesor internodesvisible stage,inflorescenceSE.02 two nodes or internodes visible stage, inflorescenceSE.02 two nodesor internodesvisible stage,stemSE.02 two nodes or internodes visible stage, stemSE.99 maximumstem lengthreached stage,inflorescenceSE.99 maximum stem length reached stage, inflorescenceSE.99 maximumstem lengthreached stage,rootSE.99 maximum stem length reached stage, root0100200300400Factor: SE.99 maximum stem length reached stage, root● ObservationsMaximum: 2Upper quartile: 2Median: 2Lower quartile: 2Minimum: 1

Per transcript expression

This is transcript data for the gene as the pipeline produced, quantile normalized and then aggregated into quartiles like we currently do for gene expression. The scatter points are results for individual assays.


The example got handpicked to be vaguely interesting - the dominant transcript switches across assay groups. Other possible cases the UI should be able to present: - one transcript (e.g. because a gene has only one exon) - many transcripts, one is always dominant - many transcripts, only one is ever dominant but not across all assay groups




Per transcript expression all on one chart

You can jitter the points slightly so they're not collinear - helps distinguish what's going on if there is a lot of assays per assay group Proposal: also show the boxplots on this chart
This has the upside of being useful even the dominant transcripts are trivial or uninteresting, also the user can draw their own conclusion about what transcript is dominant.

Relative Isoform Usage

Another idea with less data. Aims to show how many transcripts there are, which transcript is dominant (most blue in a column) and whether this changes across assay groups. Fake data, columns should add up to 100% vertically.
Created with Highcharts 5.0.140255075100Chart context menu20%20%81%81%98%98%57%57%71%71%79%79%90%90%80%80%54%54%71%71%99%99%97%97%79%79%60%60%89%89%22%22%19.5%19.5%11%11%31.5%31.5%24.5%24.5%20%20%15%15%20%20%33%33%24.5%24.5%10%10%11.5%11.5%20.5%20.5%30%30%15.5%15.5%58%58%0%0%0%0%11.5%11.5%4.5%4.5%0.5%0.5%0%0%0%0%13%13%4.5%4.5%0%0%0%0%0.5%0.5%10%10%0%0%2.03 main shoot and a…2.03 main shoot and axillary shoots visible at three nodes stage, leafcotyledon emergence …cotyledon emergence stage, leafcotyledon emergence …cotyledon emergence stage, rootwhole plant fruit form…whole plant fruit formation stage 30 to 50%, fruitwhole plant fruit form…whole plant fruit formation stage 30 to 50%, leafwhole plant fruit form…whole plant fruit formation stage 70% to final size, fruitFL.02 1/2 of flowers o…FL.02 1/2 of flowers open stage, inflorescencewhole plant fruit ripen…whole plant fruit ripening stage, fruitFL.02 1/2 of flowers o…FL.02 1/2 of flowers open stage, stemLP.03 three leaves visi…LP.03 three leaves visible stage, rootSE.00 stem elongation…SE.00 stem elongation begins stage, stemSE.02 two nodes or int…SE.02 two nodes or internodes visible stage, inflorescenceSE.02 two nodes or int…SE.02 two nodes or internodes visible stage, stemSE.99 maximum stem …SE.99 maximum stem length reached stage, inflorescenceSE.99 maximum stem …SE.99 maximum stem length reached stage, rootTRIAE_CS42_2BS_TGACv1_146768_AA0472460.1TRIAE_CS42_2BS_TGACv1_146768_AA0472460.2TRIAE_CS42_2BS_TGACv1_146768_AA0472460.3Highcharts.comSE.02 two nodes or internodes visible stage, inflorescence sold0 items onTRIAE_CS42_2BS_TGACv1_146768_AA0472460.3
TODO: other visualisations? Maybe a "stacked percentage column"?

Coexpression

Coexpression heatmap whenever available