What’s driving the response?
We explain the biology.

We translate your complex omics data into defensible biological narratives that reveal the “how” behind the phenotype, delivering actionable insight with every claim traceable to the evidence.

TraitSeq: Mechanistic Report
TraitSeq Explore →
Contents
Executive Summary
TraitSeq

Biostimulant-Induced Drought Resilience in Wheat

Transcriptomic & metabolomic profiling of biostimulant-treated wheat seedlings

Executive Summary

1. Motivation

A treatment works in the field, but what is it doing at the molecular level? This is a common challenge across the biologicals sector: field data alone cannot explain how a product works, what claims the evidence supports, or how to position it in the market. This case study demonstrates how TraitSeq addresses that challenge.

2. Mode of Action

The analysis reveals a clear mode of action involving coordinated activation of defence signalling, metabolic reprogramming, and stress-responsive pathways. Every claim in this report is traceable to the underlying statistical evidence and can be explored interactively through the TraitSeq platform.

Illustrative example. The report titles and figures shown are synthetic demonstrations of the platform output, not client deliverables.

You invested in the data.
Are you getting the return?

You generated omics data to investigate the impact of your product or strain but extracting biological meaning from the results is challenging:

  • Standard analysis delivers gene lists and enrichment tables, but not biological interpretation or insight on product performance
  • Annotation resources are scattered across dozens of databases
  • The knowledge base of gene function is ever evolving and expanding
  • Stretched teams don’t have time to fully interpret the biology

Interpreting omics data requires more than statistics. Understanding what the results reveal about product performance requires biological input that standard bioinformatics workflows don’t provide.

Where most analyses stop
analysis_report_final_v3.pdf
Differential Expression Results
3,247
DEGs (p<0.05)
1,891
Upregulated
1,356
Downregulated
Top Enriched GO Terms
GO:0006950: response to stress 2.3e-12
GO:0008152: metabolic process 4.1e-09
GO:0009987: cellular process 1.7e-08
GO:0050896: response to stimulus 3.2e-07
Recommendation

“Results indicate significant transcriptional changes across multiple biological processes. Further investigation is recommended to elucidate specific mechanistic pathways.”

?
But what does it mean for your programme?
Which pathways matter. What’s the mechanism. What to do next.
Species knowledge graphs
Maize
Zea mays
Genes annotated 106,000+
Public databases integrated 45+
Metabolic pathways mapped 600+
Transcription factors characterised 4,000+
Published studies indexed 12,000+

Every result contextualised
against all published knowledge.

TraitSeq maintains species-specific knowledge graphs that integrate annotation, pathway, and literature data from continually expanding public resources. When we analyse your data, every differentially expressed gene, every enriched pathway, every network module is interpreted against this knowledge base.

The result is a comprehensive biological narrative that answers your research question, giving your team the mechanistic evidence to make confident R&D decisions.

Research Questions + Raw Data Biological Answers

You send us

Your research questions:

  • What’s the mode of action?
  • Is the effect consistent across environments?
  • What biomarkers will translate from the lab to the field?
  • What makes this strain different?
  • Does this edit have off-target effects?

Your omics data and experimental metadata

We advise on experimental design to maximise the insight your data can deliver

Our analysis

  • Data preparation: preprocessing, QC, normalisation, batch correction
  • Multi-scale analysis: global structure, features, networks, pathways, phenotypes
  • Knowledge graph enrichment: all results linked to species-specific annotation and published literature
  • AI interpretation: all findings synthesised into a mechanistic narrative

Your data is processed in isolated cloud environments and never shared.

You get back

  • Mechanistic report: a publication-ready biological narrative answering your specific question
  • Interactive platform: explore and verify every finding yourself
  • Results bundle: all statistical outputs, tables, and figures, available for download
  • Expert walkthrough: we discuss the findings and implications with your team

1-2 week turnaround, from data upload to expert walkthrough.

Every claim traceable.
Nothing is a black box.

Every statement in your report is grounded in evidence from both the statistical analysis and the species knowledge graph, visualised for your team to explore through our interactive platform.

TraitSeq: Enrichment Analysis
GO Term Enrichment Biological Process
Contrast: Drought vs Well-watered 512 genes 87 significant
response to water deprivation 198 24 3.8e-11 5.89 ***
20 upregulated, 4 downregulated
Gene
ID
Dir
log₂FC
FDR
Sig
DREB2A
AT5G05410
+3.81
2.41e-14
***
LEA3
AT1G02820
+4.12
8.93e-13
***
RD29A
AT5G52310
+3.27
5.14e-11
***
COR15A
AT2G42540
+2.87
6.28e-10
***
P5CS1
AT2G39800
+2.94
1.67e-09
***
NCED3
AT3G14440
+2.58
3.82e-08
***
ERD10
AT1G20450
+2.43
8.91e-08
***
PIP2;1
AT3G53420
-2.43
1.28e-07
***
SLAC1
AT1G12480
+1.86
7.15e-06
***
EXPA4
AT2G39700
-1.92
4.61e-05
***
Showing 10 of 24 genes
abscisic acid-activated signalling pathway142181.24e-083.87***
14 upregulated, 4 downregulated
Gene
ID
Dir
log₂FC
FDR
Sig
RAB18
AT5G66400
+3.45
7.62e-12
***
RD29A
AT5G52310
+3.27
5.14e-11
***
NCED3
AT3G14440
+2.58
3.82e-08
***
PIP2;1
AT3G53420
-2.43
1.28e-07
***
OST1
AT4G33950
+2.31
1.82e-07
***
ABF2
AT1G45249
+2.14
6.33e-07
***
PYL4
AT2G38310
+1.94
3.17e-06
***
SLAC1
AT1G12480
+1.86
7.15e-06
***
ERD10
AT1G20450
+2.43
8.91e-08
***
PP2CA
AT3G11410
-1.47
8.93e-04
***
Showing 10 of 18 genes
regulation of stomatal closure67114.56e-063.42***
9 upregulated, 2 downregulated
Gene
ID
Dir
log₂FC
FDR
Sig
NCED3
AT3G14440
+2.58
3.82e-08
***
PIP2;1
AT3G53420
-2.43
1.28e-07
***
OST1
AT4G33950
+2.31
1.82e-07
***
ABF2
AT1G45249
+2.14
6.33e-07
***
PYL4
AT2G38310
+1.94
3.17e-06
***
MYB60
AT1G08810
-2.18
3.45e-06
***
SLAC1
AT1G12480
+1.86
7.15e-06
***
KAT1
AT5G46240
-1.68
2.14e-04
***
ALMT12
AT4G17970
+1.52
5.67e-04
***
PP2CA
AT3G11410
-1.47
8.93e-04
***
Showing 10 of 11 genes
proline biosynthetic process1248.91e-052.94***
4 upregulated
Gene
ID
Dir
log₂FC
FDR
Sig
P5CS1
AT2G39800
+2.94
1.67e-09
***
P5CS2
AT3G55610
+2.12
5.43e-07
***
P5CR
AT5G14800
+1.73
2.41e-04
***
OAT
AT5G46180
+1.41
4.82e-04
***
Showing 4 of 4 genes
response to osmotic stress156142.17e-042.51**
10 upregulated, 4 downregulated
Gene
ID
Dir
log₂FC
FDR
Sig
DREB2A
AT5G05410
+3.81
2.41e-14
***
LEA3
AT1G02820
+4.12
8.93e-13
***
RAB18
AT5G66400
+3.45
7.62e-12
***
RD29A
AT5G52310
+3.27
5.14e-11
***
COR15A
AT2G42540
+2.87
6.28e-10
***
P5CS1
AT2G39800
+2.94
1.67e-09
***
NCED3
AT3G14440
+2.58
3.82e-08
***
ERD10
AT1G20450
+2.43
8.91e-08
***
PIP2;1
AT3G53420
-2.43
1.28e-07
***
EXPA4
AT2G39700
-1.92
4.61e-05
***
Showing 10 of 14 genes
Showing 5 of 87 significant termsPage 1 of 4
DREB2A↑ Sig
AT5G05410
×
Contrast: Drought vs Well-watered
+3.81
log₂FC
2.41e-14
FDR
412
Base Mean
Function

Dehydration-responsive element binding protein 2A. Master transcription factor activating drought-responsive genes through both ABA-dependent and ABA-independent pathways. Key regulator of osmotic stress tolerance.

Expression by Condition
2 6 10 14 Drought Well-watered (n=6) (n=6)
Pathways
response to water deprivation response to heat KEGG: MAPK signalling - plant
Biological Context

DREB2A activates downstream targets including RD29A via DRE/CRT promoter elements. It operates in the ABA-independent drought signalling branch, parallel to the ABA-dependent pathway mediated by ABF2/NCED3. Co-upregulation of both branches indicates a comprehensive dual-track drought response.

Orthologs
OsDREB2A rice ZmDREB2A maize TaDREB2A wheat
Key References
Sakuma et al. (2006) Plant Cell — Functional analysis of DREB2A involved in drought-responsive gene expression
Qin et al. (2007) Plant J — Regulation and functional analysis of ZmDREB2A in response to drought and heat