Cross-Species Cereal Drought Gene Evidence and Regulatory Conservation Study
A reproducible biotechnology study of conserved and lineage-enriched drought-regulatory gene-family evidence across japonica rice, indica rice, wheat, maize, and sorghum.
Project definition
Problem statement
A 2026 source study integrates thousands of public drought transcriptome runs across cereals, but the released evidence spans many worksheets, species labels, gene-family layers, and statistical assumptions.
The engineering problem is to reduce that source into a traceable and independently testable evidence package while keeping network presence, expression, promoter motifs, family change, evolution, and functional enrichment biologically distinguishable.
Project objectives
- Verify the official source workbook before extracting declared worksheet ranges.
- Reconstruct sample, orthogroup, regulatory-edge, expression, promoter, family-change, Ka/Ks, GO, and nine-species evidence.
- Test eight predeclared conserved or lineage-enriched family-level hypotheses.
- Use distribution-free effects, resampling, rank tests, and false-discovery-rate control where appropriate.
- State clearly what the evidence supports and what still requires biological validation.
Project structure
Project components
Source extraction
Checks workbook identity, extracts thirteen declared evidence tables, retains source ranges, and isolates formula errors.
Cross-species evidence
Summarises sample coverage, orthogroups, conserved edges, and nine-species validation.
Expression and evolution
Compares C3 and C4 expression, family change, Ka/Ks, and expression-evolution relationships.
Promoter and GO evidence
Classifies cis-elements and audits functional-enrichment records without merging them into an opaque score.
Reproducibility
Regenerates fourteen result tables and sixteen figures under fixed configuration and automated tests.
Methodology
Project workflow
- 01Verify the source
The workbook byte size and MD5 are checked before any worksheet is read.
- 02Retain evidence
Declared worksheet ranges are reduced into compact CSV files with row counts and SHA-256 hashes.
- 03Run the analysis
The Python command calculates the declared summaries, effects, tests, corrections, and hypothesis matrix.
- 04Generate figures
Sixteen labelled figures are rebuilt from the retained evidence and result tables.
- 05Interpret biologically
Each result is discussed with its evidence layer, uncertainty, alternative explanation, and validation gap.
Demonstration scenario
The analysis reads thirteen retained tables, reports 5,062 source runs, 6,295 Ka/Ks pairs, 3,636 cis-elements, and recovery of all eight declared hypotheses, then regenerates fourteen result tables and sixteen figures. The student traces one conserved and one C4-enriched hypothesis from source range to statistics, figure, interpretation, and experimental gap.
Engineering
Tools and method
- Tools
- The project uses Python, Pandas, NumPy, SciPy, NetworkX, Matplotlib, OpenPyXL, Jupyter for subject analysis, simulation, and results.
- Evidence package
- Pandas and OpenPyXL prepare the declared public workbook reductions with explicit provenance.
- Statistics
- NumPy and SciPy implement bootstrap intervals, permutation tests, rank tests, effect sizes, correlations, and multiple-testing correction.
- Network analysis
- NetworkX aggregates conserved family-level edges and supports visual comparison across the five cereals.
- Figures
- Matplotlib generates the complete analytical figure set from committed data and configuration.
- Verification
- Tests, hashes, dependency audits, document audits, repository validation, and a Linux Docker run verify the handover.
Testing
Evaluation
Evaluation measures
- Recovery of all eight declared regulatory hypotheses in their stated source layer
- Traceability from each retained row to its source worksheet range and hash
- C3 and C4 expression differences with distribution-free effect sizes and intervals
- Species differences in retained family-change panels after multiple-testing correction
- Ka/Ks, promoter-motif, GO, and expression-evolution summaries kept as separate evidence
- Reproducibility across tests, result files, figures, documents, and the Linux container
Project boundaries
- A conserved family-level edge is not proof of direct transcription-factor binding or a conserved mechanism.
- The C3 and C4 comparison also differs by species and cannot establish universal photosynthetic-pathway causation.
- The study does not demonstrate drought-tolerant phenotype, field performance, breeding value, or a crop-engineering recommendation.
- Any transformation or gene-editing experiment requires institutional biosafety review and is outside the handover.
Included
- 01Python source code for extraction, statistics, evidence integration, and figures
- 02Thirteen retained evidence tables with source worksheet ranges and file hashes
- 03Fourteen result tables and sixteen analytical figures
- 0488 page project report in editable Word and PDF formats
- 0513 page setup and demonstration guide in editable Word and PDF formats
- 0660 annotated references and three licensed literature images
- 0739 automated tests with 96.81 percent branch-aware coverage
- 08Complete project files in a private GitHub repository
Project record
No information is collected on this page.
- Permanent project ID
- GP-BT-1BQK7YK
- Catalogued
- 21 Aug 2026
- Completed
- 27 Aug 2026
- Verified
- 27 Aug 2026
- Demonstration
- Included in repository
Handover
After purchase
- 01Payment is confirmed
The project is marked unavailable and cannot be purchased again.
- 02Repository access is granted
The buyer's submitted GitHub account receives access to the private repository.
- 03The purchase record is delivered
The certification sheet is prepared from the reviewed buyer details and sent privately by email.