Zebrafish genomics and its applications: vertebrate model system for understanding human cardiovascular development
Bibliographic record
Abstract
The zebrafish, Danio rerio is an excellent model for vertebrate developmental genetics. In order to characterize gene expression patterns of the zebrafish during embryonic development, a genomic resource of data and clones was initiated by large-scale partial sequencing of randomly selected cDNA clones to generate expressed sequence tags (ESTs) from zebrafish embryonic (3-day) heart cDNA library. Generation of 5,102 ESTs from the zebrafish embryonic heart cDNA library, representing the first and only catalogue of genes expressed in the embryonic zebrafish cardiovascular system. Clustering of all ESTs identified approximately 3,690 unique transcripts. Radiation hybrid mapping was performed for 102 ESTs and comparison of map positions between zebrafish and human identified new synteny groups. Further acquisition of ESTs from zebrafish adult heart and skeletal muscles cDNA libraries, coupled with the development of the 4,700 unique genes zebrafish cDNA microarray, allowed for large-scale gene expression analysis of the zebrafish during development and to the study of the effects of hypoxia on the zebrafish. In the former analysis, a total of 801 genes were identified to be differentially expressed during 5 different stages of development, including many novel developmentally regulated genes. In the latter analysis, expression profiling reveals the adaptive mechanisms of how zebrafish embryos survive under hypoxia. Hypoxia induces changes in gene expression patterns in the zebrafish embryos and these patterns are reverted back upon re-exposure to normoxia (20.8% O2). Characterizations of novel developmentally regulated genes as determined through the microarray analysis identified a novel zebrafish helix-loop-helix gene. Subsequent in situ hybridization and RT-PCR analysis confirmed that the Id7 gene is developmentally regulated. Overall, these results illustrate the power of ESTs and cDNA microarray as genomic tools for large-scale analyses of gene expression of the zebrafish during development and its responses to hypoxia. This study demonstrates the powerful utility of the EST database and the potential of cDNA microarray for the analysis of zebrafish mutants that affect various aspects of zebrafish development. Further utilizations of current resources, coupled with further additions of clones on the array should increase the power and sensitivity of this technology.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.009 | 0.004 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".