# Summary of key findings across studies
#### _Steve Yost_
The table below was generated by ChatGPT 4o after uploading the five papers.
### [ChatGPT thread](https://chatgpt.com/share/679d44a8-7df4-800d-b7e0-790f11cfb58b)
The prompts I gave were the following:
```
I've uploaded five papers. What can you find that's common to all the results? Do you see any interesting patterns?
```
It generated key findings in bullet list form for each study. I then prompted:
```
For future reference, please refer to
fgene-14-1054558.pdf as Dataset 1
fmars-07-00598.pdf as Dataset 2
fgene-12-795706.pdf as Dataset 3
1-s2.0-S0044848621004944-main.pdf as Dataset 4
1-s2.0-S1050464819311295-main.pdf as Dataset 5

Please create a table summarizing the key findings across studies, with the datasets in order in the column headings
```
### Caveat: I have not yet validated these summaries by re-examining the papers.

| Key Findings                                                               | [Dataset 1](https://github.com/Resilience-Biomarkers-for-Aquaculture/Cvirg_Pmarinus_RNAseq/blob/main/analysis_ideas.md#slide-3)                                                     | [Dataset 2](https://github.com/Resilience-Biomarkers-for-Aquaculture/Cvirg_Pmarinus_RNAseq/blob/main/analysis_ideas.md#slide-4)                                                         | [Dataset 3](https://github.com/Resilience-Biomarkers-for-Aquaculture/Cvirg_Pmarinus_RNAseq/blob/main/analysis_ideas.md#slide-5)                                                        | [Dataset 4](https://github.com/Resilience-Biomarkers-for-Aquaculture/Cvirg_Pmarinus_RNAseq/blob/main/analysis_ideas.md#slide-6)                                                   | [Dataset 5](https://github.com/Resilience-Biomarkers-for-Aquaculture/Cvirg_Pmarinus_RNAseq/blob/main/analysis_ideas.md#slide-7)                                                                   |
|:---------------------------------------------------------------------------|:--------------------------------------------------------------|:------------------------------------------------------------------|:-----------------------------------------------------------------|:------------------------------------------------------------|:----------------------------------------------------------------------------|
| Immune response differences between resistant and susceptible oysters      | Disease tolerance mechanisms; immune response trade-offs      | Epigenetic and transcriptomic changes in infected oysters         | Comparative transcriptomics in C. gigas and C. virginica         | Effects of exposure methods on survival and gene expression | Variation in transcriptomic response across families                        |
| Role of Toll-like receptors (TLRs) in immune response                      | Upregulated in tolerant oysters                               | No strong correlation with TLR methylation patterns               | Expanded and positively selected in C. virginica                 | TLR4 overexpressed in injected oysters                      | Differentially expressed in resistant oysters                               |
| C1q domain-containing proteins involved in pathogen recognition            | Associated with increased infection tolerance                 | Found to be differentially expressed under infection              | Strongly upregulated in C. virginica                             | Not a major focus                                           | Upregulated in resistant oysters                                            |
| Apoptosis regulation and upregulation of inhibitors of apoptosis (IAPs)    | Programmed cell death pathways enriched in tolerant oysters   | No clear apoptosis-related methylation effects                    | Inhibitors of apoptosis (IAPs) upregulated in resistant C. gigas | Injected oysters had higher inflammatory apoptosis response | Resistant oysters showed early apoptotic gene activation                    |
| Oxidative stress and reactive oxygen species (ROS) management              | Linked to host survival under high parasite loads             | Significant gene expression changes with infection intensity      | C. gigas better manages oxidative stress                         | Injected oysters showed more oxidative stress               | Protease inhibitors upregulated in resistant oysters                        |
| Epigenetic modifications (DNA methylation) and gene expression correlation | Transcriptomic rather than epigenetic focus                   | Higher methylation stability associated with high gene expression | Not examined in this study                                       | Not a focus of this study                                   | Not examined in this study                                                  |
| Different resistance mechanisms: proteolysis regulation vs apoptosis       | Different resistance pathways observed across oyster families | Co-expression network revealed key immune-related genes           | Stronger immune activation in susceptible C. virginica           | Differences in immune pathway activation based on exposure  | Strong early response in resistant families                                 |
| Variation in transcriptomic response timing                                | Stronger responses in tolerant oysters                        | Response varied with infection intensity                          | C. gigas responds earlier, more effectively                      | Injected oysters showed stronger immune responses           | Susceptible oysters had weaker early response but strong later inflammation |
| Effect of exposure method (injection vs feeding) on immune response        | Dose-dependent immune response                                | Field vs lab differences in expression                            | Challenge experiments confirm species differences                | Injection method led to higher mortality                    | Controlled infection model used                                             |
| Implications for selective breeding (resistance vs tolerance)              | Suggests selection for tolerance may be preferable            | Epigenetics may not predict long-term infection response          | C. gigas naturally resistant; insights for breeding programs     | Highlights need for realistic exposure models in breeding   | Timing of immune response key for resistance                                |