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# System prepended metadata

title: GeneNetwork tutorial

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# GeneNetwork convergent evolution
GeneNetwork is a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. The quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. GeneNetwork can be used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis).

## 1. Search by reproduction

![](https://i.imgur.com/kyl8jsg.png)

## 2. Sort by peak -logP

![](https://i.imgur.com/AQ4uBBO.png)

We could also sort by chromosomes, but the positions correspond to the location of the peaks (eQTLs), so it is not so useful focalized the attention only on this portion of a chromosome.

## 3. Click the first trait (BXD_21406)

Click the first trait and check the statistics. The number of samples are good and also the probability plot.

![](https://i.imgur.com/4uqn4hE.png)



If these statistics are not so good, we can click on "Transform and Filter Data" section, we can normalize using or log or quantile (Rob usually uses the last one). 

## 4. Running GEMMA

![](https://i.imgur.com/R03GkHr.png)

Log it is really high for chr10. 

## 5. Correlation study

For this locus what is the best? what correlates with this trait? go back and click on correlation section.

![](https://i.imgur.com/Ie5lK0k.png)

We can sort by samples and correlation.
But as we can see not good results, because we have high correlation but low sample sizes. It happens because there are few studies on the reproduction.

![](https://i.imgur.com/n9ElFyY.png)

## 6. After running GEMMA (5.) select peak on chr10.

![](https://i.imgur.com/sygZsJQ.png)

Orange peaks explain how parental's are differrent. Click the highest horizontal line in which there are few genes on top, click the pink lines, yellow are the genes that have a lot of variants. Where there are not orange peaks it means that are regions IBD.

We can put in view the regions of interest=101.2-105.5, and click also haplotype analyst.

![](https://i.imgur.com/JpbQ3Zr.png)

There are not a lot of genes, select genes that are big. DBA2J are greens lines, it was expected to have an half part of green and half of red.

![](https://i.imgur.com/WcPv6Cn.png)

For the last one we can see 2113 SNPs that should be distinguish the two parental strains.

## 7. Check all genes on NCBI

https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=278279, it seems that the last gene is interesting because it is present in reproductions organs.

## 8. Find papers related to this gene

https://pubmed.ncbi.nlm.nih.gov/34392169/, In these regions were found 62 protein coding genes, and the genes HSD17B2, SERPINA14, SERPINA1, SERPINA5, STAT1, NFATC1, ATP9B, CTDP1, THPO, ECE2, PSMD2, EIF4G1, EIF2B2, DVL3, POLR2H, TMTC2, and GPC6 are possible candidates for age at first birth due their function. So this gene seems correlated with the reproduction.