|V. vinifera 'OneGenE' (Vespucci 2023 dataset)|
|# genes||Queued||Executed||Last 10 days||ETA|
|The OneGenE experiments|
OneGenE aims at expanding each single gene of an organism.
The main idea of OneGenE is that if we compute the gene expansion list for each gene of an organism, we will then be able to use these expansions multiple times, to produce the final expansion list of any local gene network. With the previous gene network expansion methods, the results that we computed were affected by the knowledge of the local gene network inserted in each experiment. This means that, when we want to expand a different local gene network we cannot use the results that we already computed on the same organism. We need to schedule new ad hoc experiments for the new local gene network of interest... and this take a lot of computational time.
With OneGenE, we should be able to build a public database containing the single expansions for each gene of an organism. With this public database, we will offer the possibility to build a gene network expansion list, in very short times, by combining the already computed single expansions.
|Running||Vitis vinifera (OneGenE)|
|Grapevine (Vitis species) is among the most important fruit crops in terms of cultivated area and economic impact but also for the large requirement of pesticides. Despite this relevance, little is known about the molecular regulatory circuits underlying the physiology of this species. Clearly, a greater knowledge of the grapevine biology would have a positive effect on management practices and on breeding leading ultimately to a more sustainable viticulture.|
A “green” viticulture, that is a more sustainable grape growing which meets the needs of the present without compromising the livelihood and needs of future generations, is an emerging demand of the society. And this holds true for the Trentino province as well, where vineyards are often located next to the villages.
Today, we are in the fortunate situation of dissecting the molecular regulatory circuits of grapevine at unprecedented pace, thanks to the knowledge built up in the last 10 years. Since the discovery of the grapevine genome sequence in 2007 (Jaillon et al. Nature, Velasco et al. PlosOne) the expression of the ca. 30,000 genes it contains have been measured in dozens of controlled experiments and are publicly available (Vespucci).
|Testing||Mus musculus (OneGenE)|
This experiment aims at identifying gene networks involving mouse genes of medical relevance for Spinal Muscular Atrophy, a neurodegenerative disease representing the most common
genetic cause of infant mortality. This pathology primarily affects the nervous system and leads to atrophy of skeletal muscle. However, structural and functional impairments in several tissues and organs are also increasingly acknowledged.
Ribosome profiling (RiboSeq) has been used to investigate the translatome of samples from brain, spinal cord and liver of control and SMA mice.
|Completed||Homo Sapiens (OneGenE - FANTOM-1)|
The goal of this experiment is the identification of gene networks involving human genes of medical relevance for two broad families of human pathologies: Motor Neuron Diseases and Hematopoietic Tumors.
Human gene network expansion will take advantage of the comprehensive gene expression dataset provided by the FANTOM Project.
|On hold||Pseudomonas aeruginosa (OneGenE)|
|Pseudomonas aeruginosa is a bacterium that can be harmful for plants and animals, including us, humans. P. aeruginosa is in general a multidrug resistant bacterium that have been associated with serious illnesses (Wikipedia). For this reason, the World Health Organization (WHO), in year 2007, included P. aeruginosa in its list of bacteria for which there is urgent need of antibiotics. (WHO News Release)|
|On hold||Escherichia coli (OneGenE)|
Escherichia coli (/ˌɛʃᵻˈrɪkiə ˈkoʊlaɪ/; also known as E. coli) is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms).
Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination.
The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, and preventing colonization of the intestine with pathogenic bacteria.
E. coli is expelled into the environment within fecal matter (from Wikipedia).
Escherichia coli str. K-12 is the model organism for Gram negative bacteria. More information can be found on the corresponding NICB genome project webpage and EcoliWiki.
The Escherichia coli compendium in colombos contains expression values for 4321 genes, measured for 4077 condition contrasts. This corresponds to a total of 269 experiments and 5510 samples measured on 73 different platforms.
We used the aforementioned colombos dataset and removed genes with too few expressione values. The modified dataset contains 3343 genes. We applied the PC-IM expansion algorithm to each gene using the (tsize:200, alpha:0.05, iter:2000) parameters.