DOI: 10.5281/zenodo.7147597
title: Ensembl TSS dataset for GRCh38

description: We used the human genome reference sequence in its GRCh38.p13 version in order to have a reliable source of data in which to carry out our experiments. We chose this version because it is the most recent one available in Ensemble at the moment. However, the DNA sequence by itself is not enough, the specific TSS position of each transcript is needed. In this section, we explain the steps followed to generate the final dataset. These steps are: raw data gathering, positive instances processing, negative instances generation and data splitting by chromosomes.


First, we need an interface in order to download the raw data, which is composed by every transcript sequence in the human genome. We used Ensembl release 104 (Howe et al., 2020) and its utility BioMart (Smedley et al., 2009), which allows us to get large amounts of data easily. It also enables us to select a wide variety of interesting fields, including the transcription start and end sites. After filtering instances that present null values in any relevant field, this combination of the sequence and its flanks will form our raw dataset. Once the sequences are available, we find the TSS position (given by Ensembl) and the 2 following bases to treat it as a codon. After that, 700 bases before this codon and 300 bases after it are concatenated, getting the final sequence of 1003 nucleotides that is going to be used in our models. These specific window values have been used in (Bhandari et al., 2021) and we have kept them as we find it interesting for comparison purposes. One of the most sensitive parts of this dataset is the generation of negative instances. We cannot get this kind of data in a straightforward manner, so we need to generate it synthetically. In order to get examples of negative instances, i.e. sequences that do not represent a transcript start site, we select random DNA positions inside the transcripts that do not correspond to a TSS. Once we have selected the specific position, we get 700 bases ahead and 300 bases after it as we did with the positive instances.


Regarding the positive to negative ratio, in a similar problem, but studying TIS instead of TSS (Zhang135
et al., 2017), a ratio of 10 negative instances to each positive one was found optimal. Following this136
idea, we select 10 random positions from the transcript sequence of each positive codon and label them137
as negative instances. After this process, we end up with 1,122,113 instances: 102,488 positive and 1,019,625 negative sequences. In order to validate and test our models, we need to split this dataset into three parts: train, validation and test. We have decided to make this differentiation by chromosomes, as it is done in (Perez-Rodriguez et al., 2020). Thus, we use chromosome 16 as validation because it is a good example of a chromosome with average characteristics. Then we selected samples from chromosomes 1, 3, 13, 19 and 21 to be part of the test set and used the rest of them to train our models. Every step of this process can be replicated using the scripts available in https://github.com/JoseBarbero/EnsemblTSSPrediction.