MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments

  • Data upload
  • Downloads
  • Publications
  • Help
  • Share ▼

    Email a friend Tweet
1,358,457 requests 10/26/2017 stats: 26,744 expressed tRFs | 11,721 datasets | 117,371 genomic instances

MINTbase v2 additions

BACK to help index

In this page you can find the differences between v1 and v2.

General changes

Expression evidence. MINTbase generates all possible potential tRFs. Some of those tRFs have been reported in datasets, those tRFs are characterized as "expressed". In MINTbase v1 the user could view the expressed tRFs only by selecting "Show expressed tRFs only". Also, the information whether a tRF was expressed or not was a yes/no column in most views. In v2 we present more expression details and searching capabilities. MINTbase v2 quantifies a tRF's presence in a dataset by calculating its reads per million (RPM) and allows the user to select the minimum RPM they prefer through the search form. Furthermore, all vistas have been updated to include more details about each tRF's expression evidence. The details about the datasets are presented in "expression" vista for both versions.

Tissue keywords In MINTbase v2, the user can use tissue related keywords in the search. This can be done through a new filter in the search form. This allows the user to easily subselect tRFs, datasets etc of interest without having to navigate through multiple vistas. You can view the list of all tissue keywords used by MINTbase here.

Vista arrangement In this version of MINTbase, we increased the connectivity of the vistas. Additional links are added in most views that interconnect the other vistas. That allows the user to seamlessly travel around result representations (vistas) with issuing unnecessary intermediate searches. Additionally, we have changed the position of the vista filter in the main menu. Despite the new look, the vistas' v1 capabilities have been retained and further expanded. You can view more details about specific vista changes below.

TCGA datasets MINTbase v2 contains the tRF profiles of The Cancer Genome Atlas (TCGA) datasets. The user can use the tissue keywords to view the profiles of specific cancers or all TCGA datasets.

Genomic Loci vista

Expression evidence. Instead of reporting whether a tRF is expressed or not, v2 has two expression related columns that present more details. The first column shows the number of datasets that include the dataset with RPM at least equal or more than the selected value. The second shows the maximum RPM value that the tRF has among all datasets. Both columns link to the expression view. Note that if a tissue keyword is used, those numbers involve only the datasets with that are associated with that tissue keyword.

RNA molecule vista

Expression evidence. Instead of reporting whether a tRF is expressed or not, v2 has two expression related columns that present more details. The first column shows the number of datasets that include the dataset with RPM at least equal or more than the selected value. The second shows the maximum RPM value that the tRF has among all datasets. Both columns link to the expression view. Note that if a tissue keyword is used, those numbers involve only the datasets with that are associated with that tissue keyword.

tRNA alignment link In v2 the "RNA molecule" vista links to "tRNA alignment" vista too. A new column has been added at the end of table. When the image of the new column is clicked, the user can see the alignment of the tRF and the tRNA or select which tRNA alignment to view if the tRF has many possible parental tRNAs.

Length column. A new column "Fragment length" has been added. The column is sortable so, the user, can browse the tRFs by their length.

tRNA alignment vista

tRNA name. In v2, the user doesn't have to select a tRNA name. Once a search is submitted and if there are more than one tRNAs returned, the user will be prompted to select the tRNA of their choice before they continue. The gtRNAdb name and the number of tRFs will be displayed beside the internal tRNA names.

Search form. In v2, the search form is also added to the tRNA alignment.

Expression evidence. When the tRNA and tRFs alignment is shown, now, expression evidence per tRF is included. These evidence consists of the maximum RPM value that the tRF has among all datasets and the number of datasets that include the tRF with RPM value equal or larger than the selected. Note that if a tissue keyword is used, those numbers involve only the datasets with that are associated with that tissue keyword.

Expression vista

MINTbase unique ID column. The MINTbase unique ID (sequence derived) is now added to the "Expression" view as well.

Length column. A new column "Fragment length" has been added in the case where more than one tRFs are returned. The column is sortable so, the user, can browse the tRFs by their length.

Number of datasets column. The number of datasets column has been updated to show both the number of the datasets in which the tRF has RPM value larger or equal to the selected and the number of all datasets in which the tRF is found expressed. Note that if a tissue keyword is used, those numbers involve only the datasets with that are associated with that tissue keyword.

Summary vista

Available genomes row. A new row showing the genomes that are included in MINTbase and in which the sequence is a tRF.

RPM values and dataset statistics. The maximum RPM value of the tRF is replaced with more detailed representations of the data. We've added a new histogram that shows the number of datasets per TCGA cancer project and all of the other datasets of MINTbase. A second histogram the number of datasets per RPM value range per TCGA cancer or the other datasets of MINTbase. Finally, two box plots present the ranges of RPMs per TCGA cancer or the other datasets for regular or log2 RPMs. Those graphs are interactive and printable.