This application shows the Cis- & Trans-eQTLs estimated from GTEX data.

Authors: Farid Jacome-Velasco & Victor Trevino

The main work was done by Farid Jacome Velasco as a Master in Computational Sciences thesis. We used MatrixEQTL package to estimate eQTLs from all tissues using GTEX data, which is similar to GTEX Portal. Corrections and cofactors were used in the model. Most of the eQTLs are the same than those reported by GTEX Portal. We used different data version and filtering criteria, thus, we usually report more eQTLs than GTEX Portal. Distinct to GTEX Portal, we saved the original data points and thus the distributions per variant can be observed. Given that we used more relaxed filtering criteria (raw p < 0.01), the overall patterns of eQTL per gene can be better observed.

Cis-eQTL Applications

- Gene eQTLs
        Example for : eQTLgene.jsp?gene=POMC
- Region eQTLs for all genes and all tissues
        Example for ~LTPB1 : eQTLgenome-region.jsp?region=2:32948001-33347601
- Counts eQTLs by Gene from a region
        Example for ~LTPB1 : eQTLregion.jsp?region=2:32948001-33347601
- Returns expression levels by eQTL
        Example for DHCR24: expLevelByeQTL.jsp?chr=1&pos=54489330&gene=DHCR24&tissue=ADPSBQ&genotype=A_C
- Returns counts eQTLs by Gene from a region
        Example for ~LTPB1 : eQTLcounts.jsp?region=2:32948001-33347601

Trans-eQTL Applications

- Gene eQTLs
        Example for : TransEQTLgene.jsp?gene=POMC
- From a Position, eQTLs for all genes and all tissues
        Example for 1:143234478 : TransEQTLposition.jsp?region=1:143234478
- From a Region, eQTLs for all genes and all tissues
        Example for 1:143234000-143234999 : TransEQTLregion.jsp?region=1:143234000-143234999