PEXT
Proportion expressed across transcripts (pext) is a transcript-level annotation metric that quantifies isoform expression for variants in gnomAD v2 (hg19) across 54 GTEx tissues. The CCF tool was used to convert genome position of variants from hg19 (the original PEXT database) to hg38 (the converted GTB format PEXT database).
| Field | Description | Type |
|---|---|---|
| ensg | Ensembl gene ID | String |
| csq | Variant consequence for the transcript (annotated by the Variant Effect Predictor (VEP) version 85). | String |
| symbol | Gene symbol | String |
| lof | Lof-of-function effect (annotated by the loss-of-function transcript effect estimator (LOFTEE) package). | String |
| lof_flag | Possible reason to reject a LOF consequence. | String |
| Adipose_Subcutaneous | The Pext value for the variant in Adipose_Subcutaneous tissue. | Float |
| AdiposeVisceral_Omentum | The Pext value for the variant in AdiposeVisceral_Omentum tissue. | Float |
| AdrenalGland | The Pext value for the variant in AdrenalGland tissue. | Float |
| Artery_Aorta | The Pext value for the variant in Artery_Aorta tissue. | Float |
| Artery_Coronary | The Pext value for the variant in Artery_Coronary tissue. | Float |
| Artery_Tibial | The Pext value for the variant in Artery_Tibial tissue. | Float |
| Bladder | The Pext value for the variant in Bladder tissue. | Float |
| Brain_Amygdala | The Pext value for the variant in Brain_Amygdala tissue. | Float |
| BrainAnteriorcingulatecortex_BA24 | The Pext value for the variant in BrainAnteriorcingulatecortex_BA24 tissue. | Float |
| BrainCaudate_basalganglia | The Pext value for the variant in BrainCaudate_basalganglia tissue. | Float |
| Brain_CerebellarHemisphere | The Pext value for the variant in Brain_CerebellarHemisphere tissue. | Float |
| Brain_Cerebellum | The Pext value for the variant in Brain_Cerebellum tissue. | Float |
| Brain_Cortex | The Pext value for the variant in Brain_Cortex tissue. | Float |
| BrainFrontalCortex_BA9 | The Pext value for the variant in BrainFrontalCortex_BA9 tissue. | Float |
| Brain_Hippocampus | The Pext value for the variant in Brain_Hippocampus tissue. | Float |
| Brain_Hypothalamus | The Pext value for the variant in Brain_Hypothalamus tissue. | Float |
| BrainNucleusaccumbens_basalganglia | The Pext value for the variant in BrainNucleusaccumbens_basalganglia tissue. | Float |
| BrainPutamen_basalganglia | The Pext value for the variant in BrainPutamen_basalganglia tissue. | Float |
| BrainSpinalcord_cervicalc_1 | The Pext value for the variant in BrainSpinalcord_cervicalc_1 tissue. | Float |
| Brain_Substantianigra | The Pext value for the variant in Brain_Substantianigra tissue. | Float |
| Breast_MammaryTissuePext | The Pext value for the variant in Breast_MammaryTissuePext tissue. | Float |
| Cells_EBV_transformedlymphocytes | The Pext value for the variant in Cells_EBV_transformedlymphocytes tissue. | Float |
| Cells_Transformedfibroblasts | The Pext value for the variant in Cells_Transformedfibroblasts tissue. | Float |
| Cervix_Ectocervix | The Pext value for the variant in Cervix_Ectocervix tissue. | Float |
| Cervix_Endocervix | The Pext value for the variant in Cervix_Endocervix tissue. | Float |
| Colon_Sigmoid | The Pext value for the variant in Colon_Sigmoid tissue. | Float |
| Colon_Transverse | The Pext value for the variant in Colon_Transverse tissue. | Float |
| Esophagus_GastroesophagealJunction | The Pext value for the variant in Esophagus_GastroesophagealJunction tissue. | Float |
| Esophagus_Mucosa | The Pext value for the variant in Esophagus_Mucosa tissue. | Float |
| Esophagus_Muscularis | The Pext value for the variant in Esophagus_Muscularis tissue. | Float |
| FallopianTube | The Pext value for the variant in FallopianTube tissue. | Float |
| Heart_AtrialAppendage | The Pext value for the variant in Heart_AtrialAppendage tissue. | Float |
| Heart_LeftVentricle | The Pext value for the variant in Heart_LeftVentricle tissue. | Float |
| Kidney_Cortex | The Pext value for the variant in Kidney_Cortex tissue. | Float |
| Liver | The Pext value for the variant in Liver tissue. | Float |
| Lung | The Pext value for the variant in Lung tissue. | Float |
| MinorSalivaryGland | The Pext value for the variant in MinorSalivaryGland tissue. | Float |
| Muscle_Skeletal | The Pext value for the variant in Muscle_Skeletal tissue. | Float |
| Nerve_Tibial | The Pext value for the variant in Nerve_Tibial tissue. | Float |
| Ovary | The Pext value for the variant in Ovary tissue. | Float |
| Pancreas | The Pext value for the variant in Pancreas tissue. | Float |
| Pituitary | The Pext value for the variant in Pituitary tissue. | Float |
| Prostate | The Pext value for the variant in Prostate tissue. | Float |
| SkinNotSunExposed_Suprapubic | The Pext value for the variant in SkinNotSunExposed_Suprapubic tissue. | Float |
| SkinSunExposed_Lowerleg | The Pext value for the variant in SkinSunExposed_Lowerleg tissue. | Float |
| SmallIntestine_TerminalIleum | The Pext value for the variant in SmallIntestine_TerminalIleum tissue. | Float |
| Spleen | The Pext value for the variant in Spleen tissue. | Float |
| Stomach | The Pext value for the variant in Stomach tissue. | Float |
| Testis | The Pext value for the variant in Testis tissue. | Float |
| Thyroid | The Pext value for the variant in Thyroid tissue. | Float |
| Uterus | The Pext value for the variant in Uterus tissue. | Float |
| Vagina | The Pext value for the variant in Vagina tissue. | Float |
| WholeBlood | The Pext value for the variant in WholeBlood tissue. | Float |
| mean_proportion | The mean Pext value for the variant across GTEx tissues. | Float |