Tissue transcriptomics
HPA collects transcriptomic data from the three databases (HPA, GTEx and FANTOM5). For HPA RNAseq total RNA was extracted from the tissue samples healthy individuals (Accession no: PRJEB4337, Ensembl: ENSG00000130234 (version 92.38) using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The extracted RNA samples were analyzed using either an Experion automated electrophoresis system (Bio-Rad Laboratories, Hercules, CA, USA) with the standard-sensitivity RNA chip or an Agilent 2100 Bioanalyzer system (Agilent Biotechnologies, Palo Alto, USA) with the RNA 6000 Nano Labchip Kit. Sample samples of high RNA quality (RNA Integrity Number > 7.5) were used for the mRNA sequencing. mRNA sequencing was performed on Illumina HiSeq2000 and 2500 machines (Illumina, San Diego, CA, USA) using the standard Illumina RNA-seq protocol (with a read length of 2x100 bases). For estimation of transcript abundance Kallisto v0.43.1 was used (https://pachterlab.github.io/kallisto/about). The normalized Tags Per Million (TPM) for each gene from the three databases were calculated and included in the Human Protein Atlas. Each tissue was categorized for the intensity of gene expression using a cutoff value of 1 NX as a limit for detection across all tissues. A tissue was categorized (i) enriched if it had NX level at least four times higher than other tissues, (ii) low specificity if NX ≥ 1 in at least one tissue, (iii) Not detected if NX < 1 in all tissues.