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.