Analysis of gene expression data

First, the mRNA expression data of ITIH family in normal tissues were obtained from the Genotype-Tissue Expression (GTEx) project [18]. To confirm the expression patterns of ITIHs in normal tissues, we then consulted the HPA (Human protein atlas) and FANTOM5 dataset from the human protein atlas database (http://www.proteinatlas.org/) [19]. Transcripts of ITIHs across different cell types in the liver tissue were visualized using Single Cell Expression Atlas (https://www.ebi.ac.uk/gxa/sc/home). Expression data of ITIHs for over 1000 cancer cell lines were accessed from Cancer Cell Line Encyclopedia (CCLE) (https://www.broadinstitute.org/ccle) [20]. RNA-seq data of 64 cell lines from The Human Protein Atlas (HPA) ((https://www.proteinatlas.org/) [19] were utilized to validate expression patterns of ITIHs in different cancer cell lines.

To explore the expression differences of ITIHs between tumor and the corresponding normal tissues across different cancer types, we analyzed TCGA RNA-seq data of 20 cancer types with matched normal samples (7900 tumor and 724 normal). Then, expression data from GTEx were combined with TCGA data, in order to extend the analyses to more cancer types and enlarged samples sizes. The expression levels of ITIHs in human blood exosomes were obtained from exoRBase (http://www.exorbase.org/) [11]. In addition, we explored the expression levels of ITIHs in different pathologic stages across pan-cancers using the “Stage Plot” module of GEPIA2 web server (http://gepia2.cancer-pku.cn/#analysis) [12]. To validate the differential expression of ITIH1 between LIHC and normal tissue, we further retrieved five datasets from Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) under accession number {"type":"entrez-geo","attrs":{"text":"GSE1898","term_id":"1898"}}GSE1898, {"type":"entrez-geo","attrs":{"text":"GSE39791","term_id":"39791"}}GSE39791, {"type":"entrez-geo","attrs":{"text":"GSE45436","term_id":"45436"}}GSE45436, {"type":"entrez-geo","attrs":{"text":"GSE6764","term_id":"6764"}}GSE6764, and {"type":"entrez-geo","attrs":{"text":"GSE84598","term_id":"84598"}}GSE84598.