3.1 IRX4 expression from publicly available datasets
We initially checked the expression of IRX4 gene from the Genotype-Tissue Expression (GTEX) portal62 and found expression in multiple tissues, including breast, oesophagus, heart, salivary gland, prostate, skin and vagina (Figure S1). We found an increased expression of this gene in the prostate, skin, vagina and oesophagus compared to other tissues. Furthermore, we checked if the expression at the transcript level correlated with any cancer-specific RNA seq data. We used GeneVestigator to identify the top hits for higher expression ofIRX4 gene 63. Amongst the initial hits, the expression of IRX4 was found to be higher in malignant prostate cancer cells and oesophagus squamous cell carcinoma (Figure S2).
The transcriptomic data also indicated the expression of this gene in breast, skin and brain tumours highlighting the importance of this gene in cancer study. Next, we went ahead to check the expression of IRX4 protein using multiple databases and datasets. This protein was found to be expressed only in the MCF7 breast cancer cell line according to the ProtemicsDB, which uses Mass Spectrometry (MS) data to quantify protein (Figure S3). To further identify if the expression of IRX4 did correlate with any MS specific data, we used PaxDB to identify proteins and proteome-wide levels (Figure 1). Interestingly, we found evidence of the protein in multiple datasets, which are represented as ppm. H727 cells, which are epithelial lung bronchus cells, showed higher protein expression than its total proteome. Low expression of the gene was observed in the lung tissue. The Global Proteome Machine (GPM) is a well-curated protein expression database consisting of peptides from multiple species 64. According to this database, the expression of IRX4 was found in cell-lines HCT116, epithelial colorectal carcinoma cells, HEK293 and embryonic human kidney cells. B cells and Ascitic fluid too showed expression of the protein, highlighting the vast range of expression patterns for this protein.