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.