Table 1.
List of the database and server utilize in the study
| Database | Data type | Analysis type | Dataset | Website link |
|---|---|---|---|---|
| ONCOMINE | Gene expression | Cancer vs. normal analysis |
1. Broad Tumorscape 2. Cell Line Panel 3. DNA Copy Number 4. Multi-Cancer Panel 5. Normal Tissue Panel 6. TCGA Datasets |
(https://www.ONCOMINE.org/resource/login.html) |
| GEPIA2 | Gene expression | Gene expression profile across all tumor samples and paired normal tissues | TCGA/GTEx dataset | (http://gepia2.cancer-pku.cn/) |
| GENT2 | Gene expression | Tissue-wide gene expression profile across paired tissues | Public gene expression data sets | (http://gent2.appex.kr/gent2/) |
| UALCAN | Transcript per million | Transcript per million RNA molecule was compared across different categories | TCGA | (http://ualcan.path.uab.edu/index.html) |
| UALCAN | Promoter DNA methylation | Promoter DNA methylation was compared across different categories using beta value | TCGA | (http://ualcan.path.uab.edu/index.html) |
| cBioPortal | Genomic alteration | Frequency of mutation, amplification , deep deletion and multiple alterations across specific cancer was analyzed | TCGA | (http://www.cbioportal.org/) |
| Mutation | Mutation across TAP1 protein was determined for specific cancer | |||
| Mutation and copy number alterations | Mutation and copy number alteration was identified in TAP1 mRNA expression for specific cancer | |||
| The Human Protein Atlas | Protein expression | Protein expression data was compared across different categories using immunohistochemistry. | The tissue atlas | (http://www.proteinatlas.org/) |
| PrognoScan | Gene expression and patient prognosis | Gene expression was analyzed comparing patient prognosis such as overall survival (OS), disease-free survival (DFS) and relapse-free survival for cancer and normal patient | Public cancer microarray datasets | (http://dna00.bio.kyutech.ac.jp/PrognoScan/) (https://kmplot.com/analysis/) |
| R2: Genomics Analysis and Visualization Platform | Positively co-expressed genes | Identification and visualization of positively co-expressed genes of different cancers | TCGA | |
| Enricher | Positively co-expressed genes | Signaling pathway and gene ontology analysis of positively co-expressed genes in KEGG human pathways 2019, Panther 2016, GO Biological Process, GO Molecular Function (2018) and GO Cellular Component ranking by p-value | TCGA | (http://amp.pharm.mssm.edu/Enrichr/enrich#) |