| Tumor | Detail |
|---|---|
| ESCC | Esophageal squamous cell Carcinoma |
| LUSC | Lung squamous cell carcinoma |
| GBM | Glioblastoma multiforme |
| HNSC | Head and Neck squamous cell carcinoma |
| PAAD | Pancreatic adenocarcinoma |
| LUAD | Lung adenocarcinoma |
| UCEC | Uterine Corpus Endometrial Carcinoma |
| KIRC | Kidney renal clear cell carcinoma |
| LIHC | Liver hepatocellular carcinoma |
| OV | Ovarian serous cystadenocarcinoma |
| STAD | Stomach adenocarcinoma |
| BRCA | Breast invasive carcinoma |
| COAD | Colon adenocarcinoma |
MaxQuant software (version 2.0.2.0) was used to analyze MS raw files. If the “internal reference”, such as a mixed sample, exists, the reference channel will be set according to the corresponding plex, and the normalization method will be set as ‘Weighted ratio to reference channel’. The expression ratios output by MaxQuant were log2-transformed and normalized using the median centering method across proteins and phosphorylation sites.
the meaning of ‘log2 (median)’ represented the log2 transformed median value of normalized expression of proteins or phosphorylation. log2 (median) (N) represented the log2 transformed median value in normal samples. log2 (median) (T) represented the log2 transformed median value in tumor samples.
The differential expression analysis is displayed by pie chart.
Red square represents proteins or phosphorylation sites that are up regulated in tumor.
Blue square represents proteins or phosphorylation sites that are down regulated in tumor.
The differential expression analysis is displayed by volcano plot.
X-axis represents log2-transformed fold change of tumor samples over non-tumor samples.
Y-axis represents negative log10-transformed q-value which are calculated by the Wilcoxon signed-rank test and corrected by the Benjamini-Hochberg tutorial.
Input set: All proteins from 'Table of differential profile' base on cutoff specified by users
Method: Over Representation Analysis (ORA) is a widely used approach to determine whether known biological functions or processes are over-represented (= enriched) in an experimentally-derived gene list, e.g. a list of differentially expressed genes (DEGs).The p-value can be calculated by hypergeometric distribution.
Database: Gene Ontology, KEGG, Hallmark, Reactome, WikiPathway