Additional file 1 of Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer
Creators: name: Li, Lingling
name: Liu, Hui
name: Li, Yan
name: Guo, Chunmei
name: Wang, Bing
name: Shen, Dan
name: Zhang, Qiao
name: Ding, Chen
Publisher: name: figshare
Year: 2022
Subjects: Biophysics
Biochemistry
Medicine
Cell Biology
Chemical Sciences not elsewhere classified
Mathematical Sciences not elsewhere classified
Cancer

description: Additional file 1: Supplementary Fig. S1. Overview of the proteomic profiles of EESCC and EDAC. a Schematic illustration of the samples and experimental workflow. b The number of the patient cases, identified proteins, and phosphosites in EESCC and EDAC. c Venn diagram showing the overlaps of the identified proteins (left) and phosphosites (right) in 3 EESCC patients. d Venn diagram showing the overlaps of the identified proteins (left) and phosphosites (right) in 3 EDAC patients. Supplementary Fig. S2. The phosphoproteomic features of tumor tissues compared with paired normal tissues in in EESCC and EDAC. a PCA analysis showing distinct separation between the tumor tissues and paired normal tissues in EESCC at the phosphoprotein level. b Volcano analysis depicted the differential expressed proteins of the tumor tissues and paired normal tissues in EESCC at the phosphoprotein level. c Bar chart presenting the functional pathways in up-regulated and down-regulated pathways in EESCC at the phosphoprotein level. d PCA analysis showing distinct separation between the tumor tissues and paired normal tissues in EDAC at the phosphoprotein level. e Volcano analysis depicted the differential expressed proteins of the tumor tissues and paired normal tissues in EDAC at the phosphoprotein level. f Bar chart presenting the functional pathways in up-regulated and down-regulated pathways in EDAC at the phosphoprotein level. Supplementary Fig. S3. Phosphoproteomic characteristics of EESCC and EDAC phosphoproteome. a Venn diagram representing the overlaps of the identification (left) and Pearson’s correlation coefficients (right) between proteome and phosphoproteome in EESCC. b Venn diagram representing the overlaps of the identification (left) and Pearson’s correlation coefficients (right) between proteome and phosphoproteome in EDAC. c PCA analysis showing distinct separation between normal tissues of EESCC and EDAC at the protein (left) and phosphoprotein (right) levels. d Volcano analysis depicted the differential expressed proteins of EESCC and EDAC. e Volcano analysis depicted the differential phosphorylation (left) and bar chart showing the functional pathways (right) in EESCC and EDAC phosphoproteome. f Phosphoproteins in functional pathways that were differentially expressed in EESCC (left) and EDAC (right) at protein and phosphoprotein levels. g Pearson’s correlation coefficients indicated significantly positive association between RB1 (T3730) and EGFR (T693). Supplementary Fig. S4. Eight major classifications of cytokines identified in early-stage gastrointestinal cancer. All the classified types (left) and the proteins of the cytokines identified in EESCC (middle) and EDAC (right) were shown. Supplementary Fig. S5. Major kinases in EESCC and EDAC. a A Kinome Tree of EESCC (purple) and EDAC (red) mapped to human kinases datasets. b The distribution of the major kinases types in EESCC (left) and EDAC (right).