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Gene: PDGFA |
Gene summary for PDGFA |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDGFA | Gene ID | 5154 |
| Gene name | platelet derived growth factor subunit A | |
| Gene Alias | PDGF-A | |
| Cytomap | 7p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P04085 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5154 | PDGFA | LZE4T | Human | Esophagus | ESCC | 8.53e-26 | 6.69e-01 | 0.0811 |
| 5154 | PDGFA | LZE5T | Human | Esophagus | ESCC | 1.97e-02 | 2.25e-01 | 0.0514 |
| 5154 | PDGFA | LZE7T | Human | Esophagus | ESCC | 1.11e-05 | 4.20e-01 | 0.0667 |
| 5154 | PDGFA | LZE8T | Human | Esophagus | ESCC | 5.86e-08 | 2.07e-01 | 0.067 |
| 5154 | PDGFA | LZE22T | Human | Esophagus | ESCC | 2.97e-03 | 3.36e-01 | 0.068 |
| 5154 | PDGFA | P1T-E | Human | Esophagus | ESCC | 6.66e-07 | 5.58e-01 | 0.0875 |
| 5154 | PDGFA | P2T-E | Human | Esophagus | ESCC | 1.92e-78 | 1.33e+00 | 0.1177 |
| 5154 | PDGFA | P4T-E | Human | Esophagus | ESCC | 2.45e-05 | 2.40e-01 | 0.1323 |
| 5154 | PDGFA | P5T-E | Human | Esophagus | ESCC | 9.99e-23 | 4.14e-01 | 0.1327 |
| 5154 | PDGFA | P8T-E | Human | Esophagus | ESCC | 3.79e-18 | 3.80e-01 | 0.0889 |
| 5154 | PDGFA | P9T-E | Human | Esophagus | ESCC | 4.92e-14 | 3.12e-01 | 0.1131 |
| 5154 | PDGFA | P10T-E | Human | Esophagus | ESCC | 1.74e-68 | 1.19e+00 | 0.116 |
| 5154 | PDGFA | P11T-E | Human | Esophagus | ESCC | 2.64e-35 | 1.22e+00 | 0.1426 |
| 5154 | PDGFA | P12T-E | Human | Esophagus | ESCC | 1.39e-42 | 7.29e-01 | 0.1122 |
| 5154 | PDGFA | P15T-E | Human | Esophagus | ESCC | 5.16e-25 | 5.56e-01 | 0.1149 |
| 5154 | PDGFA | P16T-E | Human | Esophagus | ESCC | 4.54e-61 | 1.06e+00 | 0.1153 |
| 5154 | PDGFA | P17T-E | Human | Esophagus | ESCC | 2.47e-05 | 5.71e-01 | 0.1278 |
| 5154 | PDGFA | P19T-E | Human | Esophagus | ESCC | 4.74e-05 | 7.64e-01 | 0.1662 |
| 5154 | PDGFA | P20T-E | Human | Esophagus | ESCC | 5.36e-19 | 5.63e-01 | 0.1124 |
| 5154 | PDGFA | P21T-E | Human | Esophagus | ESCC | 1.38e-47 | 8.86e-01 | 0.1617 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0010563111 | Esophagus | ESCC | negative regulation of phosphorus metabolic process | 274/8552 | 442/18723 | 2.32e-12 | 9.41e-11 | 274 |
| GO:0045936111 | Esophagus | ESCC | negative regulation of phosphate metabolic process | 273/8552 | 441/18723 | 3.18e-12 | 1.25e-10 | 273 |
| GO:0048732111 | Esophagus | ESCC | gland development | 269/8552 | 436/18723 | 7.81e-12 | 2.95e-10 | 269 |
| GO:007190016 | Esophagus | ESCC | regulation of protein serine/threonine kinase activity | 227/8552 | 359/18723 | 1.12e-11 | 4.10e-10 | 227 |
| GO:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:00435888 | Esophagus | ESCC | skin development | 163/8552 | 263/18723 | 6.48e-08 | 1.14e-06 | 163 |
| GO:000854410 | Esophagus | ESCC | epidermis development | 193/8552 | 324/18723 | 2.87e-07 | 4.19e-06 | 193 |
| GO:0032970111 | Esophagus | ESCC | regulation of actin filament-based process | 231/8552 | 397/18723 | 2.91e-07 | 4.20e-06 | 231 |
| GO:0032956111 | Esophagus | ESCC | regulation of actin cytoskeleton organization | 210/8552 | 358/18723 | 4.40e-07 | 6.00e-06 | 210 |
| GO:004206027 | Esophagus | ESCC | wound healing | 243/8552 | 422/18723 | 4.62e-07 | 6.25e-06 | 243 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:00719029 | Esophagus | ESCC | positive regulation of protein serine/threonine kinase activity | 124/8552 | 200/18723 | 2.27e-06 | 2.61e-05 | 124 |
| GO:004677710 | Esophagus | ESCC | protein autophosphorylation | 138/8552 | 227/18723 | 2.98e-06 | 3.38e-05 | 138 |
| GO:00066446 | Esophagus | ESCC | phospholipid metabolic process | 218/8552 | 383/18723 | 5.37e-06 | 5.59e-05 | 218 |
| GO:004814414 | Esophagus | ESCC | fibroblast proliferation | 57/8552 | 81/18723 | 5.83e-06 | 6.03e-05 | 57 |
| GO:002261216 | Esophagus | ESCC | gland morphogenesis | 78/8552 | 118/18723 | 5.83e-06 | 6.03e-05 | 78 |
| GO:004586018 | Esophagus | ESCC | positive regulation of protein kinase activity | 219/8552 | 386/18723 | 6.91e-06 | 6.97e-05 | 219 |
| GO:003367420 | Esophagus | ESCC | positive regulation of kinase activity | 260/8552 | 467/18723 | 7.26e-06 | 7.22e-05 | 260 |
| GO:00480087 | Esophagus | ESCC | platelet-derived growth factor receptor signaling pathway | 42/8552 | 56/18723 | 7.62e-06 | 7.54e-05 | 42 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05418211 | Esophagus | ESCC | Fluid shear stress and atherosclerosis | 109/4205 | 139/8465 | 2.00e-12 | 3.72e-11 | 1.90e-11 | 109 |
| hsa0521516 | Esophagus | ESCC | Prostate cancer | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa0451020 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
| hsa0152110 | Esophagus | ESCC | EGFR tyrosine kinase inhibitor resistance | 55/4205 | 79/8465 | 2.44e-04 | 8.78e-04 | 4.50e-04 | 55 |
| hsa0521417 | Esophagus | ESCC | Glioma | 52/4205 | 75/8465 | 4.20e-04 | 1.45e-03 | 7.43e-04 | 52 |
| hsa052028 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0481028 | Esophagus | ESCC | Regulation of actin cytoskeleton | 133/4205 | 229/8465 | 5.94e-03 | 1.48e-02 | 7.56e-03 | 133 |
| hsa052319 | Esophagus | ESCC | Choline metabolism in cancer | 61/4205 | 98/8465 | 7.97e-03 | 1.92e-02 | 9.84e-03 | 61 |
| hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa05418310 | Esophagus | ESCC | Fluid shear stress and atherosclerosis | 109/4205 | 139/8465 | 2.00e-12 | 3.72e-11 | 1.90e-11 | 109 |
| hsa0521517 | Esophagus | ESCC | Prostate cancer | 72/4205 | 97/8465 | 6.12e-07 | 4.10e-06 | 2.10e-06 | 72 |
| hsa04510111 | Esophagus | ESCC | Focal adhesion | 127/4205 | 203/8465 | 1.25e-04 | 4.99e-04 | 2.56e-04 | 127 |
| hsa0152115 | Esophagus | ESCC | EGFR tyrosine kinase inhibitor resistance | 55/4205 | 79/8465 | 2.44e-04 | 8.78e-04 | 4.50e-04 | 55 |
| hsa0521418 | Esophagus | ESCC | Glioma | 52/4205 | 75/8465 | 4.20e-04 | 1.45e-03 | 7.43e-04 | 52 |
| hsa0520213 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa04810112 | Esophagus | ESCC | Regulation of actin cytoskeleton | 133/4205 | 229/8465 | 5.94e-03 | 1.48e-02 | 7.56e-03 | 133 |
| hsa0523114 | Esophagus | ESCC | Choline metabolism in cancer | 61/4205 | 98/8465 | 7.97e-03 | 1.92e-02 | 9.84e-03 | 61 |
| hsa0415114 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa0451021 | Liver | Cirrhotic | Focal adhesion | 93/2530 | 203/8465 | 9.27e-07 | 1.10e-05 | 6.80e-06 | 93 |
| hsa0481021 | Liver | Cirrhotic | Regulation of actin cytoskeleton | 100/2530 | 229/8465 | 5.28e-06 | 5.50e-05 | 3.39e-05 | 100 |
| Page: 1 2 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Breast | ADJ |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Breast | ADJ |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Breast | DCIS |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Breast | DCIS |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Breast | Healthy |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Breast | Healthy |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Breast | IDC |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Breast | IDC |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Cervix | ADJ |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Cervix | ADJ |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Cervix | CC |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Cervix | CC |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | Cervix | Precancer |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | Cervix | Precancer |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | CRC | CRC |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | CRC | CRC |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | CRC | FAP |
| PDGFA | PDGFRA | PDGFA_PDGFRA | PDGF | CRC | MSS |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | CRC | MSS |
| PDGFA | PDGFRB | PDGFA_PDGFRB | PDGF | CRC | SER |
| Page: 1 2 3 4 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PDGFA | SNV | Missense_Mutation | novel | c.571N>C | p.Glu191Gln | p.E191Q | P04085 | protein_coding | tolerated(0.21) | possibly_damaging(0.793) | TCGA-VS-A9UH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PDGFA | insertion | Frame_Shift_Ins | novel | c.606dupA | p.Arg203ThrfsTer74 | p.R203Tfs*74 | P04085 | protein_coding | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
| PDGFA | SNV | Missense_Mutation | rs184796222 | c.431G>A | p.Arg144His | p.R144H | P04085 | protein_coding | deleterious(0.02) | probably_damaging(0.965) | TCGA-A6-6782-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PDGFA | SNV | Missense_Mutation | novel | c.25N>T | p.Leu9Phe | p.L9F | P04085 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PDGFA | SNV | Missense_Mutation | rs570502707 | c.614N>T | p.Arg205Ile | p.R205I | P04085 | protein_coding | deleterious(0.01) | probably_damaging(0.986) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PDGFA | SNV | Missense_Mutation | rs145010817 | c.532G>A | p.Ala178Thr | p.A178T | P04085 | protein_coding | tolerated(1) | benign(0.005) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
| PDGFA | SNV | Missense_Mutation | c.362N>T | p.Pro121Leu | p.P121L | P04085 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CK-4950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folfox | SD | |
| PDGFA | SNV | Missense_Mutation | rs775727803 | c.343N>A | p.Ala115Thr | p.A115T | P04085 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-DM-A288-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
| PDGFA | SNV | Missense_Mutation | novel | c.100G>A | p.Ala34Thr | p.A34T | P04085 | protein_coding | tolerated(0.05) | possibly_damaging(0.519) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PDGFA | SNV | Missense_Mutation | rs533180683 | c.539C>T | p.Ala180Val | p.A180V | P04085 | protein_coding | tolerated(0.18) | benign(0.085) | TCGA-AJ-A3BH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 5154 | PDGFA | GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME, KINASE | inhibitor | SUNITINIB | SUNITINIB | |
| 5154 | PDGFA | GROWTH FACTOR, CELL SURFACE, DRUGGABLE GENOME, KINASE | Squalamine | SQUALAMINE |
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