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Gene: SAA4 |
Gene summary for SAA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SAA4 | Gene ID | 6291 |
| Gene name | serum amyloid A4, constitutive | |
| Gene Alias | C-SAA | |
| Cytomap | 11p15.1 | |
| Gene Type | protein-coding | GO ID | GO:0002526 | UniProtAcc | P35542 |
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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 |
| 6291 | SAA4 | HCC1_Meng | Human | Liver | HCC | 7.17e-34 | 1.05e-01 | 0.0246 |
| 6291 | SAA4 | HCC2_Meng | Human | Liver | HCC | 4.33e-03 | -1.40e-01 | 0.0107 |
| 6291 | SAA4 | Pt13.a | Human | Liver | HCC | 3.88e-32 | 8.26e-01 | 0.021 |
| 6291 | SAA4 | Pt13.b | Human | Liver | HCC | 8.55e-49 | 6.48e-01 | 0.0251 |
| 6291 | SAA4 | Pt13.c | Human | Liver | HCC | 1.90e-05 | 5.76e-01 | 0.0076 |
| 6291 | SAA4 | S029 | Human | Liver | HCC | 8.81e-06 | 8.57e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00025262 | Liver | HCC | acute inflammatory response | 62/7958 | 112/18723 | 4.06e-03 | 1.77e-02 | 62 |
| GO:00069532 | Liver | HCC | acute-phase response | 30/7958 | 49/18723 | 6.31e-03 | 2.57e-02 | 30 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| SAA4 | SNV | Missense_Mutation | rs201435531 | c.233N>A | p.Arg78His | p.R78H | P35542 | protein_coding | deleterious(0) | benign(0.228) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| SAA4 | SNV | Missense_Mutation | c.386A>C | p.Lys129Thr | p.K129T | P35542 | protein_coding | deleterious(0) | benign(0.348) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| SAA4 | SNV | Missense_Mutation | rs762589722 | c.203N>A | p.Gly68Glu | p.G68E | P35542 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SAA4 | SNV | Missense_Mutation | rs146072546 | c.355N>A | p.Asp119Asn | p.D119N | P35542 | protein_coding | tolerated(1) | benign(0.001) | TCGA-AZ-6606-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folfiri | PD |
| SAA4 | SNV | Missense_Mutation | novel | c.145A>C | p.Asn49His | p.N49H | P35542 | protein_coding | tolerated(0.09) | benign(0.017) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| SAA4 | SNV | Missense_Mutation | novel | c.259N>G | p.Ile87Val | p.I87V | P35542 | protein_coding | tolerated(0.59) | benign(0.007) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SAA4 | SNV | Missense_Mutation | rs753574341 | c.64N>T | p.Arg22Cys | p.R22C | P35542 | protein_coding | deleterious(0.04) | benign(0.005) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SAA4 | SNV | Missense_Mutation | novel | c.129N>T | p.Met43Ile | p.M43I | P35542 | protein_coding | deleterious(0.01) | benign(0) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SAA4 | SNV | Missense_Mutation | c.262N>T | p.Asp88Tyr | p.D88Y | P35542 | protein_coding | tolerated(0.1) | benign(0.001) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SAA4 | SNV | Missense_Mutation | rs565392562 | c.359G>A | p.Arg120His | p.R120H | P35542 | protein_coding | tolerated(1) | benign(0) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
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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 |
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