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Gene: MSR1 |
Gene summary for MSR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MSR1 | Gene ID | 4481 |
| Gene name | macrophage scavenger receptor 1 | |
| Gene Alias | CD204 | |
| Cytomap | 8p22 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | P21757 |
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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 |
| 4481 | MSR1 | HCC2 | Human | Liver | HCC | 1.24e-04 | 1.36e+00 | 0.5341 |
| 4481 | MSR1 | Pt13.a | Human | Liver | HCC | 2.14e-02 | 1.47e-01 | 0.021 |
| 4481 | MSR1 | Pt13.c | Human | Liver | HCC | 3.11e-08 | 4.80e-01 | 0.0076 |
| 4481 | MSR1 | Pt14.d | Human | Liver | HCC | 3.79e-19 | 5.10e-01 | 0.0143 |
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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). |
| 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:005123521 | Liver | HCC | maintenance of location | 185/7958 | 327/18723 | 1.70e-07 | 3.12e-06 | 185 |
| GO:000689821 | Liver | HCC | receptor-mediated endocytosis | 134/7958 | 244/18723 | 5.73e-05 | 5.31e-04 | 134 |
| GO:001087621 | Liver | HCC | lipid localization | 228/7958 | 448/18723 | 1.80e-04 | 1.41e-03 | 228 |
| GO:00199152 | Liver | HCC | lipid storage | 53/7958 | 87/18723 | 4.01e-04 | 2.71e-03 | 53 |
| GO:000686921 | Liver | HCC | lipid transport | 198/7958 | 398/18723 | 1.92e-03 | 9.78e-03 | 198 |
| GO:00303012 | Liver | HCC | cholesterol transport | 65/7958 | 117/18723 | 2.95e-03 | 1.38e-02 | 65 |
| GO:00108832 | Liver | HCC | regulation of lipid storage | 35/7958 | 57/18723 | 3.08e-03 | 1.43e-02 | 35 |
| GO:00159182 | Liver | HCC | sterol transport | 71/7958 | 130/18723 | 3.49e-03 | 1.58e-02 | 71 |
| GO:0010878 | Liver | HCC | cholesterol storage | 15/7958 | 21/18723 | 7.03e-03 | 2.80e-02 | 15 |
| GO:00107422 | Liver | HCC | macrophage derived foam cell differentiation | 24/7958 | 38/18723 | 8.20e-03 | 3.22e-02 | 24 |
| GO:00900772 | Liver | HCC | foam cell differentiation | 24/7958 | 38/18723 | 8.20e-03 | 3.22e-02 | 24 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414521 | Liver | HCC | Phagosome | 93/4020 | 152/8465 | 4.27e-04 | 1.88e-03 | 1.05e-03 | 93 |
| hsa0414531 | Liver | HCC | Phagosome | 93/4020 | 152/8465 | 4.27e-04 | 1.88e-03 | 1.05e-03 | 93 |
| 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 |
| MSR1 | SNV | Missense_Mutation | c.59C>A | p.Ser20Tyr | p.S20Y | P21757 | protein_coding | deleterious(0.01) | possibly_damaging(0.87) | TCGA-BH-A202-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR | |
| MSR1 | SNV | Missense_Mutation | rs141819994 | c.970N>A | p.Gly324Arg | p.G324R | P21757 | protein_coding | deleterious(0) | possibly_damaging(0.55) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| MSR1 | SNV | Missense_Mutation | c.596N>A | p.Gly199Asp | p.G199D | P21757 | protein_coding | tolerated(0.5) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| MSR1 | SNV | Missense_Mutation | novel | c.43N>C | p.Asp15His | p.D15H | P21757 | protein_coding | deleterious(0.01) | possibly_damaging(0.684) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| MSR1 | SNV | Missense_Mutation | c.150N>C | p.Lys50Asn | p.K50N | P21757 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| MSR1 | SNV | Missense_Mutation | c.1145N>A | p.Arg382His | p.R382H | P21757 | protein_coding | deleterious(0.01) | benign(0.09) | TCGA-VS-A94W-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| MSR1 | SNV | Missense_Mutation | c.815N>C | p.Gln272Pro | p.Q272P | P21757 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3956-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| MSR1 | SNV | Missense_Mutation | novel | c.810N>T | p.Leu270Phe | p.L270F | P21757 | protein_coding | tolerated(0.06) | benign(0.088) | TCGA-AA-3979-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| MSR1 | SNV | Missense_Mutation | rs13306549 | c.313G>A | p.Glu105Lys | p.E105K | P21757 | protein_coding | tolerated(0.28) | benign(0.007) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| MSR1 | SNV | Missense_Mutation | c.898G>T | p.Gly300Cys | p.G300C | P21757 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| 4481 | MSR1 | EXTERNAL SIDE OF PLASMA MEMBRANE, DRUGGABLE GENOME | H2O2 | 15316030 |
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