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Gene: MS4A2 |
Gene summary for MS4A2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MS4A2 | Gene ID | 2206 |
| Gene name | membrane spanning 4-domains A2 | |
| Gene Alias | APY | |
| Cytomap | 11q12.1 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | Q01362 |
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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 |
| 2206 | MS4A2 | CA_HPV_1 | Human | Cervix | CC | 8.58e-19 | -7.09e-01 | 0.0264 |
| 2206 | MS4A2 | CA_HPV_3 | Human | Cervix | CC | 8.28e-05 | -4.49e-01 | 0.0414 |
| 2206 | MS4A2 | N_HPV_2 | Human | Cervix | N_HPV | 5.12e-10 | -6.44e-01 | -0.0131 |
| 2206 | MS4A2 | CCI_1 | Human | Cervix | CC | 1.46e-05 | -9.18e-01 | 0.528 |
| 2206 | MS4A2 | CCI_2 | Human | Cervix | CC | 5.47e-05 | -9.18e-01 | 0.5249 |
| 2206 | MS4A2 | CCI_3 | Human | Cervix | CC | 7.16e-08 | -9.18e-01 | 0.516 |
| 2206 | MS4A2 | CCII_1 | Human | Cervix | CC | 2.06e-11 | -9.18e-01 | 0.3249 |
| 2206 | MS4A2 | Tumor | Human | Cervix | CC | 5.21e-31 | -9.18e-01 | 0.1241 |
| 2206 | MS4A2 | sample1 | Human | Cervix | CC | 2.49e-09 | -9.18e-01 | 0.0959 |
| 2206 | MS4A2 | sample3 | Human | Cervix | CC | 4.93e-29 | -9.18e-01 | 0.1387 |
| 2206 | MS4A2 | H2 | Human | Cervix | HSIL_HPV | 2.93e-28 | -8.98e-01 | 0.0632 |
| 2206 | MS4A2 | L1 | Human | Cervix | CC | 1.21e-12 | -9.18e-01 | 0.0802 |
| 2206 | MS4A2 | T1 | Human | Cervix | CC | 1.18e-21 | -9.18e-01 | 0.0918 |
| 2206 | MS4A2 | T2 | Human | Cervix | CC | 1.22e-04 | -9.18e-01 | 0.0709 |
| 2206 | MS4A2 | T3 | Human | Cervix | CC | 1.21e-28 | -9.18e-01 | 0.1389 |
| 2206 | MS4A2 | HCC1 | Human | Liver | HCC | 1.73e-10 | 1.17e+00 | 0.5336 |
| 2206 | MS4A2 | HCC2 | Human | Liver | HCC | 1.58e-22 | 1.31e+00 | 0.5341 |
| 2206 | MS4A2 | HCC5 | Human | Liver | HCC | 8.95e-17 | 1.11e+00 | 0.4932 |
| 2206 | MS4A2 | EOLP-1 | Human | Oral cavity | EOLP | 1.02e-07 | 5.10e-01 | -0.0202 |
| 2206 | MS4A2 | EOLP-2 | Human | Oral cavity | EOLP | 7.24e-29 | 8.63e-01 | -0.0203 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:00027644 | Cervix | CC | immune response-regulating signaling pathway | 97/2311 | 468/18723 | 1.49e-07 | 7.07e-06 | 97 |
| GO:00380933 | Cervix | CC | Fc receptor signaling pathway | 19/2311 | 50/18723 | 3.42e-06 | 9.17e-05 | 19 |
| GO:0038095 | Cervix | CC | Fc-epsilon receptor signaling pathway | 11/2311 | 24/18723 | 5.28e-05 | 7.88e-04 | 11 |
| GO:0002768 | Cervix | CC | immune response-regulating cell surface receptor signaling pathway | 59/2311 | 315/18723 | 6.64e-04 | 6.11e-03 | 59 |
| GO:000276411 | Cervix | HSIL_HPV | immune response-regulating signaling pathway | 46/737 | 468/18723 | 1.17e-08 | 1.30e-06 | 46 |
| GO:00027681 | Cervix | HSIL_HPV | immune response-regulating cell surface receptor signaling pathway | 32/737 | 315/18723 | 9.80e-07 | 4.68e-05 | 32 |
| GO:003809311 | Cervix | HSIL_HPV | Fc receptor signaling pathway | 8/737 | 50/18723 | 6.88e-04 | 9.21e-03 | 8 |
| GO:000276421 | Cervix | N_HPV | immune response-regulating signaling pathway | 36/534 | 468/18723 | 7.52e-08 | 7.81e-06 | 36 |
| GO:00027682 | Cervix | N_HPV | immune response-regulating cell surface receptor signaling pathway | 22/534 | 315/18723 | 1.11e-04 | 2.18e-03 | 22 |
| GO:000276413 | Oral cavity | EOLP | immune response-regulating signaling pathway | 108/2218 | 468/18723 | 4.04e-12 | 7.34e-10 | 108 |
| GO:003809313 | Oral cavity | EOLP | Fc receptor signaling pathway | 19/2218 | 50/18723 | 1.84e-06 | 4.26e-05 | 19 |
| GO:00027683 | Oral cavity | EOLP | immune response-regulating cell surface receptor signaling pathway | 66/2218 | 315/18723 | 2.44e-06 | 5.45e-05 | 66 |
| GO:00380951 | Oral cavity | EOLP | Fc-epsilon receptor signaling pathway | 10/2218 | 24/18723 | 2.17e-04 | 2.16e-03 | 10 |
| GO:000276422 | Oral cavity | NEOLP | immune response-regulating signaling pathway | 74/2005 | 468/18723 | 3.90e-04 | 3.63e-03 | 74 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0407110 | Cervix | CC | Sphingolipid signaling pathway | 35/1267 | 121/8465 | 5.70e-05 | 3.93e-04 | 2.32e-04 | 35 |
| hsa04664 | Cervix | CC | Fc epsilon RI signaling pathway | 22/1267 | 68/8465 | 2.35e-04 | 1.31e-03 | 7.77e-04 | 22 |
| hsa053107 | Cervix | CC | Asthma | 11/1267 | 31/8465 | 3.82e-03 | 1.36e-02 | 8.03e-03 | 11 |
| hsa0407113 | Cervix | CC | Sphingolipid signaling pathway | 35/1267 | 121/8465 | 5.70e-05 | 3.93e-04 | 2.32e-04 | 35 |
| hsa046641 | Cervix | CC | Fc epsilon RI signaling pathway | 22/1267 | 68/8465 | 2.35e-04 | 1.31e-03 | 7.77e-04 | 22 |
| hsa0531012 | Cervix | CC | Asthma | 11/1267 | 31/8465 | 3.82e-03 | 1.36e-02 | 8.03e-03 | 11 |
| hsa0407141 | Oral cavity | EOLP | Sphingolipid signaling pathway | 44/1218 | 121/8465 | 1.19e-09 | 3.51e-08 | 2.07e-08 | 44 |
| hsa046642 | Oral cavity | EOLP | Fc epsilon RI signaling pathway | 23/1218 | 68/8465 | 4.23e-05 | 2.01e-04 | 1.19e-04 | 23 |
| hsa040722 | Oral cavity | EOLP | Phospholipase D signaling pathway | 31/1218 | 148/8465 | 1.82e-02 | 4.67e-02 | 2.76e-02 | 31 |
| hsa0407151 | Oral cavity | EOLP | Sphingolipid signaling pathway | 44/1218 | 121/8465 | 1.19e-09 | 3.51e-08 | 2.07e-08 | 44 |
| hsa0466411 | Oral cavity | EOLP | Fc epsilon RI signaling pathway | 23/1218 | 68/8465 | 4.23e-05 | 2.01e-04 | 1.19e-04 | 23 |
| hsa0407211 | Oral cavity | EOLP | Phospholipase D signaling pathway | 31/1218 | 148/8465 | 1.82e-02 | 4.67e-02 | 2.76e-02 | 31 |
| hsa0407161 | Oral cavity | NEOLP | Sphingolipid signaling pathway | 36/1112 | 121/8465 | 1.11e-06 | 1.21e-05 | 7.64e-06 | 36 |
| hsa0407171 | Oral cavity | NEOLP | Sphingolipid signaling pathway | 36/1112 | 121/8465 | 1.11e-06 | 1.21e-05 | 7.64e-06 | 36 |
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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 |
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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. |
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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 |
| MS4A2 | SNV | Missense_Mutation | c.727N>T | p.Asp243Tyr | p.D243Y | Q01362 | protein_coding | deleterious(0) | possibly_damaging(0.817) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MS4A2 | SNV | Missense_Mutation | novel | c.23N>A | p.Arg8Lys | p.R8K | Q01362 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-AR-A2LH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| MS4A2 | SNV | Missense_Mutation | c.472T>C | p.Tyr158His | p.Y158H | Q01362 | protein_coding | deleterious(0.01) | probably_damaging(0.969) | TCGA-WL-A834-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | paclitaxel | SD | |
| MS4A2 | SNV | Missense_Mutation | novel | c.569N>C | p.Ile190Thr | p.I190T | Q01362 | protein_coding | deleterious(0) | possibly_damaging(0.883) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MS4A2 | SNV | Missense_Mutation | c.592N>C | p.Ser198Pro | p.S198P | Q01362 | protein_coding | tolerated(0.26) | probably_damaging(0.94) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| MS4A2 | SNV | Missense_Mutation | c.509N>T | p.Thr170Ile | p.T170I | Q01362 | protein_coding | tolerated(0.1) | benign(0.005) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| MS4A2 | SNV | Missense_Mutation | c.364A>T | p.Asn122Tyr | p.N122Y | Q01362 | protein_coding | tolerated(0.16) | possibly_damaging(0.678) | TCGA-DY-A1DF-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| MS4A2 | SNV | Missense_Mutation | novel | c.20G>T | p.Arg7Met | p.R7M | Q01362 | protein_coding | deleterious(0) | benign(0.258) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MS4A2 | SNV | Missense_Mutation | c.271N>T | p.Asp91Tyr | p.D91Y | Q01362 | protein_coding | deleterious(0.05) | possibly_damaging(0.855) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| MS4A2 | SNV | Missense_Mutation | c.31N>G | p.Leu11Val | p.L11V | Q01362 | protein_coding | deleterious(0.01) | possibly_damaging(0.486) | TCGA-AP-A0LI-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | paclitaxel | 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 |
| 2206 | MS4A2 | EXTERNAL SIDE OF PLASMA MEMBRANE | OMALIZUMAB | OMALIZUMAB | ||
| 2206 | MS4A2 | EXTERNAL SIDE OF PLASMA MEMBRANE | R112 |
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