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Gene: FAM172A |
Gene summary for FAM172A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | FAM172A | Gene ID | 83989 |
| Gene name | family with sequence similarity 172 member A | |
| Gene Alias | C5orf21 | |
| Cytomap | 5q15 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q8WUF8 |
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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 |
| 83989 | FAM172A | CCI_1 | Human | Cervix | CC | 1.35e-02 | 5.34e-01 | 0.528 |
| 83989 | FAM172A | CCI_2 | Human | Cervix | CC | 1.76e-10 | 1.19e+00 | 0.5249 |
| 83989 | FAM172A | CCI_3 | Human | Cervix | CC | 1.41e-10 | 8.32e-01 | 0.516 |
| 83989 | FAM172A | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.71e-21 | -7.44e-01 | 0.0155 |
| 83989 | FAM172A | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.85e-02 | -4.40e-01 | -0.1808 |
| 83989 | FAM172A | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.12e-04 | -6.31e-01 | -0.1207 |
| 83989 | FAM172A | HTA11_696_2000001011 | Human | Colorectum | AD | 3.04e-08 | -4.38e-01 | -0.1464 |
| 83989 | FAM172A | HTA11_866_2000001011 | Human | Colorectum | AD | 4.44e-03 | -3.45e-01 | -0.1001 |
| 83989 | FAM172A | HTA11_9408_2000001011 | Human | Colorectum | AD | 1.12e-02 | -8.34e-01 | 0.0451 |
| 83989 | FAM172A | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.05e-05 | 5.93e-01 | 0.0588 |
| 83989 | FAM172A | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.08e-05 | 5.71e-01 | 0.281 |
| 83989 | FAM172A | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.09e-02 | 5.94e-01 | 0.3859 |
| 83989 | FAM172A | A001-C-207 | Human | Colorectum | FAP | 2.22e-03 | -2.87e-01 | 0.1278 |
| 83989 | FAM172A | A015-C-203 | Human | Colorectum | FAP | 4.78e-32 | -4.54e-01 | -0.1294 |
| 83989 | FAM172A | A015-C-204 | Human | Colorectum | FAP | 2.82e-06 | -3.77e-01 | -0.0228 |
| 83989 | FAM172A | A014-C-040 | Human | Colorectum | FAP | 8.36e-05 | -3.94e-01 | -0.1184 |
| 83989 | FAM172A | A002-C-201 | Human | Colorectum | FAP | 5.82e-16 | -4.62e-01 | 0.0324 |
| 83989 | FAM172A | A001-C-119 | Human | Colorectum | FAP | 5.72e-13 | -7.25e-01 | -0.1557 |
| 83989 | FAM172A | A001-C-108 | Human | Colorectum | FAP | 3.77e-16 | -3.73e-01 | -0.0272 |
| 83989 | FAM172A | A002-C-205 | Human | Colorectum | FAP | 1.76e-23 | -4.54e-01 | -0.1236 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:004348410 | Cervix | CC | regulation of RNA splicing | 42/2311 | 148/18723 | 1.25e-07 | 6.24e-06 | 42 |
| GO:19033119 | Cervix | CC | regulation of mRNA metabolic process | 64/2311 | 288/18723 | 1.71e-06 | 5.64e-05 | 64 |
| GO:004802410 | Cervix | CC | regulation of mRNA splicing, via spliceosome | 28/2311 | 101/18723 | 2.41e-05 | 4.19e-04 | 28 |
| GO:00488634 | Cervix | CC | stem cell differentiation | 46/2311 | 206/18723 | 4.11e-05 | 6.36e-04 | 46 |
| GO:00063257 | Cervix | CC | chromatin organization | 78/2311 | 409/18723 | 5.40e-05 | 8.02e-04 | 78 |
| GO:00506849 | Cervix | CC | regulation of mRNA processing | 33/2311 | 137/18723 | 1.06e-04 | 1.35e-03 | 33 |
| GO:000838010 | Cervix | CC | RNA splicing | 76/2311 | 434/18723 | 9.79e-04 | 8.19e-03 | 76 |
| GO:000037710 | Cervix | CC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000039810 | Cervix | CC | mRNA splicing, via spliceosome | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000037510 | Cervix | CC | RNA splicing, via transesterification reactions | 55/2311 | 324/18723 | 8.61e-03 | 4.44e-02 | 55 |
| GO:00487624 | Cervix | CC | mesenchymal cell differentiation | 42/2311 | 236/18723 | 9.12e-03 | 4.60e-02 | 42 |
| GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
| GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
| GO:1903311 | Colorectum | AD | regulation of mRNA metabolic process | 117/3918 | 288/18723 | 1.69e-14 | 4.23e-12 | 117 |
| GO:0043484 | Colorectum | AD | regulation of RNA splicing | 70/3918 | 148/18723 | 6.47e-13 | 1.16e-10 | 70 |
| GO:0048024 | Colorectum | AD | regulation of mRNA splicing, via spliceosome | 50/3918 | 101/18723 | 1.62e-10 | 1.56e-08 | 50 |
| GO:0050684 | Colorectum | AD | regulation of mRNA processing | 61/3918 | 137/18723 | 4.23e-10 | 3.58e-08 | 61 |
| GO:0000380 | Colorectum | AD | alternative mRNA splicing, via spliceosome | 33/3918 | 77/18723 | 1.13e-05 | 2.55e-04 | 33 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| 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 |
| FAM172A | SNV | Missense_Mutation | rs758166608 | c.1007N>A | p.Arg336Gln | p.R336Q | Q8WUF8 | protein_coding | tolerated(1) | benign(0.003) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| FAM172A | SNV | Missense_Mutation | c.497N>T | p.Ala166Val | p.A166V | Q8WUF8 | protein_coding | deleterious(0.01) | probably_damaging(0.946) | TCGA-AR-A251-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| FAM172A | SNV | Missense_Mutation | c.1133N>A | p.Ser378Tyr | p.S378Y | Q8WUF8 | protein_coding | deleterious(0) | possibly_damaging(0.895) | TCGA-BH-A1FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| FAM172A | SNV | Missense_Mutation | rs200535189 | c.779N>G | p.Tyr260Cys | p.Y260C | Q8WUF8 | protein_coding | tolerated(0.17) | benign(0) | TCGA-GM-A2DM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR |
| FAM172A | insertion | Nonsense_Mutation | novel | c.31_32insATAAACCTCTCATAAAATATCAGTAA | p.Leu11TyrfsTer9 | p.L11Yfs*9 | Q8WUF8 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| FAM172A | SNV | Missense_Mutation | c.652G>C | p.Asp218His | p.D218H | Q8WUF8 | protein_coding | deleterious(0.03) | possibly_damaging(0.866) | TCGA-C5-A7UH-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| FAM172A | SNV | Missense_Mutation | novel | c.388N>A | p.Glu130Lys | p.E130K | Q8WUF8 | protein_coding | tolerated(0.05) | benign(0.025) | TCGA-VS-A9V5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| FAM172A | SNV | Missense_Mutation | rs761232649 | c.925N>A | p.Asp309Asn | p.D309N | Q8WUF8 | protein_coding | deleterious(0.01) | benign(0.088) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| FAM172A | SNV | Missense_Mutation | novel | c.503N>T | p.Arg168Ile | p.R168I | Q8WUF8 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| FAM172A | insertion | Frame_Shift_Ins | novel | c.928_929insCTCACACCCATTCATCTCAGCAC | p.Val310AlafsTer9 | p.V310Afs*9 | Q8WUF8 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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 |
| Page: 1 |
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