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Gene: TNFRSF12A |
Gene summary for TNFRSF12A |
Gene summary. |
Gene information | Species | Human | Gene symbol | TNFRSF12A | Gene ID | 51330 |
Gene name | TNF receptor superfamily member 12A | |
Gene Alias | CD266 | |
Cytomap | 16p13.3 | |
Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | Q9NP84 |
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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 |
51330 | TNFRSF12A | GSM4909277 | Human | Breast | Precancer | 4.17e-06 | 6.32e-01 | 0.0177 |
51330 | TNFRSF12A | GSM4909281 | Human | Breast | IDC | 9.02e-08 | -4.33e-01 | 0.21 |
51330 | TNFRSF12A | GSM4909285 | Human | Breast | IDC | 2.90e-11 | -4.36e-01 | 0.21 |
51330 | TNFRSF12A | GSM4909286 | Human | Breast | IDC | 1.48e-18 | -6.80e-01 | 0.1081 |
51330 | TNFRSF12A | GSM4909288 | Human | Breast | IDC | 1.26e-03 | -6.25e-01 | 0.0988 |
51330 | TNFRSF12A | GSM4909292 | Human | Breast | IDC | 2.15e-04 | -7.83e-01 | 0.1236 |
51330 | TNFRSF12A | GSM4909293 | Human | Breast | IDC | 8.47e-17 | -5.77e-01 | 0.1581 |
51330 | TNFRSF12A | GSM4909294 | Human | Breast | IDC | 1.65e-07 | -4.98e-01 | 0.2022 |
51330 | TNFRSF12A | GSM4909296 | Human | Breast | IDC | 6.50e-09 | -4.31e-01 | 0.1524 |
51330 | TNFRSF12A | GSM4909297 | Human | Breast | IDC | 6.42e-13 | -4.57e-01 | 0.1517 |
51330 | TNFRSF12A | GSM4909298 | Human | Breast | IDC | 3.17e-06 | -3.90e-01 | 0.1551 |
51330 | TNFRSF12A | GSM4909301 | Human | Breast | IDC | 2.24e-16 | -6.39e-01 | 0.1577 |
51330 | TNFRSF12A | GSM4909304 | Human | Breast | IDC | 1.41e-06 | -4.81e-01 | 0.1636 |
51330 | TNFRSF12A | GSM4909306 | Human | Breast | IDC | 1.31e-05 | -4.20e-01 | 0.1564 |
51330 | TNFRSF12A | GSM4909307 | Human | Breast | IDC | 2.55e-13 | -5.66e-01 | 0.1569 |
51330 | TNFRSF12A | GSM4909308 | Human | Breast | IDC | 8.71e-07 | -4.71e-01 | 0.158 |
51330 | TNFRSF12A | GSM4909311 | Human | Breast | IDC | 1.62e-34 | -7.31e-01 | 0.1534 |
51330 | TNFRSF12A | GSM4909312 | Human | Breast | IDC | 5.35e-17 | -5.55e-01 | 0.1552 |
51330 | TNFRSF12A | GSM4909317 | Human | Breast | IDC | 3.97e-02 | -3.54e-01 | 0.1355 |
51330 | TNFRSF12A | GSM4909319 | Human | Breast | IDC | 1.79e-27 | -5.18e-01 | 0.1563 |
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Transcriptomic changes along malignancy continuum. |
∗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:0061041110 | Thyroid | ATC | regulation of wound healing | 61/6293 | 134/18723 | 2.69e-03 | 1.23e-02 | 61 |
GO:1903034111 | Thyroid | ATC | regulation of response to wounding | 71/6293 | 167/18723 | 9.88e-03 | 3.61e-02 | 71 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Breast | DCIS |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Breast | Healthy |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Cervix | ADJ |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Cervix | Healthy |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Cervix | Precancer |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Endometrium | AEH |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Endometrium | EEC |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Endometrium | Healthy |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Esophagus | ESCC |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | HNSCC | ADJ |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | HNSCC | Healthy |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | HNSCC | OSCC |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | HNSCC | Precancer |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Liver | Healthy |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Lung | AAH |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Lung | IAC |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Lung | MIAC |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Lung | Precancer |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Prostate | BPH |
TNFSF12 | TNFRSF12A | TNFSF12_TNFRSF12A | TWEAK | Prostate | Healthy |
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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 |
TNFRSF12A | deletion | Frame_Shift_Del | novel | c.226delC | p.Arg76GlyfsTer11 | p.R76Gfs*11 | Q9NP84 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
TNFRSF12A | SNV | Missense_Mutation | rs201879993 | c.358N>A | p.Glu120Lys | p.E120K | Q9NP84 | protein_coding | tolerated(0.15) | benign(0.192) | TCGA-4J-AA1J-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
TNFRSF12A | SNV | Missense_Mutation | c.305G>A | p.Arg102Lys | p.R102K | Q9NP84 | protein_coding | tolerated(0.15) | probably_damaging(0.924) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
TNFRSF12A | SNV | Missense_Mutation | c.244N>T | p.Leu82Phe | p.L82F | Q9NP84 | protein_coding | tolerated(0.06) | probably_damaging(0.999) | TCGA-38-4629-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
TNFRSF12A | SNV | Missense_Mutation | novel | c.332C>G | p.Thr111Ser | p.T111S | Q9NP84 | protein_coding | tolerated(0.06) | probably_damaging(0.968) | TCGA-75-6211-01 | Lung | lung adenocarcinoma | Female | Unknown | I/II | Unknown | Unknown | PD |
TNFRSF12A | SNV | Missense_Mutation | novel | c.46N>T | p.Gly16Trp | p.G16W | Q9NP84 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-77-7335-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
TNFRSF12A | SNV | Missense_Mutation | novel | c.277N>A | p.Gly93Arg | p.G93R | Q9NP84 | protein_coding | deleterious(0.03) | possibly_damaging(0.588) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response |
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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 |
51330 | TNFRSF12A | DRUGGABLE GENOME | Enavatuzumab | ENAVATUZUMAB | ||
51330 | TNFRSF12A | DRUGGABLE GENOME | agonist | CHEMBL1743011 | ENAVATUZUMAB | |
51330 | TNFRSF12A | DRUGGABLE GENOME | 178101760 |
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