|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: TNFRSF11A |
Gene summary for TNFRSF11A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TNFRSF11A | Gene ID | 8792 |
| Gene name | TNF receptor superfamily member 11a | |
| Gene Alias | CD265 | |
| Cytomap | 18q21.33 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q9Y6Q6 |
Top |
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 |
| 8792 | TNFRSF11A | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.22e-03 | -3.19e-01 | 0.0674 |
| 8792 | TNFRSF11A | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.46e-04 | -2.96e-01 | 0.294 |
| 8792 | TNFRSF11A | HTA11_99999971662_82457 | Human | Colorectum | MSS | 8.94e-16 | -5.14e-01 | 0.3859 |
| 8792 | TNFRSF11A | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.65e-03 | -5.20e-01 | 0.2585 |
| 8792 | TNFRSF11A | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.22e-22 | -5.75e-01 | 0.3005 |
| 8792 | TNFRSF11A | A015-C-203 | Human | Colorectum | FAP | 1.11e-21 | -3.50e-01 | -0.1294 |
| 8792 | TNFRSF11A | A015-C-204 | Human | Colorectum | FAP | 3.44e-03 | -2.18e-01 | -0.0228 |
| 8792 | TNFRSF11A | A014-C-040 | Human | Colorectum | FAP | 3.21e-02 | 9.56e-02 | -0.1184 |
| 8792 | TNFRSF11A | A002-C-201 | Human | Colorectum | FAP | 8.51e-10 | -3.53e-01 | 0.0324 |
| 8792 | TNFRSF11A | A002-C-203 | Human | Colorectum | FAP | 2.95e-02 | -9.20e-02 | 0.2786 |
| 8792 | TNFRSF11A | A001-C-119 | Human | Colorectum | FAP | 6.98e-09 | -4.78e-01 | -0.1557 |
| 8792 | TNFRSF11A | A001-C-108 | Human | Colorectum | FAP | 3.87e-13 | -1.28e-01 | -0.0272 |
| 8792 | TNFRSF11A | A002-C-205 | Human | Colorectum | FAP | 1.43e-17 | -4.41e-01 | -0.1236 |
| 8792 | TNFRSF11A | A015-C-006 | Human | Colorectum | FAP | 1.71e-08 | -3.57e-01 | -0.0994 |
| 8792 | TNFRSF11A | A015-C-106 | Human | Colorectum | FAP | 2.80e-08 | -1.21e-01 | -0.0511 |
| 8792 | TNFRSF11A | A002-C-114 | Human | Colorectum | FAP | 6.95e-14 | -4.19e-01 | -0.1561 |
| 8792 | TNFRSF11A | A015-C-104 | Human | Colorectum | FAP | 3.37e-25 | -4.24e-01 | -0.1899 |
| 8792 | TNFRSF11A | A001-C-014 | Human | Colorectum | FAP | 1.75e-10 | -2.79e-01 | 0.0135 |
| 8792 | TNFRSF11A | A002-C-016 | Human | Colorectum | FAP | 3.39e-16 | -2.83e-01 | 0.0521 |
| 8792 | TNFRSF11A | A015-C-002 | Human | Colorectum | FAP | 2.41e-06 | -3.21e-01 | -0.0763 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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. |
Top |
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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
| GO:0030099 | Colorectum | AD | myeloid cell differentiation | 119/3918 | 381/18723 | 1.24e-06 | 4.01e-05 | 119 |
| GO:0030879 | Colorectum | AD | mammary gland development | 53/3918 | 137/18723 | 1.46e-06 | 4.58e-05 | 53 |
| GO:0007623 | Colorectum | AD | circadian rhythm | 72/3918 | 210/18723 | 4.50e-06 | 1.21e-04 | 72 |
| GO:0048511 | Colorectum | AD | rhythmic process | 94/3918 | 298/18723 | 1.00e-05 | 2.34e-04 | 94 |
| GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
| GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
| GO:0001894 | Colorectum | AD | tissue homeostasis | 81/3918 | 268/18723 | 1.96e-04 | 2.62e-03 | 81 |
| GO:0051047 | Colorectum | AD | positive regulation of secretion | 90/3918 | 310/18723 | 4.11e-04 | 4.66e-03 | 90 |
| GO:1903532 | Colorectum | AD | positive regulation of secretion by cell | 82/3918 | 282/18723 | 6.85e-04 | 7.00e-03 | 82 |
| GO:0045860 | Colorectum | AD | positive regulation of protein kinase activity | 107/3918 | 386/18723 | 8.01e-04 | 7.92e-03 | 107 |
| GO:0015732 | Colorectum | AD | prostaglandin transport | 10/3918 | 18/18723 | 1.31e-03 | 1.15e-02 | 10 |
| GO:0010876 | Colorectum | AD | lipid localization | 120/3918 | 448/18723 | 1.59e-03 | 1.33e-02 | 120 |
| GO:0006869 | Colorectum | AD | lipid transport | 108/3918 | 398/18723 | 1.67e-03 | 1.39e-02 | 108 |
| GO:0071900 | Colorectum | AD | regulation of protein serine/threonine kinase activity | 98/3918 | 359/18723 | 2.18e-03 | 1.73e-02 | 98 |
| GO:2000191 | Colorectum | AD | regulation of fatty acid transport | 14/3918 | 32/18723 | 3.03e-03 | 2.25e-02 | 14 |
| GO:0051091 | Colorectum | AD | positive regulation of DNA-binding transcription factor activity | 73/3918 | 260/18723 | 3.52e-03 | 2.54e-02 | 73 |
| GO:0002573 | Colorectum | AD | myeloid leukocyte differentiation | 60/3918 | 208/18723 | 4.03e-03 | 2.81e-02 | 60 |
| GO:0071902 | Colorectum | AD | positive regulation of protein serine/threonine kinase activity | 58/3918 | 200/18723 | 4.09e-03 | 2.84e-02 | 58 |
| GO:0032310 | Colorectum | AD | prostaglandin secretion | 8/3918 | 15/18723 | 5.67e-03 | 3.64e-02 | 8 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| TNFRSF11A | SNV | Missense_Mutation | c.214N>A | p.Gly72Ser | p.G72S | Q9Y6Q6 | protein_coding | deleterious(0) | probably_damaging(0.915) | TCGA-A8-A07I-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| TNFRSF11A | SNV | Missense_Mutation | c.955G>A | p.Ala319Thr | p.A319T | Q9Y6Q6 | protein_coding | tolerated(0.46) | benign(0.005) | TCGA-AR-A24U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| TNFRSF11A | SNV | Missense_Mutation | rs750355755 | c.571N>A | p.Asp191Asn | p.D191N | Q9Y6Q6 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-E2-A14Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD |
| TNFRSF11A | SNV | Missense_Mutation | rs372282611 | c.1669N>A | p.Glu557Lys | p.E557K | Q9Y6Q6 | protein_coding | deleterious(0.01) | probably_damaging(0.977) | TCGA-E2-A159-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| TNFRSF11A | insertion | Frame_Shift_Ins | novel | c.208_209insT | p.Pro70LeufsTer6 | p.P70Lfs*6 | Q9Y6Q6 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| TNFRSF11A | insertion | In_Frame_Ins | novel | c.209_210insGCTCCTCCATGTACCAGTGAGAAGCATTATGAGCAT | p.Pro70_Cys71insLeuLeuHisValProValArgSerIleMetSerIle | p.P70_C71insLLHVPVRSIMSI | Q9Y6Q6 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| TNFRSF11A | deletion | Frame_Shift_Del | novel | c.856delN | p.Leu286TyrfsTer3 | p.L286Yfs*3 | Q9Y6Q6 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TNFRSF11A | SNV | Missense_Mutation | novel | c.89N>C | p.Ile30Thr | p.I30T | Q9Y6Q6 | protein_coding | deleterious(0) | benign(0.214) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TNFRSF11A | SNV | Missense_Mutation | novel | c.1580N>A | p.Gly527Glu | p.G527E | Q9Y6Q6 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-C5-A8XK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| TNFRSF11A | SNV | Missense_Mutation | c.559A>G | p.Thr187Ala | p.T187A | Q9Y6Q6 | protein_coding | deleterious(0) | possibly_damaging(0.586) | TCGA-A6-3807-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Ancillary | leucovorin | SD |
| Page: 1 2 3 4 5 6 7 |
Top |
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 |
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | Pyrazolones | 26398624 | ||
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | 178101759 | |||
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | propionic acid derivatives | 26398624 | ||
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | diclofenac | DICLOFENAC | 26398624 | |
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | risperidone | RISPERIDONE | ||
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | acetaminophen | ACETAMINOPHEN | 26398624 | |
| 8792 | TNFRSF11A | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | aspirin | ASPIRIN | 26398624 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |