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Gene: TNFRSF1B |
Gene summary for TNFRSF1B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TNFRSF1B | Gene ID | 7133 |
| Gene name | TNF receptor superfamily member 1B | |
| Gene Alias | CD120b | |
| Cytomap | 1p36.22 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | P20333 |
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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 |
| 7133 | TNFRSF1B | S41 | Human | Liver | Cirrhotic | 1.23e-02 | 3.41e-01 | -0.0343 |
| 7133 | TNFRSF1B | HCC2 | Human | Liver | HCC | 1.29e-21 | 2.76e+00 | 0.5341 |
| 7133 | TNFRSF1B | HCC5 | Human | Liver | HCC | 6.87e-19 | 2.49e+00 | 0.4932 |
| 7133 | TNFRSF1B | Pt13.b | Human | Liver | HCC | 6.48e-03 | 4.04e-02 | 0.0251 |
| 7133 | TNFRSF1B | S028 | Human | Liver | HCC | 1.58e-03 | 3.48e-01 | 0.2503 |
| 7133 | TNFRSF1B | S029 | Human | Liver | HCC | 2.53e-03 | 4.19e-01 | 0.2581 |
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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:004217612 | Liver | Cirrhotic | regulation of protein catabolic process | 181/4634 | 391/18723 | 7.94e-21 | 2.77e-18 | 181 |
| GO:000989612 | Liver | Cirrhotic | positive regulation of catabolic process | 215/4634 | 492/18723 | 1.13e-20 | 3.56e-18 | 215 |
| GO:190136111 | Liver | Cirrhotic | organic cyclic compound catabolic process | 213/4634 | 495/18723 | 1.58e-19 | 3.67e-17 | 213 |
| GO:003133112 | Liver | Cirrhotic | positive regulation of cellular catabolic process | 190/4634 | 427/18723 | 1.94e-19 | 4.18e-17 | 190 |
| GO:001943911 | Liver | Cirrhotic | aromatic compound catabolic process | 202/4634 | 467/18723 | 6.93e-19 | 1.28e-16 | 202 |
| GO:004427011 | Liver | Cirrhotic | cellular nitrogen compound catabolic process | 195/4634 | 451/18723 | 2.99e-18 | 4.94e-16 | 195 |
| GO:004670011 | Liver | Cirrhotic | heterocycle catabolic process | 192/4634 | 445/18723 | 7.17e-18 | 1.12e-15 | 192 |
| GO:004586212 | Liver | Cirrhotic | positive regulation of proteolysis | 163/4634 | 372/18723 | 4.18e-16 | 5.14e-14 | 163 |
| GO:004573212 | Liver | Cirrhotic | positive regulation of protein catabolic process | 112/4634 | 231/18723 | 3.89e-15 | 4.21e-13 | 112 |
| GO:003465511 | Liver | Cirrhotic | nucleobase-containing compound catabolic process | 171/4634 | 407/18723 | 9.07e-15 | 9.33e-13 | 171 |
| GO:009719312 | Liver | Cirrhotic | intrinsic apoptotic signaling pathway | 130/4634 | 288/18723 | 2.69e-14 | 2.45e-12 | 130 |
| GO:000640111 | Liver | Cirrhotic | RNA catabolic process | 126/4634 | 278/18723 | 4.64e-14 | 4.10e-12 | 126 |
| GO:009719112 | Liver | Cirrhotic | extrinsic apoptotic signaling pathway | 97/4634 | 219/18723 | 1.82e-10 | 9.11e-09 | 97 |
| GO:007099712 | Liver | Cirrhotic | neuron death | 141/4634 | 361/18723 | 9.56e-10 | 4.38e-08 | 141 |
| GO:19012147 | Liver | Cirrhotic | regulation of neuron death | 122/4634 | 319/18723 | 5.17e-08 | 1.62e-06 | 122 |
| GO:004348711 | Liver | Cirrhotic | regulation of RNA stability | 73/4634 | 170/18723 | 1.44e-07 | 3.87e-06 | 73 |
| GO:00336192 | Liver | Cirrhotic | membrane protein proteolysis | 31/4634 | 57/18723 | 1.55e-06 | 3.02e-05 | 31 |
| GO:19012156 | Liver | Cirrhotic | negative regulation of neuron death | 80/4634 | 208/18723 | 7.55e-06 | 1.15e-04 | 80 |
| GO:00065092 | Liver | Cirrhotic | membrane protein ectodomain proteolysis | 24/4634 | 43/18723 | 1.30e-05 | 1.82e-04 | 24 |
| GO:000756812 | Liver | Cirrhotic | aging | 117/4634 | 339/18723 | 3.13e-05 | 3.91e-04 | 117 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501414 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
| hsa0502214 | Liver | Cirrhotic | Pathways of neurodegeneration - multiple diseases | 217/2530 | 476/8465 | 7.30e-14 | 2.03e-12 | 1.25e-12 | 217 |
| hsa0501415 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
| hsa0502215 | Liver | Cirrhotic | Pathways of neurodegeneration - multiple diseases | 217/2530 | 476/8465 | 7.30e-14 | 2.03e-12 | 1.25e-12 | 217 |
| hsa0501422 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa0502222 | Liver | HCC | Pathways of neurodegeneration - multiple diseases | 298/4020 | 476/8465 | 6.59e-12 | 1.30e-10 | 7.22e-11 | 298 |
| hsa046684 | Liver | HCC | TNF signaling pathway | 73/4020 | 114/8465 | 2.53e-04 | 1.19e-03 | 6.63e-04 | 73 |
| hsa0501432 | Liver | HCC | Amyotrophic lateral sclerosis | 252/4020 | 364/8465 | 8.85e-18 | 7.41e-16 | 4.12e-16 | 252 |
| hsa0502232 | Liver | HCC | Pathways of neurodegeneration - multiple diseases | 298/4020 | 476/8465 | 6.59e-12 | 1.30e-10 | 7.22e-11 | 298 |
| hsa0466811 | Liver | HCC | TNF signaling pathway | 73/4020 | 114/8465 | 2.53e-04 | 1.19e-03 | 6.63e-04 | 73 |
| 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 |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Breast | ADJ |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Breast | DCIS |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Breast | Healthy |
| LTA | TNFRSF1B | LTA_TNFRSF1B | LT | Cervix | ADJ |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Cervix | CC |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Cervix | Healthy |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Cervix | Precancer |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Endometrium | ADJ |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Endometrium | AEH |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Endometrium | EEC |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Endometrium | Healthy |
| LTA | TNFRSF1B | LTA_TNFRSF1B | LT | Esophagus | ESCC |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | GC | ADJ |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | HNSCC | ADJ |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | HNSCC | OSCC |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | HNSCC | Precancer |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Liver | Healthy |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Liver | Precancer |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Lung | AAH |
| TNF | TNFRSF1B | TNF_TNFRSF1B | TNF | Lung | ADJ |
| 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 |
| TNFRSF1B | SNV | Missense_Mutation | rs778973992 | c.1003N>T | p.Ala335Ser | p.A335S | P20333 | protein_coding | tolerated(0.08) | benign(0.283) | TCGA-3C-AALJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| TNFRSF1B | SNV | Missense_Mutation | rs571590743 | c.1291C>T | p.Arg431Trp | p.R431W | P20333 | protein_coding | deleterious(0.02) | benign(0.251) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TNFRSF1B | SNV | Missense_Mutation | c.643N>T | p.His215Tyr | p.H215Y | P20333 | protein_coding | tolerated(1) | benign(0) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| TNFRSF1B | SNV | Missense_Mutation | c.1261N>A | p.Val421Ile | p.V421I | P20333 | protein_coding | tolerated(0.29) | probably_damaging(0.981) | TCGA-BH-A1FH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| TNFRSF1B | SNV | Missense_Mutation | novel | c.931A>G | p.Thr311Ala | p.T311A | P20333 | protein_coding | tolerated(1) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TNFRSF1B | SNV | Missense_Mutation | novel | c.363G>T | p.Arg121Ser | p.R121S | P20333 | protein_coding | tolerated(0.35) | benign(0.02) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| TNFRSF1B | SNV | Missense_Mutation | c.1333G>A | p.Glu445Lys | p.E445K | P20333 | protein_coding | deleterious(0.03) | benign(0.116) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| TNFRSF1B | SNV | Missense_Mutation | c.1193N>A | p.Ser398Tyr | p.S398Y | P20333 | protein_coding | deleterious(0.01) | possibly_damaging(0.641) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| TNFRSF1B | SNV | Missense_Mutation | c.143N>G | p.Gln48Arg | p.Q48R | P20333 | protein_coding | tolerated(0.21) | benign(0.001) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| TNFRSF1B | SNV | Missense_Mutation | novel | c.1118N>A | p.Gly373Asp | p.G373D | P20333 | protein_coding | deleterious(0.01) | probably_damaging(0.916) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| 7133 | TNFRSF1B | DRUGGABLE GENOME | CARBAMAZEPINE | CARBAMAZEPINE | 15565432 | |
| 7133 | TNFRSF1B | DRUGGABLE GENOME | ACTINOMYCIN D | 11125300 | ||
| 7133 | TNFRSF1B | DRUGGABLE GENOME | infliximab | INFLIXIMAB | 25850964,18565259,25537528,22129793 | |
| 7133 | TNFRSF1B | DRUGGABLE GENOME | 178101766 | |||
| 7133 | TNFRSF1B | DRUGGABLE GENOME | LITHIUM | LITHIUM | 15565432 | |
| 7133 | TNFRSF1B | DRUGGABLE GENOME | Tumor necrosis factor alpha (TNF-alpha) inhibitors | 25850964,18565259,25537528,22129793 | ||
| 7133 | TNFRSF1B | DRUGGABLE GENOME | etanercept | ETANERCEPT | 30075559 | |
| 7133 | TNFRSF1B | DRUGGABLE GENOME | 178101757 | |||
| 7133 | TNFRSF1B | DRUGGABLE GENOME | STAVUDINE | STAVUDINE | 9430255 | |
| 7133 | TNFRSF1B | DRUGGABLE GENOME | DIDANOSINE | DIDANOSINE | 9430255 |
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