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Gene: LTBR |
Gene summary for LTBR |
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Gene information | Species | Human | Gene symbol | LTBR | Gene ID | 4055 |
Gene name | lymphotoxin beta receptor | |
Gene Alias | D12S370 | |
Cytomap | 12p13.31 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P36941 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
4055 | LTBR | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.34e-10 | 4.53e-01 | -0.1808 |
4055 | LTBR | HTA11_78_2000001011 | Human | Colorectum | AD | 1.89e-03 | 2.59e-01 | -0.1088 |
4055 | LTBR | HTA11_347_2000001011 | Human | Colorectum | AD | 1.83e-13 | 4.73e-01 | -0.1954 |
4055 | LTBR | HTA11_83_2000001011 | Human | Colorectum | SER | 1.90e-03 | 3.67e-01 | -0.1526 |
4055 | LTBR | HTA11_696_2000001011 | Human | Colorectum | AD | 7.47e-04 | 2.97e-01 | -0.1464 |
4055 | LTBR | HTA11_866_2000001011 | Human | Colorectum | AD | 7.22e-06 | 3.73e-01 | -0.1001 |
4055 | LTBR | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.63e-18 | 6.61e-01 | -0.059 |
4055 | LTBR | HTA11_546_2000001011 | Human | Colorectum | AD | 3.36e-04 | 3.35e-01 | -0.0842 |
4055 | LTBR | HTA11_866_3004761011 | Human | Colorectum | AD | 5.58e-08 | 3.82e-01 | 0.096 |
4055 | LTBR | HTA11_4255_2000001011 | Human | Colorectum | SER | 4.17e-02 | 4.22e-01 | 0.0446 |
4055 | LTBR | HTA11_10623_2000001011 | Human | Colorectum | AD | 9.36e-03 | 3.99e-01 | -0.0177 |
4055 | LTBR | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.53e-08 | 4.72e-01 | 0.0338 |
4055 | LTBR | HTA11_7696_3000711011 | Human | Colorectum | AD | 4.79e-02 | 2.93e-01 | 0.0674 |
4055 | LTBR | HTA11_7469_2000001011 | Human | Colorectum | AD | 4.77e-03 | 6.22e-01 | -0.0124 |
4055 | LTBR | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.61e-05 | 4.76e-01 | 0.0588 |
4055 | LTBR | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.23e-10 | 5.79e-01 | 0.3859 |
4055 | LTBR | HTA11_99999974143_84620 | Human | Colorectum | MSS | 5.27e-03 | 2.48e-01 | 0.3005 |
4055 | LTBR | A015-C-203 | Human | Colorectum | FAP | 6.87e-03 | -9.40e-02 | -0.1294 |
4055 | LTBR | A002-C-016 | Human | Colorectum | FAP | 9.78e-05 | -1.38e-01 | 0.0521 |
4055 | LTBR | A001-C-203 | Human | Colorectum | FAP | 1.63e-02 | -1.14e-01 | -0.0481 |
Page: 1 2 3 4 5 6 7 8 |
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∗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 |
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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 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:2001233 | Colorectum | AD | regulation of apoptotic signaling pathway | 119/3918 | 356/18723 | 2.14e-08 | 1.21e-06 | 119 |
GO:0030099 | Colorectum | AD | myeloid cell differentiation | 119/3918 | 381/18723 | 1.24e-06 | 4.01e-05 | 119 |
GO:0043123 | Colorectum | AD | positive regulation of I-kappaB kinase/NF-kappaB signaling | 60/3918 | 186/18723 | 1.91e-04 | 2.56e-03 | 60 |
GO:0071496 | Colorectum | AD | cellular response to external stimulus | 94/3918 | 320/18723 | 1.98e-04 | 2.64e-03 | 94 |
GO:0043122 | Colorectum | AD | regulation of I-kappaB kinase/NF-kappaB signaling | 76/3918 | 249/18723 | 2.17e-04 | 2.85e-03 | 76 |
GO:0097191 | Colorectum | AD | extrinsic apoptotic signaling pathway | 68/3918 | 219/18723 | 2.64e-04 | 3.27e-03 | 68 |
GO:0051403 | Colorectum | AD | stress-activated MAPK cascade | 72/3918 | 239/18723 | 4.77e-04 | 5.25e-03 | 72 |
GO:0031098 | Colorectum | AD | stress-activated protein kinase signaling cascade | 74/3918 | 247/18723 | 4.80e-04 | 5.27e-03 | 74 |
GO:0007249 | Colorectum | AD | I-kappaB kinase/NF-kappaB signaling | 82/3918 | 281/18723 | 6.09e-04 | 6.40e-03 | 82 |
GO:2001235 | Colorectum | AD | positive regulation of apoptotic signaling pathway | 42/3918 | 126/18723 | 7.85e-04 | 7.84e-03 | 42 |
GO:0070302 | Colorectum | AD | regulation of stress-activated protein kinase signaling cascade | 58/3918 | 195/18723 | 2.21e-03 | 1.74e-02 | 58 |
GO:0032872 | Colorectum | AD | regulation of stress-activated MAPK cascade | 57/3918 | 192/18723 | 2.51e-03 | 1.92e-02 | 57 |
GO:0002573 | Colorectum | AD | myeloid leukocyte differentiation | 60/3918 | 208/18723 | 4.03e-03 | 2.81e-02 | 60 |
GO:20012331 | Colorectum | SER | regulation of apoptotic signaling pathway | 101/2897 | 356/18723 | 3.05e-10 | 4.07e-08 | 101 |
GO:00971911 | Colorectum | SER | extrinsic apoptotic signaling pathway | 58/2897 | 219/18723 | 1.76e-05 | 5.22e-04 | 58 |
GO:20012351 | Colorectum | SER | positive regulation of apoptotic signaling pathway | 36/2897 | 126/18723 | 1.29e-04 | 2.63e-03 | 36 |
GO:2001236 | Colorectum | SER | regulation of extrinsic apoptotic signaling pathway | 39/2897 | 151/18723 | 6.67e-04 | 8.94e-03 | 39 |
GO:00714961 | Colorectum | SER | cellular response to external stimulus | 70/2897 | 320/18723 | 1.40e-03 | 1.53e-02 | 70 |
GO:00300991 | Colorectum | SER | myeloid cell differentiation | 80/2897 | 381/18723 | 2.28e-03 | 2.18e-02 | 80 |
GO:00310981 | Colorectum | SER | stress-activated protein kinase signaling cascade | 54/2897 | 247/18723 | 4.65e-03 | 3.67e-02 | 54 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04066 | Colorectum | AD | HIF-1 signaling pathway | 48/2092 | 109/8465 | 7.25e-06 | 7.84e-05 | 5.00e-05 | 48 |
hsa05166 | Colorectum | AD | Human T-cell leukemia virus 1 infection | 72/2092 | 222/8465 | 5.24e-03 | 2.44e-02 | 1.55e-02 | 72 |
hsa040661 | Colorectum | AD | HIF-1 signaling pathway | 48/2092 | 109/8465 | 7.25e-06 | 7.84e-05 | 5.00e-05 | 48 |
hsa051661 | Colorectum | AD | Human T-cell leukemia virus 1 infection | 72/2092 | 222/8465 | 5.24e-03 | 2.44e-02 | 1.55e-02 | 72 |
hsa040662 | Colorectum | SER | HIF-1 signaling pathway | 36/1580 | 109/8465 | 2.27e-04 | 2.15e-03 | 1.56e-03 | 36 |
hsa040663 | Colorectum | SER | HIF-1 signaling pathway | 36/1580 | 109/8465 | 2.27e-04 | 2.15e-03 | 1.56e-03 | 36 |
hsa040664 | Colorectum | MSS | HIF-1 signaling pathway | 39/1875 | 109/8465 | 7.61e-04 | 5.00e-03 | 3.06e-03 | 39 |
hsa051662 | Colorectum | MSS | Human T-cell leukemia virus 1 infection | 68/1875 | 222/8465 | 1.84e-03 | 9.61e-03 | 5.89e-03 | 68 |
hsa040665 | Colorectum | MSS | HIF-1 signaling pathway | 39/1875 | 109/8465 | 7.61e-04 | 5.00e-03 | 3.06e-03 | 39 |
hsa051663 | Colorectum | MSS | Human T-cell leukemia virus 1 infection | 68/1875 | 222/8465 | 1.84e-03 | 9.61e-03 | 5.89e-03 | 68 |
hsa040666 | Colorectum | FAP | HIF-1 signaling pathway | 38/1404 | 109/8465 | 2.43e-06 | 4.28e-05 | 2.60e-05 | 38 |
hsa040667 | Colorectum | FAP | HIF-1 signaling pathway | 38/1404 | 109/8465 | 2.43e-06 | 4.28e-05 | 2.60e-05 | 38 |
hsa05166211 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0406629 | Esophagus | ESCC | HIF-1 signaling pathway | 75/4205 | 109/8465 | 3.66e-05 | 1.68e-04 | 8.60e-05 | 75 |
hsa040645 | Esophagus | ESCC | NF-kappa B signaling pathway | 67/4205 | 104/8465 | 1.62e-03 | 4.89e-03 | 2.50e-03 | 67 |
hsa05166310 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa04066113 | Esophagus | ESCC | HIF-1 signaling pathway | 75/4205 | 109/8465 | 3.66e-05 | 1.68e-04 | 8.60e-05 | 75 |
hsa0406412 | Esophagus | ESCC | NF-kappa B signaling pathway | 67/4205 | 104/8465 | 1.62e-03 | 4.89e-03 | 2.50e-03 | 67 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Breast | DCIS |
LTa1b2 | LTBR | LTA_LTB_LTBR | LT | Cervix | ADJ |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Cervix | CC |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Cervix | Healthy |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Cervix | Precancer |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Endometrium | Healthy |
LTa1b2 | LTBR | LTA_LTB_LTBR | LT | Esophagus | ESCC |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Esophagus | ESCC |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | HNSCC | ADJ |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | HNSCC | OSCC |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Liver | Healthy |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Liver | Precancer |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Prostate | BPH |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Prostate | Tumor |
TNFSF14 | LTBR | TNFSF14_LTBR | LIGHT | Skin | cSCC |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
LTBR | SNV | Missense_Mutation | novel | c.1153N>T | p.Pro385Ser | p.P385S | P36941 | protein_coding | tolerated_low_confidence(0.07) | probably_damaging(0.986) | TCGA-CV-A468-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
LTBR | SNV | Missense_Mutation | rs541718272 | c.1238N>T | p.Ala413Val | p.A413V | P36941 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-P3-A5QE-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
LTBR | SNV | Missense_Mutation | rs778597764 | c.625A>G | p.Thr209Ala | p.T209A | P36941 | protein_coding | tolerated(0.72) | benign(0.001) | TCGA-EJ-5499-01 | Prostate | prostate adenocarcinoma | Male | <65 | 7 | Unknown | Unknown | SD |
LTBR | SNV | Missense_Mutation | novel | c.403T>G | p.Trp135Gly | p.W135G | P36941 | protein_coding | tolerated(0.33) | benign(0) | TCGA-HC-A632-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | SD |
LTBR | SNV | Missense_Mutation | c.1037A>G | p.Asn346Ser | p.N346S | P36941 | protein_coding | tolerated(0.21) | benign(0.015) | TCGA-HU-A4GF-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
LTBR | SNV | Missense_Mutation | novel | c.188N>A | p.Pro63Gln | p.P63Q | P36941 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-EM-A2CL-01 | Thyroid | thyroid carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
LTBR | SNV | Missense_Mutation | c.1006G>T | p.Gly336Trp | p.G336W | P36941 | protein_coding | deleterious(0.02) | probably_damaging(0.979) | TCGA-H2-A26U-01 | Thyroid | thyroid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
4055 | LTBR | DRUGGABLE GENOME | 178101763 | |||
4055 | LTBR | DRUGGABLE GENOME | Baminercept | BAMINERCEPT | ||
4055 | LTBR | DRUGGABLE GENOME | HCBE-11 | HCBE-11 |
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