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Gene: TBP |
Gene summary for TBP |
Gene summary. |
Gene information | Species | Human | Gene symbol | TBP | Gene ID | 6908 |
Gene name | TATA-box binding protein | |
Gene Alias | GTF2D | |
Cytomap | 6q27 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P20226 |
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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 |
6908 | TBP | LZE4T | Human | Esophagus | ESCC | 3.49e-05 | 2.16e-01 | 0.0811 |
6908 | TBP | LZE7T | Human | Esophagus | ESCC | 2.90e-07 | 4.81e-01 | 0.0667 |
6908 | TBP | LZE8T | Human | Esophagus | ESCC | 1.25e-07 | 2.29e-01 | 0.067 |
6908 | TBP | LZE22T | Human | Esophagus | ESCC | 2.13e-02 | 2.55e-01 | 0.068 |
6908 | TBP | LZE24T | Human | Esophagus | ESCC | 8.64e-20 | 4.70e-01 | 0.0596 |
6908 | TBP | LZE6T | Human | Esophagus | ESCC | 7.23e-04 | 1.94e-01 | 0.0845 |
6908 | TBP | P1T-E | Human | Esophagus | ESCC | 1.35e-03 | 2.34e-01 | 0.0875 |
6908 | TBP | P2T-E | Human | Esophagus | ESCC | 3.80e-22 | 3.37e-01 | 0.1177 |
6908 | TBP | P4T-E | Human | Esophagus | ESCC | 8.86e-24 | 4.98e-01 | 0.1323 |
6908 | TBP | P5T-E | Human | Esophagus | ESCC | 1.88e-18 | 3.62e-01 | 0.1327 |
6908 | TBP | P8T-E | Human | Esophagus | ESCC | 3.29e-19 | 2.92e-01 | 0.0889 |
6908 | TBP | P9T-E | Human | Esophagus | ESCC | 1.89e-09 | 1.70e-01 | 0.1131 |
6908 | TBP | P10T-E | Human | Esophagus | ESCC | 2.81e-24 | 3.88e-01 | 0.116 |
6908 | TBP | P11T-E | Human | Esophagus | ESCC | 2.33e-09 | 3.77e-01 | 0.1426 |
6908 | TBP | P12T-E | Human | Esophagus | ESCC | 7.43e-17 | 3.06e-01 | 0.1122 |
6908 | TBP | P15T-E | Human | Esophagus | ESCC | 2.05e-18 | 4.13e-01 | 0.1149 |
6908 | TBP | P16T-E | Human | Esophagus | ESCC | 9.44e-29 | 5.30e-01 | 0.1153 |
6908 | TBP | P17T-E | Human | Esophagus | ESCC | 5.80e-08 | 2.44e-01 | 0.1278 |
6908 | TBP | P19T-E | Human | Esophagus | ESCC | 2.04e-09 | 8.31e-01 | 0.1662 |
6908 | TBP | P20T-E | Human | Esophagus | ESCC | 4.59e-21 | 3.76e-01 | 0.1124 |
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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:2000756 | Liver | Cirrhotic | regulation of peptidyl-lysine acetylation | 30/4634 | 63/18723 | 6.83e-05 | 7.74e-04 | 30 |
GO:00092622 | Liver | Cirrhotic | deoxyribonucleotide metabolic process | 23/4634 | 44/18723 | 7.87e-05 | 8.61e-04 | 23 |
GO:003105611 | Liver | Cirrhotic | regulation of histone modification | 59/4634 | 152/18723 | 8.28e-05 | 9.02e-04 | 59 |
GO:00353047 | Liver | Cirrhotic | regulation of protein dephosphorylation | 39/4634 | 90/18723 | 8.57e-05 | 9.25e-04 | 39 |
GO:0009219 | Liver | Cirrhotic | pyrimidine deoxyribonucleotide metabolic process | 15/4634 | 24/18723 | 9.76e-05 | 1.03e-03 | 15 |
GO:0043967 | Liver | Cirrhotic | histone H4 acetylation | 31/4634 | 67/18723 | 1.03e-04 | 1.06e-03 | 31 |
GO:00091654 | Liver | Cirrhotic | nucleotide biosynthetic process | 89/4634 | 254/18723 | 1.45e-04 | 1.40e-03 | 89 |
GO:1901983 | Liver | Cirrhotic | regulation of protein acetylation | 34/4634 | 77/18723 | 1.53e-04 | 1.46e-03 | 34 |
GO:19012934 | Liver | Cirrhotic | nucleoside phosphate biosynthetic process | 89/4634 | 256/18723 | 1.97e-04 | 1.82e-03 | 89 |
GO:000647011 | Liver | Cirrhotic | protein dephosphorylation | 96/4634 | 281/18723 | 2.32e-04 | 2.11e-03 | 96 |
GO:000226212 | Liver | Cirrhotic | myeloid cell homeostasis | 59/4634 | 157/18723 | 2.33e-04 | 2.11e-03 | 59 |
GO:00303242 | Liver | Cirrhotic | lung development | 65/4634 | 177/18723 | 2.49e-04 | 2.25e-03 | 65 |
GO:00303232 | Liver | Cirrhotic | respiratory tube development | 66/4634 | 181/18723 | 2.82e-04 | 2.49e-03 | 66 |
GO:000717911 | Liver | Cirrhotic | transforming growth factor beta receptor signaling pathway | 71/4634 | 198/18723 | 3.02e-04 | 2.65e-03 | 71 |
GO:0006220 | Liver | Cirrhotic | pyrimidine nucleotide metabolic process | 24/4634 | 50/18723 | 3.06e-04 | 2.68e-03 | 24 |
GO:000155811 | Liver | Cirrhotic | regulation of cell growth | 132/4634 | 414/18723 | 5.53e-04 | 4.36e-03 | 132 |
GO:20007361 | Liver | Cirrhotic | regulation of stem cell differentiation | 26/4634 | 58/18723 | 6.65e-04 | 5.04e-03 | 26 |
GO:01400565 | Liver | Cirrhotic | organelle localization by membrane tethering | 32/4634 | 77/18723 | 8.65e-04 | 6.23e-03 | 32 |
GO:00091416 | Liver | Cirrhotic | nucleoside triphosphate metabolic process | 43/4634 | 112/18723 | 9.31e-04 | 6.62e-03 | 43 |
GO:001631111 | Liver | Cirrhotic | dephosphorylation | 130/4634 | 417/18723 | 1.58e-03 | 1.03e-02 | 130 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
hsa05166211 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0520325 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
hsa030222 | Esophagus | ESCC | Basal transcription factors | 35/4205 | 45/8465 | 1.01e-04 | 4.06e-04 | 2.08e-04 | 35 |
hsa0501638 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
hsa05166310 | Esophagus | ESCC | Human T-cell leukemia virus 1 infection | 164/4205 | 222/8465 | 8.13e-14 | 2.09e-12 | 1.07e-12 | 164 |
hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0520335 | Esophagus | ESCC | Viral carcinogenesis | 137/4205 | 204/8465 | 2.47e-07 | 1.88e-06 | 9.62e-07 | 137 |
hsa0501736 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
hsa0302211 | Esophagus | ESCC | Basal transcription factors | 35/4205 | 45/8465 | 1.01e-04 | 4.06e-04 | 2.08e-04 | 35 |
hsa0501622 | Liver | HCC | Huntington disease | 219/4020 | 306/8465 | 3.06e-18 | 3.42e-16 | 1.90e-16 | 219 |
hsa0516622 | Liver | HCC | Human T-cell leukemia virus 1 infection | 139/4020 | 222/8465 | 3.17e-06 | 2.79e-05 | 1.55e-05 | 139 |
hsa0501721 | Liver | HCC | Spinocerebellar ataxia | 92/4020 | 143/8465 | 3.20e-05 | 1.88e-04 | 1.04e-04 | 92 |
hsa051652 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
hsa052032 | Liver | HCC | Viral carcinogenesis | 117/4020 | 204/8465 | 2.68e-03 | 8.98e-03 | 5.00e-03 | 117 |
hsa0501632 | Liver | HCC | Huntington disease | 219/4020 | 306/8465 | 3.06e-18 | 3.42e-16 | 1.90e-16 | 219 |
hsa0516632 | Liver | HCC | Human T-cell leukemia virus 1 infection | 139/4020 | 222/8465 | 3.17e-06 | 2.79e-05 | 1.55e-05 | 139 |
hsa0501731 | Liver | HCC | Spinocerebellar ataxia | 92/4020 | 143/8465 | 3.20e-05 | 1.88e-04 | 1.04e-04 | 92 |
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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 |
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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 |
∗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 |
TBP | SNV | Missense_Mutation | novel | c.101A>G | p.Tyr34Cys | p.Y34C | P20226 | protein_coding | deleterious_low_confidence(0.03) | probably_damaging(0.993) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
TBP | SNV | Missense_Mutation | c.392C>G | p.Pro131Arg | p.P131R | P20226 | protein_coding | deleterious(0.01) | benign(0.296) | TCGA-AN-A0FK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
TBP | SNV | Missense_Mutation | c.713C>A | p.Ala238Asp | p.A238D | P20226 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A0FL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
TBP | SNV | Missense_Mutation | novel | c.940N>A | p.Gly314Ser | p.G314S | P20226 | protein_coding | deleterious(0.01) | probably_damaging(0.997) | TCGA-BH-A0HW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
TBP | SNV | Missense_Mutation | novel | c.821T>C | p.Val274Ala | p.V274A | P20226 | protein_coding | tolerated(0.43) | probably_damaging(0.996) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
TBP | SNV | Missense_Mutation | c.722N>C | p.Val241Ala | p.V241A | P20226 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
TBP | SNV | Missense_Mutation | c.671C>T | p.Ala224Val | p.A224V | P20226 | protein_coding | deleterious(0.01) | probably_damaging(0.984) | TCGA-D5-6931-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
TBP | SNV | Missense_Mutation | novel | c.70N>C | p.Gly24Arg | p.G24R | P20226 | protein_coding | tolerated_low_confidence(0.29) | benign(0.123) | TCGA-AG-A01J-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
TBP | insertion | Frame_Shift_Ins | novel | c.864_865insC | p.Gly290TrpfsTer27 | p.G290Wfs*27 | P20226 | protein_coding | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
TBP | SNV | Missense_Mutation | rs756227958 | c.556N>T | p.Arg186Cys | p.R186C | P20226 | protein_coding | deleterious(0) | probably_damaging(0.945) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
6908 | TBP | TRANSCRIPTION FACTOR | HORMONES | 7848271 | ||
6908 | TBP | TRANSCRIPTION FACTOR | RETINOIC ACID | 8413615 | ||
6908 | TBP | TRANSCRIPTION FACTOR | VP-16 | ETOPOSIDE PHOSPHATE | 1646402 |
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