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Gene: AMT |
Gene summary for AMT |
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Gene information | Species | Human | Gene symbol | AMT | Gene ID | 275 |
Gene name | aminomethyltransferase | |
Gene Alias | GCE | |
Cytomap | 3p21.31 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | A0A024R2U7 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
275 | AMT | HCC1_Meng | Human | Liver | HCC | 2.62e-95 | 1.65e-01 | 0.0246 |
275 | AMT | HCC2_Meng | Human | Liver | HCC | 3.00e-03 | -2.33e-03 | 0.0107 |
275 | AMT | cirrhotic1 | Human | Liver | Cirrhotic | 1.38e-02 | 8.85e-02 | 0.0202 |
275 | AMT | cirrhotic2 | Human | Liver | Cirrhotic | 8.19e-04 | 1.33e-01 | 0.0201 |
275 | AMT | HCC1 | Human | Liver | HCC | 5.22e-06 | 3.21e+00 | 0.5336 |
275 | AMT | HCC2 | Human | Liver | HCC | 1.20e-02 | 1.68e+00 | 0.5341 |
275 | AMT | S015 | Human | Liver | HCC | 6.02e-04 | 3.38e-01 | 0.2375 |
275 | AMT | S016 | Human | Liver | HCC | 2.72e-03 | 2.44e-01 | 0.2243 |
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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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00016678 | Breast | Precancer | ameboidal-type cell migration | 47/1080 | 475/18723 | 2.19e-04 | 3.35e-03 | 47 |
GO:00160497 | Breast | Precancer | cell growth | 46/1080 | 482/18723 | 5.63e-04 | 7.16e-03 | 46 |
GO:00353049 | Breast | Precancer | regulation of protein dephosphorylation | 14/1080 | 90/18723 | 6.16e-04 | 7.72e-03 | 14 |
GO:00192164 | Breast | Precancer | regulation of lipid metabolic process | 34/1080 | 331/18723 | 8.14e-04 | 9.55e-03 | 34 |
GO:00015587 | Breast | Precancer | regulation of cell growth | 39/1080 | 414/18723 | 1.81e-03 | 1.78e-02 | 39 |
GO:00011015 | Breast | Precancer | response to acid chemical | 16/1080 | 135/18723 | 4.85e-03 | 3.67e-02 | 16 |
GO:01501158 | Breast | Precancer | cell-substrate junction organization | 13/1080 | 101/18723 | 5.30e-03 | 3.94e-02 | 13 |
GO:01501168 | Breast | Precancer | regulation of cell-substrate junction organization | 10/1080 | 71/18723 | 7.33e-03 | 4.88e-02 | 10 |
GO:000166714 | Breast | IDC | ameboidal-type cell migration | 64/1434 | 475/18723 | 6.65e-06 | 2.05e-04 | 64 |
GO:001921612 | Breast | IDC | regulation of lipid metabolic process | 45/1434 | 331/18723 | 1.21e-04 | 2.24e-03 | 45 |
GO:003530414 | Breast | IDC | regulation of protein dephosphorylation | 18/1434 | 90/18723 | 1.39e-04 | 2.48e-03 | 18 |
GO:00192184 | Breast | IDC | regulation of steroid metabolic process | 18/1434 | 100/18723 | 5.40e-04 | 6.96e-03 | 18 |
GO:001604913 | Breast | IDC | cell growth | 56/1434 | 482/18723 | 1.16e-03 | 1.26e-02 | 56 |
GO:000155813 | Breast | IDC | regulation of cell growth | 49/1434 | 414/18723 | 1.55e-03 | 1.55e-02 | 49 |
GO:007233012 | Breast | IDC | monocarboxylic acid biosynthetic process | 29/1434 | 214/18723 | 1.91e-03 | 1.83e-02 | 29 |
GO:001605313 | Breast | IDC | organic acid biosynthetic process | 39/1434 | 316/18723 | 2.13e-03 | 1.99e-02 | 39 |
GO:000110112 | Breast | IDC | response to acid chemical | 20/1434 | 135/18723 | 3.28e-03 | 2.75e-02 | 20 |
GO:004639413 | Breast | IDC | carboxylic acid biosynthetic process | 38/1434 | 314/18723 | 3.39e-03 | 2.83e-02 | 38 |
GO:00431126 | Breast | IDC | receptor metabolic process | 23/1434 | 166/18723 | 4.04e-03 | 3.25e-02 | 23 |
GO:00030125 | Breast | IDC | muscle system process | 50/1434 | 452/18723 | 5.52e-03 | 4.05e-02 | 50 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0120021 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
hsa006304 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
hsa00260 | Liver | Cirrhotic | Glycine, serine and threonine metabolism | 22/2530 | 40/8465 | 7.85e-04 | 4.51e-03 | 2.78e-03 | 22 |
hsa0120031 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
hsa0063011 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
hsa002601 | Liver | Cirrhotic | Glycine, serine and threonine metabolism | 22/2530 | 40/8465 | 7.85e-04 | 4.51e-03 | 2.78e-03 | 22 |
hsa0120041 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
hsa0063021 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
hsa006702 | Liver | HCC | One carbon pool by folate | 17/4020 | 20/8465 | 6.04e-04 | 2.50e-03 | 1.39e-03 | 17 |
hsa002602 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
hsa0120051 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
hsa0063031 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
hsa0067011 | Liver | HCC | One carbon pool by folate | 17/4020 | 20/8465 | 6.04e-04 | 2.50e-03 | 1.39e-03 | 17 |
hsa002603 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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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 |
AMT | insertion | Frame_Shift_Ins | novel | c.59_60insC | p.Ala21GlyfsTer7 | p.A21Gfs*7 | P48728 | protein_coding | TCGA-D1-A1NY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD | ||
AMT | SNV | Missense_Mutation | novel | c.935T>G | p.Leu312Arg | p.L312R | P48728 | protein_coding | deleterious(0) | probably_damaging(0.916) | TCGA-22-1002-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
AMT | SNV | Missense_Mutation | novel | c.1017G>C | p.Met339Ile | p.M339I | P48728 | protein_coding | tolerated(0.18) | benign(0) | TCGA-CN-A63T-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | CR |
AMT | SNV | Missense_Mutation | novel | c.1052G>T | p.Cys351Phe | p.C351F | P48728 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-CV-A45W-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
AMT | SNV | Missense_Mutation | c.1155N>C | p.Gln385His | p.Q385H | P48728 | protein_coding | tolerated(0.46) | benign(0.011) | TCGA-HC-A6AL-01 | Prostate | prostate adenocarcinoma | Male | <65 | 7 | Unknown | Unknown | SD | |
AMT | SNV | Missense_Mutation | c.1071N>T | p.Lys357Asn | p.K357N | P48728 | protein_coding | tolerated(0.1) | possibly_damaging(0.715) | TCGA-BR-6565-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
AMT | SNV | Missense_Mutation | c.53N>C | p.Phe18Ser | p.F18S | P48728 | protein_coding | tolerated(0.41) | benign(0.001) | TCGA-BR-8363-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
AMT | SNV | Missense_Mutation | rs150649086 | c.29N>A | p.Arg10His | p.R10H | P48728 | protein_coding | tolerated_low_confidence(0.39) | benign(0) | TCGA-CG-4442-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
AMT | SNV | Missense_Mutation | rs34812788 | c.152N>T | p.Ala51Val | p.A51V | P48728 | protein_coding | deleterious(0.05) | benign(0.003) | TCGA-VQ-A8PB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | CR |
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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 |
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