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Gene: GRAMD1B |
Gene summary for GRAMD1B |
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Gene information | Species | Human | Gene symbol | GRAMD1B | Gene ID | 57476 |
Gene name | GRAM domain containing 1B | |
Gene Alias | LINC01059 | |
Cytomap | 11q24.1 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q3KR37 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
57476 | GRAMD1B | HCC2_Meng | Human | Liver | HCC | 1.24e-04 | 1.24e-02 | 0.0107 |
57476 | GRAMD1B | cirrhotic3 | Human | Liver | Cirrhotic | 2.72e-02 | 9.28e-02 | 0.0215 |
57476 | GRAMD1B | HCC2 | Human | Liver | HCC | 3.95e-05 | 1.30e+00 | 0.5341 |
57476 | GRAMD1B | S027 | Human | Liver | HCC | 1.37e-04 | 4.58e-01 | 0.2446 |
57476 | GRAMD1B | S028 | Human | Liver | HCC | 5.09e-11 | 5.26e-01 | 0.2503 |
57476 | GRAMD1B | S029 | Human | Liver | HCC | 1.23e-16 | 6.47e-01 | 0.2581 |
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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:005508811 | Liver | Cirrhotic | lipid homeostasis | 74/4634 | 167/18723 | 2.46e-08 | 8.51e-07 | 74 |
GO:004263211 | Liver | Cirrhotic | cholesterol homeostasis | 46/4634 | 96/18723 | 7.15e-07 | 1.52e-05 | 46 |
GO:005509211 | Liver | Cirrhotic | sterol homeostasis | 46/4634 | 97/18723 | 1.04e-06 | 2.13e-05 | 46 |
GO:009730512 | Liver | Cirrhotic | response to alcohol | 96/4634 | 253/18723 | 1.97e-06 | 3.65e-05 | 96 |
GO:001087611 | Liver | Cirrhotic | lipid localization | 147/4634 | 448/18723 | 6.24e-05 | 7.12e-04 | 147 |
GO:000686911 | Liver | Cirrhotic | lipid transport | 128/4634 | 398/18723 | 4.54e-04 | 3.69e-03 | 128 |
GO:001591811 | Liver | Cirrhotic | sterol transport | 48/4634 | 130/18723 | 1.32e-03 | 8.83e-03 | 48 |
GO:00973061 | Liver | Cirrhotic | cellular response to alcohol | 36/4634 | 93/18723 | 1.97e-03 | 1.23e-02 | 36 |
GO:0036314 | Liver | Cirrhotic | response to sterol | 17/4634 | 36/18723 | 2.82e-03 | 1.63e-02 | 17 |
GO:01200091 | Liver | Cirrhotic | intermembrane lipid transfer | 21/4634 | 48/18723 | 3.06e-03 | 1.73e-02 | 21 |
GO:00550882 | Liver | HCC | lipid homeostasis | 103/7958 | 167/18723 | 4.27e-07 | 7.18e-06 | 103 |
GO:009730522 | Liver | HCC | response to alcohol | 138/7958 | 253/18723 | 6.91e-05 | 6.26e-04 | 138 |
GO:001087621 | Liver | HCC | lipid localization | 228/7958 | 448/18723 | 1.80e-04 | 1.41e-03 | 228 |
GO:005509221 | Liver | HCC | sterol homeostasis | 59/7958 | 97/18723 | 2.06e-04 | 1.58e-03 | 59 |
GO:01200092 | Liver | HCC | intermembrane lipid transfer | 33/7958 | 48/18723 | 2.12e-04 | 1.63e-03 | 33 |
GO:004263221 | Liver | HCC | cholesterol homeostasis | 58/7958 | 96/18723 | 2.99e-04 | 2.13e-03 | 58 |
GO:000686921 | Liver | HCC | lipid transport | 198/7958 | 398/18723 | 1.92e-03 | 9.78e-03 | 198 |
GO:00363141 | Liver | HCC | response to sterol | 24/7958 | 36/18723 | 2.95e-03 | 1.38e-02 | 24 |
GO:00159182 | Liver | HCC | sterol transport | 71/7958 | 130/18723 | 3.49e-03 | 1.58e-02 | 71 |
GO:0070723 | Liver | HCC | response to cholesterol | 20/7958 | 31/18723 | 1.11e-02 | 4.09e-02 | 20 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
GRAMD1B | SNV | Missense_Mutation | novel | c.823N>A | p.Glu275Lys | p.E275K | Q3KR37 | protein_coding | tolerated(0.05) | benign(0.14) | TCGA-94-8490-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
GRAMD1B | SNV | Missense_Mutation | rs753231387 | c.583G>T | p.Ala195Ser | p.A195S | Q3KR37 | protein_coding | deleterious(0) | benign(0.057) | TCGA-O2-A52Q-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
GRAMD1B | deletion | Frame_Shift_Del | novel | c.1960delN | p.Tyr654ThrfsTer19 | p.Y654Tfs*19 | Q3KR37 | protein_coding | TCGA-91-6829-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
GRAMD1B | SNV | Missense_Mutation | rs373808855 | c.928N>A | p.Pro310Thr | p.P310T | Q3KR37 | protein_coding | tolerated(0.07) | benign(0.097) | TCGA-CN-A63U-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
GRAMD1B | SNV | Missense_Mutation | novel | c.112N>A | p.Gly38Arg | p.G38R | Q3KR37 | protein_coding | tolerated(0.09) | possibly_damaging(0.563) | TCGA-CV-7568-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
GRAMD1B | SNV | Missense_Mutation | novel | c.739N>T | p.Asp247Tyr | p.D247Y | Q3KR37 | protein_coding | deleterious(0.01) | possibly_damaging(0.594) | TCGA-F7-A50I-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
GRAMD1B | SNV | Missense_Mutation | c.575N>T | p.Ser192Leu | p.S192L | Q3KR37 | protein_coding | deleterious(0) | possibly_damaging(0.716) | TCGA-HD-7832-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
GRAMD1B | SNV | Missense_Mutation | c.1528C>T | p.Arg510Cys | p.R510C | Q3KR37 | protein_coding | tolerated(0.22) | benign(0.21) | TCGA-BR-7707-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
GRAMD1B | SNV | Missense_Mutation | rs757313912 | c.1775N>T | p.Thr592Met | p.T592M | Q3KR37 | protein_coding | tolerated(0.25) | possibly_damaging(0.646) | TCGA-BR-8078-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GRAMD1B | SNV | Missense_Mutation | c.149C>T | p.Ser50Leu | p.S50L | Q3KR37 | protein_coding | deleterious(0.02) | benign(0.173) | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | 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 |
57476 | GRAMD1B | TRANSPORTER | lithium | LITHIUM | 29121268 |
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