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Gene: GRAMD1A |
Gene summary for GRAMD1A |
Gene summary. |
Gene information | Species | Human | Gene symbol | GRAMD1A | Gene ID | 57655 |
Gene name | GRAM domain containing 1A | |
Gene Alias | KIAA1533 | |
Cytomap | 19q13.11 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q96CP6 |
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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 |
57655 | GRAMD1A | P130T-E | Human | Esophagus | ESCC | 1.87e-56 | 1.12e+00 | 0.1676 |
57655 | GRAMD1A | HCC1_Meng | Human | Liver | HCC | 4.89e-43 | 1.01e-01 | 0.0246 |
57655 | GRAMD1A | HCC2_Meng | Human | Liver | HCC | 1.79e-26 | 2.30e-01 | 0.0107 |
57655 | GRAMD1A | HCC2 | Human | Liver | HCC | 2.46e-02 | 1.84e+00 | 0.5341 |
57655 | GRAMD1A | Pt13.b | Human | Liver | HCC | 1.81e-07 | 1.87e-01 | 0.0251 |
57655 | GRAMD1A | S014 | Human | Liver | HCC | 1.90e-23 | 6.96e-01 | 0.2254 |
57655 | GRAMD1A | S015 | Human | Liver | HCC | 2.73e-17 | 7.48e-01 | 0.2375 |
57655 | GRAMD1A | S016 | Human | Liver | HCC | 1.51e-18 | 6.54e-01 | 0.2243 |
57655 | GRAMD1A | S029 | Human | Liver | HCC | 1.07e-02 | 2.37e-01 | 0.2581 |
57655 | GRAMD1A | C04 | Human | Oral cavity | OSCC | 9.37e-09 | 5.50e-01 | 0.2633 |
57655 | GRAMD1A | C21 | Human | Oral cavity | OSCC | 4.32e-24 | 8.27e-01 | 0.2678 |
57655 | GRAMD1A | C30 | Human | Oral cavity | OSCC | 4.66e-26 | 1.10e+00 | 0.3055 |
57655 | GRAMD1A | C38 | Human | Oral cavity | OSCC | 4.40e-08 | 1.08e+00 | 0.172 |
57655 | GRAMD1A | C43 | Human | Oral cavity | OSCC | 6.33e-29 | 5.30e-01 | 0.1704 |
57655 | GRAMD1A | C51 | Human | Oral cavity | OSCC | 1.78e-11 | 6.11e-01 | 0.2674 |
57655 | GRAMD1A | C06 | Human | Oral cavity | OSCC | 6.77e-07 | 1.06e+00 | 0.2699 |
57655 | GRAMD1A | C08 | Human | Oral cavity | OSCC | 8.04e-29 | 6.68e-01 | 0.1919 |
57655 | GRAMD1A | C09 | Human | Oral cavity | OSCC | 7.02e-04 | 2.88e-01 | 0.1431 |
57655 | GRAMD1A | LN22 | Human | Oral cavity | OSCC | 3.53e-02 | 4.38e-01 | 0.1733 |
57655 | GRAMD1A | LP15 | Human | Oral cavity | LP | 2.85e-05 | 5.87e-01 | 0.2174 |
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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:0010876 | Colorectum | AD | lipid localization | 120/3918 | 448/18723 | 1.59e-03 | 1.33e-02 | 120 |
GO:0006869 | Colorectum | AD | lipid transport | 108/3918 | 398/18723 | 1.67e-03 | 1.39e-02 | 108 |
GO:0097305 | Colorectum | AD | response to alcohol | 71/3918 | 253/18723 | 4.01e-03 | 2.80e-02 | 71 |
GO:00973051 | Colorectum | MSS | response to alcohol | 66/3467 | 253/18723 | 1.73e-03 | 1.54e-02 | 66 |
GO:00108761 | Colorectum | MSS | lipid localization | 104/3467 | 448/18723 | 6.76e-03 | 4.38e-02 | 104 |
GO:00068691 | Colorectum | FAP | lipid transport | 81/2622 | 398/18723 | 2.84e-04 | 3.76e-03 | 81 |
GO:00973053 | Colorectum | FAP | response to alcohol | 55/2622 | 253/18723 | 5.05e-04 | 5.78e-03 | 55 |
GO:0097306 | Colorectum | FAP | cellular response to alcohol | 25/2622 | 93/18723 | 7.87e-04 | 8.29e-03 | 25 |
GO:00108762 | Colorectum | FAP | lipid localization | 85/2622 | 448/18723 | 1.92e-03 | 1.63e-02 | 85 |
GO:0097305111 | Esophagus | ESCC | response to alcohol | 138/8552 | 253/18723 | 2.70e-03 | 1.14e-02 | 138 |
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:01200092 | Liver | HCC | intermembrane lipid transfer | 33/7958 | 48/18723 | 2.12e-04 | 1.63e-03 | 33 |
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 |
GO:009730519 | Oral cavity | OSCC | response to alcohol | 127/7305 | 253/18723 | 1.81e-04 | 1.24e-03 | 127 |
GO:0097305110 | Oral cavity | LP | response to alcohol | 80/4623 | 253/18723 | 7.24e-03 | 4.05e-02 | 80 |
GO:0097305113 | Thyroid | PTC | response to alcohol | 107/5968 | 253/18723 | 2.92e-04 | 2.07e-03 | 107 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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 |
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 |
GRAMD1A | SNV | Missense_Mutation | novel | c.1481N>G | p.Ser494Cys | p.S494C | Q96CP6 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
GRAMD1A | SNV | Missense_Mutation | c.1534N>A | p.Glu512Lys | p.E512K | Q96CP6 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
GRAMD1A | SNV | Missense_Mutation | rs375746328 | c.1976N>T | p.Thr659Met | p.T659M | Q96CP6 | protein_coding | deleterious(0) | possibly_damaging(0.762) | TCGA-AC-A6IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GRAMD1A | SNV | Missense_Mutation | novel | c.689A>C | p.Tyr230Ser | p.Y230S | Q96CP6 | protein_coding | tolerated(0.07) | probably_damaging(0.994) | TCGA-BH-A203-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
GRAMD1A | SNV | Missense_Mutation | c.382G>A | p.Glu128Lys | p.E128K | Q96CP6 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
GRAMD1A | SNV | Missense_Mutation | novel | c.695N>T | p.Ser232Phe | p.S232F | Q96CP6 | protein_coding | deleterious(0.04) | benign(0.148) | TCGA-ZJ-AAXU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
GRAMD1A | SNV | Missense_Mutation | rs769848875 | c.512N>T | p.Thr171Met | p.T171M | Q96CP6 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GRAMD1A | SNV | Missense_Mutation | novel | c.520N>A | p.Glu174Lys | p.E174K | Q96CP6 | protein_coding | deleterious(0) | possibly_damaging(0.881) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GRAMD1A | SNV | Missense_Mutation | rs754266755 | c.1526C>T | p.Ser509Leu | p.S509L | Q96CP6 | protein_coding | deleterious(0.02) | benign(0.117) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
GRAMD1A | SNV | Missense_Mutation | rs759830313 | c.1360N>A | p.Gly454Ser | p.G454S | Q96CP6 | protein_coding | tolerated(0.11) | benign(0.028) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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 |
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