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Gene: GAR1 |
Gene summary for GAR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GAR1 | Gene ID | 54433 |
| Gene name | GAR1 ribonucleoprotein | |
| Gene Alias | NOLA1 | |
| Cytomap | 4q25 | |
| Gene Type | protein-coding | GO ID | GO:0000154 | UniProtAcc | A0A024RDJ3 |
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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 |
| 54433 | GAR1 | P130T-E | Human | Esophagus | ESCC | 9.71e-25 | 5.84e-01 | 0.1676 |
| 54433 | GAR1 | HCC1_Meng | Human | Liver | HCC | 7.35e-63 | 1.26e-01 | 0.0246 |
| 54433 | GAR1 | HCC2_Meng | Human | Liver | HCC | 4.19e-30 | 1.59e-01 | 0.0107 |
| 54433 | GAR1 | cirrhotic1 | Human | Liver | Cirrhotic | 2.25e-08 | 1.36e-01 | 0.0202 |
| 54433 | GAR1 | cirrhotic2 | Human | Liver | Cirrhotic | 9.93e-07 | 1.25e-01 | 0.0201 |
| 54433 | GAR1 | cirrhotic3 | Human | Liver | Cirrhotic | 1.83e-03 | 1.37e-01 | 0.0215 |
| 54433 | GAR1 | Pt13.b | Human | Liver | HCC | 2.04e-07 | 1.12e-01 | 0.0251 |
| 54433 | GAR1 | S014 | Human | Liver | HCC | 6.24e-09 | 3.90e-01 | 0.2254 |
| 54433 | GAR1 | S015 | Human | Liver | HCC | 3.22e-09 | 5.68e-01 | 0.2375 |
| 54433 | GAR1 | S016 | Human | Liver | HCC | 8.34e-12 | 5.70e-01 | 0.2243 |
| 54433 | GAR1 | S027 | Human | Liver | HCC | 6.24e-07 | 8.51e-01 | 0.2446 |
| 54433 | GAR1 | S028 | Human | Liver | HCC | 1.29e-22 | 1.04e+00 | 0.2503 |
| 54433 | GAR1 | S029 | Human | Liver | HCC | 1.98e-19 | 1.15e+00 | 0.2581 |
| 54433 | GAR1 | C04 | Human | Oral cavity | OSCC | 8.49e-28 | 1.48e+00 | 0.2633 |
| 54433 | GAR1 | C21 | Human | Oral cavity | OSCC | 1.89e-42 | 1.55e+00 | 0.2678 |
| 54433 | GAR1 | C30 | Human | Oral cavity | OSCC | 3.87e-28 | 1.26e+00 | 0.3055 |
| 54433 | GAR1 | C38 | Human | Oral cavity | OSCC | 9.43e-06 | 6.62e-01 | 0.172 |
| 54433 | GAR1 | C43 | Human | Oral cavity | OSCC | 8.98e-27 | 6.25e-01 | 0.1704 |
| 54433 | GAR1 | C46 | Human | Oral cavity | OSCC | 4.85e-18 | 4.91e-01 | 0.1673 |
| 54433 | GAR1 | C51 | Human | Oral cavity | OSCC | 1.88e-11 | 8.47e-01 | 0.2674 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:000072319 | Esophagus | ESCC | telomere maintenance | 99/8552 | 131/18723 | 2.68e-12 | 1.08e-10 | 99 |
| GO:007189716 | Esophagus | ESCC | DNA biosynthetic process | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:000700418 | Esophagus | ESCC | telomere maintenance via telomerase | 56/8552 | 69/18723 | 1.40e-09 | 3.30e-08 | 56 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:001083319 | Esophagus | ESCC | telomere maintenance via telomere lengthening | 61/8552 | 81/18723 | 5.24e-08 | 9.37e-07 | 61 |
| GO:000627816 | Esophagus | ESCC | RNA-dependent DNA biosynthetic process | 56/8552 | 75/18723 | 3.03e-07 | 4.30e-06 | 56 |
| GO:003220014 | Esophagus | ESCC | telomere organization | 99/8552 | 159/18723 | 1.77e-05 | 1.57e-04 | 99 |
| GO:00015221 | Esophagus | ESCC | pseudouridine synthesis | 16/8552 | 18/18723 | 1.78e-04 | 1.15e-03 | 16 |
| GO:0000154 | Esophagus | ESCC | rRNA modification | 26/8552 | 37/18723 | 2.16e-03 | 9.62e-03 | 26 |
| GO:00311182 | Esophagus | ESCC | rRNA pseudouridine synthesis | 9/8552 | 10/18723 | 5.09e-03 | 1.92e-02 | 9 |
| GO:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
| GO:004225412 | Liver | Cirrhotic | ribosome biogenesis | 154/4634 | 299/18723 | 1.18e-23 | 6.72e-21 | 154 |
| GO:000636412 | Liver | Cirrhotic | rRNA processing | 115/4634 | 225/18723 | 1.12e-17 | 1.64e-15 | 115 |
| GO:00160724 | Liver | Cirrhotic | rRNA metabolic process | 119/4634 | 236/18723 | 1.19e-17 | 1.70e-15 | 119 |
| Page: 1 2 3 4 5 6 |
| 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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| GAR1 | SNV | Missense_Mutation | c.31N>G | p.Phe11Val | p.F11V | Q9NY12 | protein_coding | tolerated_low_confidence(0.27) | benign(0.031) | TCGA-A2-A04U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| GAR1 | SNV | Missense_Mutation | c.268A>G | p.Thr90Ala | p.T90A | Q9NY12 | protein_coding | tolerated(0.56) | benign(0.371) | TCGA-EK-A2RA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GAR1 | insertion | Frame_Shift_Ins | novel | c.628_629insAGGTA | p.Gly210GlufsTer12 | p.G210Efs*12 | Q9NY12 | protein_coding | TCGA-AG-A023-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| GAR1 | SNV | Missense_Mutation | c.395N>G | p.Asn132Ser | p.N132S | Q9NY12 | protein_coding | deleterious(0) | possibly_damaging(0.869) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| GAR1 | SNV | Missense_Mutation | c.392N>G | p.Glu131Gly | p.E131G | Q9NY12 | protein_coding | deleterious(0) | possibly_damaging(0.817) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| GAR1 | SNV | Missense_Mutation | novel | c.26N>A | p.Gly9Glu | p.G9E | Q9NY12 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.921) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GAR1 | SNV | Missense_Mutation | novel | c.101N>A | p.Gly34Asp | p.G34D | Q9NY12 | protein_coding | tolerated_low_confidence(0.2) | probably_damaging(0.959) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| GAR1 | SNV | Missense_Mutation | c.249N>G | p.Asp83Glu | p.D83E | Q9NY12 | protein_coding | tolerated(1) | possibly_damaging(0.779) | TCGA-38-4629-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| GAR1 | SNV | Missense_Mutation | c.554N>A | p.Arg185Lys | p.R185K | Q9NY12 | protein_coding | tolerated_low_confidence(0.24) | benign(0.237) | TCGA-55-A490-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD | |
| GAR1 | SNV | Missense_Mutation | c.514N>T | p.Gly172Cys | p.G172C | Q9NY12 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.887) | TCGA-75-5126-01 | Lung | lung adenocarcinoma | Female | Unknown | III/IV | 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 |
| Page: 1 |
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