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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 | LZE4T | Human | Esophagus | ESCC | 1.94e-03 | 1.81e-01 | 0.0811 |
| 54433 | GAR1 | LZE7T | Human | Esophagus | ESCC | 1.92e-06 | 3.01e-01 | 0.0667 |
| 54433 | GAR1 | LZE8T | Human | Esophagus | ESCC | 1.25e-03 | 1.04e-02 | 0.067 |
| 54433 | GAR1 | LZE20T | Human | Esophagus | ESCC | 6.55e-06 | 1.79e-02 | 0.0662 |
| 54433 | GAR1 | LZE22T | Human | Esophagus | ESCC | 9.02e-04 | 1.99e-01 | 0.068 |
| 54433 | GAR1 | LZE24T | Human | Esophagus | ESCC | 7.65e-14 | 1.52e-01 | 0.0596 |
| 54433 | GAR1 | LZE6T | Human | Esophagus | ESCC | 4.40e-03 | 1.50e-01 | 0.0845 |
| 54433 | GAR1 | P1T-E | Human | Esophagus | ESCC | 1.07e-06 | 1.23e-01 | 0.0875 |
| 54433 | GAR1 | P2T-E | Human | Esophagus | ESCC | 9.43e-23 | 5.70e-01 | 0.1177 |
| 54433 | GAR1 | P4T-E | Human | Esophagus | ESCC | 6.10e-21 | 6.17e-01 | 0.1323 |
| 54433 | GAR1 | P5T-E | Human | Esophagus | ESCC | 1.71e-09 | 1.21e-01 | 0.1327 |
| 54433 | GAR1 | P8T-E | Human | Esophagus | ESCC | 2.50e-20 | 1.67e-01 | 0.0889 |
| 54433 | GAR1 | P9T-E | Human | Esophagus | ESCC | 5.87e-12 | 2.40e-01 | 0.1131 |
| 54433 | GAR1 | P10T-E | Human | Esophagus | ESCC | 1.12e-15 | 2.24e-01 | 0.116 |
| 54433 | GAR1 | P11T-E | Human | Esophagus | ESCC | 9.37e-09 | 1.45e-01 | 0.1426 |
| 54433 | GAR1 | P12T-E | Human | Esophagus | ESCC | 2.95e-20 | 3.87e-01 | 0.1122 |
| 54433 | GAR1 | P15T-E | Human | Esophagus | ESCC | 4.17e-20 | 2.58e-01 | 0.1149 |
| 54433 | GAR1 | P16T-E | Human | Esophagus | ESCC | 5.86e-21 | 3.05e-01 | 0.1153 |
| 54433 | GAR1 | P17T-E | Human | Esophagus | ESCC | 4.40e-03 | 3.32e-01 | 0.1278 |
| 54433 | GAR1 | P19T-E | Human | Esophagus | ESCC | 1.49e-05 | 3.82e-01 | 0.1662 |
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| 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:00015222 | Skin | cSCC | pseudouridine synthesis | 11/4864 | 18/18723 | 1.74e-03 | 1.06e-02 | 11 |
| GO:00311183 | Skin | cSCC | rRNA pseudouridine synthesis | 7/4864 | 10/18723 | 4.43e-03 | 2.29e-02 | 7 |
| GO:00094513 | Skin | cSCC | RNA modification | 58/4864 | 167/18723 | 7.33e-03 | 3.47e-02 | 58 |
| GO:0022613113 | Thyroid | PTC | ribonucleoprotein complex biogenesis | 292/5968 | 463/18723 | 3.24e-44 | 2.05e-40 | 292 |
| GO:0042254113 | Thyroid | PTC | ribosome biogenesis | 202/5968 | 299/18723 | 3.47e-37 | 5.47e-34 | 202 |
| GO:0006364112 | Thyroid | PTC | rRNA processing | 156/5968 | 225/18723 | 5.58e-31 | 5.03e-28 | 156 |
| GO:0016072112 | Thyroid | PTC | rRNA metabolic process | 160/5968 | 236/18723 | 5.68e-30 | 3.58e-27 | 160 |
| GO:003447018 | Thyroid | PTC | ncRNA processing | 215/5968 | 395/18723 | 7.14e-21 | 1.22e-18 | 215 |
| GO:00346608 | Thyroid | PTC | ncRNA metabolic process | 239/5968 | 485/18723 | 5.54e-16 | 4.26e-14 | 239 |
| GO:0000723111 | Thyroid | PTC | telomere maintenance | 74/5968 | 131/18723 | 4.85e-09 | 1.26e-07 | 74 |
| GO:0007004111 | Thyroid | PTC | telomere maintenance via telomerase | 43/5968 | 69/18723 | 1.88e-07 | 3.48e-06 | 43 |
| GO:0010833111 | Thyroid | PTC | telomere maintenance via telomere lengthening | 46/5968 | 81/18723 | 3.10e-06 | 4.04e-05 | 46 |
| GO:0006278110 | Thyroid | PTC | RNA-dependent DNA biosynthetic process | 43/5968 | 75/18723 | 4.61e-06 | 5.66e-05 | 43 |
| GO:00322009 | Thyroid | PTC | telomere organization | 74/5968 | 159/18723 | 7.46e-05 | 6.43e-04 | 74 |
| GO:0071897110 | Thyroid | PTC | DNA biosynthetic process | 82/5968 | 180/18723 | 7.98e-05 | 6.81e-04 | 82 |
| GO:002261334 | Thyroid | ATC | ribonucleoprotein complex biogenesis | 292/6293 | 463/18723 | 3.05e-39 | 9.63e-36 | 292 |
| GO:004225434 | Thyroid | ATC | ribosome biogenesis | 203/6293 | 299/18723 | 3.63e-34 | 4.59e-31 | 203 |
| GO:000636432 | Thyroid | ATC | rRNA processing | 157/6293 | 225/18723 | 9.02e-29 | 5.70e-26 | 157 |
| GO:001607232 | Thyroid | ATC | rRNA metabolic process | 161/6293 | 236/18723 | 1.02e-27 | 5.89e-25 | 161 |
| GO:003447021 | Thyroid | ATC | ncRNA processing | 216/6293 | 395/18723 | 3.14e-18 | 3.98e-16 | 216 |
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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 |
| 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 |
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