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Gene: FARSA |
Gene summary for FARSA |
Gene summary. |
Gene information | Species | Human | Gene symbol | FARSA | Gene ID | 2193 |
Gene name | phenylalanyl-tRNA synthetase subunit alpha | |
Gene Alias | CML33 | |
Cytomap | 19p13.13 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | Q6IBR2 |
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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 |
2193 | FARSA | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.51e-08 | 3.80e-01 | -0.0811 |
2193 | FARSA | HTA11_78_2000001011 | Human | Colorectum | AD | 5.02e-05 | 2.62e-01 | -0.1088 |
2193 | FARSA | HTA11_347_2000001011 | Human | Colorectum | AD | 2.34e-08 | 3.32e-01 | -0.1954 |
2193 | FARSA | HTA11_83_2000001011 | Human | Colorectum | SER | 9.10e-05 | 4.00e-01 | -0.1526 |
2193 | FARSA | HTA11_696_2000001011 | Human | Colorectum | AD | 4.71e-14 | 4.44e-01 | -0.1464 |
2193 | FARSA | HTA11_866_2000001011 | Human | Colorectum | AD | 1.66e-05 | 2.57e-01 | -0.1001 |
2193 | FARSA | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.53e-18 | 6.06e-01 | -0.059 |
2193 | FARSA | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.11e-03 | 4.17e-01 | -0.1706 |
2193 | FARSA | HTA11_546_2000001011 | Human | Colorectum | AD | 1.82e-02 | 3.32e-01 | -0.0842 |
2193 | FARSA | HTA11_866_3004761011 | Human | Colorectum | AD | 5.18e-08 | 3.15e-01 | 0.096 |
2193 | FARSA | HTA11_8622_2000001021 | Human | Colorectum | SER | 2.13e-04 | 5.00e-01 | 0.0528 |
2193 | FARSA | HTA11_7663_2000001011 | Human | Colorectum | SER | 3.02e-03 | 4.11e-01 | 0.0131 |
2193 | FARSA | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.37e-17 | 5.50e-01 | 0.0674 |
2193 | FARSA | HTA11_6818_2000001011 | Human | Colorectum | AD | 4.76e-02 | 3.48e-01 | 0.0112 |
2193 | FARSA | HTA11_6818_2000001021 | Human | Colorectum | AD | 9.25e-10 | 4.47e-01 | 0.0588 |
2193 | FARSA | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.13e-11 | 4.14e-01 | 0.294 |
2193 | FARSA | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.49e-08 | 4.19e-01 | 0.281 |
2193 | FARSA | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.55e-19 | 6.64e-01 | 0.3859 |
2193 | FARSA | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.12e-02 | 3.14e-01 | 0.2585 |
2193 | FARSA | HTA11_99999974143_84620 | Human | Colorectum | MSS | 8.18e-07 | 2.76e-01 | 0.3005 |
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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:0006418 | Colorectum | AD | tRNA aminoacylation for protein translation | 19/3918 | 41/18723 | 2.37e-04 | 3.03e-03 | 19 |
GO:0043039 | Colorectum | AD | tRNA aminoacylation | 19/3918 | 44/18723 | 7.13e-04 | 7.21e-03 | 19 |
GO:0043038 | Colorectum | AD | amino acid activation | 19/3918 | 45/18723 | 9.94e-04 | 9.28e-03 | 19 |
GO:0006520 | Colorectum | AD | cellular amino acid metabolic process | 81/3918 | 284/18723 | 1.37e-03 | 1.19e-02 | 81 |
GO:00064181 | Colorectum | SER | tRNA aminoacylation for protein translation | 17/2897 | 41/18723 | 5.75e-05 | 1.35e-03 | 17 |
GO:00430391 | Colorectum | SER | tRNA aminoacylation | 17/2897 | 44/18723 | 1.64e-04 | 3.12e-03 | 17 |
GO:00430381 | Colorectum | SER | amino acid activation | 17/2897 | 45/18723 | 2.25e-04 | 3.91e-03 | 17 |
GO:00065201 | Colorectum | SER | cellular amino acid metabolic process | 61/2897 | 284/18723 | 4.20e-03 | 3.41e-02 | 61 |
GO:00346606 | Esophagus | HGIN | ncRNA metabolic process | 104/2587 | 485/18723 | 2.26e-06 | 8.23e-05 | 104 |
GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
GO:00512623 | Esophagus | ESCC | protein tetramerization | 54/8552 | 87/18723 | 1.50e-03 | 7.06e-03 | 54 |
GO:00512592 | Esophagus | ESCC | protein complex oligomerization | 130/8552 | 238/18723 | 3.29e-03 | 1.36e-02 | 130 |
GO:00346603 | Liver | Cirrhotic | ncRNA metabolic process | 173/4634 | 485/18723 | 3.64e-08 | 1.21e-06 | 173 |
GO:000652011 | Liver | Cirrhotic | cellular amino acid metabolic process | 103/4634 | 284/18723 | 8.88e-06 | 1.30e-04 | 103 |
GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
GO:00065202 | Liver | HCC | cellular amino acid metabolic process | 167/7958 | 284/18723 | 1.91e-08 | 4.56e-07 | 167 |
GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
GO:0051262 | Liver | HCC | protein tetramerization | 50/7958 | 87/18723 | 3.42e-03 | 1.55e-02 | 50 |
GO:0051290 | Liver | HCC | protein heterotetramerization | 12/7958 | 15/18723 | 3.56e-03 | 1.59e-02 | 12 |
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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 |
FARSA | SNV | Missense_Mutation | rs368745199 | c.277N>A | p.Glu93Lys | p.E93K | Q9Y285 | protein_coding | tolerated(0.18) | benign(0.003) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD |
FARSA | SNV | Missense_Mutation | novel | c.1330C>G | p.Leu444Val | p.L444V | Q9Y285 | protein_coding | tolerated(0.09) | possibly_damaging(0.632) | TCGA-AA-A024-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
FARSA | SNV | Missense_Mutation | novel | c.749N>C | p.Asn250Thr | p.N250T | Q9Y285 | protein_coding | deleterious(0.02) | possibly_damaging(0.886) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
FARSA | SNV | Missense_Mutation | c.974N>A | p.Arg325Gln | p.R325Q | Q9Y285 | protein_coding | deleterious(0.01) | possibly_damaging(0.893) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
FARSA | SNV | Missense_Mutation | c.1264N>C | p.Tyr422His | p.Y422H | Q9Y285 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-CM-5861-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
FARSA | SNV | Missense_Mutation | rs375272364 | c.812N>A | p.Arg271His | p.R271H | Q9Y285 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-G4-6320-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | oxaliplatin | SD |
FARSA | SNV | Missense_Mutation | novel | c.1250T>C | p.Met417Thr | p.M417T | Q9Y285 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
FARSA | SNV | Missense_Mutation | c.1304N>T | p.Ser435Leu | p.S435L | Q9Y285 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A0VQ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
FARSA | SNV | Missense_Mutation | novel | c.883N>T | p.Arg295Trp | p.R295W | Q9Y285 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
FARSA | SNV | Missense_Mutation | novel | c.1072C>T | p.Arg358Trp | p.R358W | Q9Y285 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A3BG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | 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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