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Gene: SMARCAL1 |
Gene summary for SMARCAL1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SMARCAL1 | Gene ID | 50485 |
| Gene name | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 | |
| Gene Alias | HARP | |
| Cytomap | 2q35 | |
| Gene Type | protein-coding | GO ID | GO:0000723 | UniProtAcc | Q9NZC9 |
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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 |
| 50485 | SMARCAL1 | LZE4T | Human | Esophagus | ESCC | 1.11e-02 | 6.91e-02 | 0.0811 |
| 50485 | SMARCAL1 | LZE8T | Human | Esophagus | ESCC | 5.06e-07 | 1.36e-01 | 0.067 |
| 50485 | SMARCAL1 | LZE24T | Human | Esophagus | ESCC | 1.13e-06 | 1.01e-01 | 0.0596 |
| 50485 | SMARCAL1 | P1T-E | Human | Esophagus | ESCC | 3.36e-03 | 1.26e-01 | 0.0875 |
| 50485 | SMARCAL1 | P2T-E | Human | Esophagus | ESCC | 4.12e-11 | 1.80e-01 | 0.1177 |
| 50485 | SMARCAL1 | P4T-E | Human | Esophagus | ESCC | 3.28e-09 | 1.16e-01 | 0.1323 |
| 50485 | SMARCAL1 | P8T-E | Human | Esophagus | ESCC | 3.23e-08 | 1.40e-01 | 0.0889 |
| 50485 | SMARCAL1 | P9T-E | Human | Esophagus | ESCC | 3.05e-03 | 8.13e-02 | 0.1131 |
| 50485 | SMARCAL1 | P10T-E | Human | Esophagus | ESCC | 6.40e-04 | 7.30e-02 | 0.116 |
| 50485 | SMARCAL1 | P11T-E | Human | Esophagus | ESCC | 1.30e-06 | 2.17e-01 | 0.1426 |
| 50485 | SMARCAL1 | P12T-E | Human | Esophagus | ESCC | 5.84e-17 | 2.05e-01 | 0.1122 |
| 50485 | SMARCAL1 | P15T-E | Human | Esophagus | ESCC | 5.33e-09 | 1.78e-01 | 0.1149 |
| 50485 | SMARCAL1 | P16T-E | Human | Esophagus | ESCC | 1.55e-13 | 2.12e-01 | 0.1153 |
| 50485 | SMARCAL1 | P17T-E | Human | Esophagus | ESCC | 1.70e-03 | 2.18e-01 | 0.1278 |
| 50485 | SMARCAL1 | P19T-E | Human | Esophagus | ESCC | 1.02e-04 | 2.30e-01 | 0.1662 |
| 50485 | SMARCAL1 | P20T-E | Human | Esophagus | ESCC | 6.09e-20 | 2.60e-01 | 0.1124 |
| 50485 | SMARCAL1 | P21T-E | Human | Esophagus | ESCC | 2.36e-16 | 1.92e-01 | 0.1617 |
| 50485 | SMARCAL1 | P22T-E | Human | Esophagus | ESCC | 2.45e-08 | 1.54e-01 | 0.1236 |
| 50485 | SMARCAL1 | P23T-E | Human | Esophagus | ESCC | 1.36e-09 | 9.89e-02 | 0.108 |
| 50485 | SMARCAL1 | P24T-E | Human | Esophagus | ESCC | 6.31e-15 | 2.01e-01 | 0.1287 |
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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 |
| ∗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:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:000072319 | Esophagus | ESCC | telomere maintenance | 99/8552 | 131/18723 | 2.68e-12 | 1.08e-10 | 99 |
| GO:00062612 | Esophagus | ESCC | DNA-dependent DNA replication | 100/8552 | 151/18723 | 2.61e-07 | 3.94e-06 | 100 |
| GO:00063024 | Esophagus | ESCC | double-strand break repair | 152/8552 | 251/18723 | 1.33e-06 | 1.62e-05 | 152 |
| GO:00062754 | Esophagus | ESCC | regulation of DNA replication | 73/8552 | 107/18723 | 1.97e-06 | 2.28e-05 | 73 |
| GO:003220014 | Esophagus | ESCC | telomere organization | 99/8552 | 159/18723 | 1.77e-05 | 1.57e-04 | 99 |
| GO:0006303 | Esophagus | ESCC | double-strand break repair via nonhomologous end joining | 43/8552 | 66/18723 | 1.10e-03 | 5.53e-03 | 43 |
| GO:0090329 | Esophagus | ESCC | regulation of DNA-dependent DNA replication | 30/8552 | 46/18723 | 5.91e-03 | 2.18e-02 | 30 |
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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 |
| SMARCAL1 | SNV | Missense_Mutation | rs119473037 | c.1933N>T | p.Arg645Cys | p.R645C | Q9NZC9 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SMARCAL1 | SNV | Missense_Mutation | c.2673N>C | p.Glu891Asp | p.E891D | Q9NZC9 | protein_coding | tolerated(0.18) | benign(0.01) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SMARCAL1 | SNV | Missense_Mutation | c.1698N>T | p.Met566Ile | p.M566I | Q9NZC9 | protein_coding | deleterious(0.03) | benign(0.026) | TCGA-AN-A0FD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SMARCAL1 | SNV | Missense_Mutation | c.445N>G | p.Gln149Glu | p.Q149E | Q9NZC9 | protein_coding | tolerated(0.29) | benign(0.095) | TCGA-C8-A1HK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SMARCAL1 | SNV | Missense_Mutation | c.542N>G | p.Ser181Cys | p.S181C | Q9NZC9 | protein_coding | tolerated(0.09) | benign(0.005) | TCGA-C8-A1HK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SMARCAL1 | SNV | Missense_Mutation | rs370663120 | c.1030G>A | p.Glu344Lys | p.E344K | Q9NZC9 | protein_coding | deleterious(0.05) | possibly_damaging(0.608) | TCGA-D8-A1JJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD |
| SMARCAL1 | SNV | Missense_Mutation | c.2106C>G | p.Phe702Leu | p.F702L | Q9NZC9 | protein_coding | deleterious(0) | possibly_damaging(0.472) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| SMARCAL1 | deletion | Frame_Shift_Del | novel | c.898delC | p.Gln300SerfsTer83 | p.Q300Sfs*83 | Q9NZC9 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| SMARCAL1 | deletion | Frame_Shift_Del | novel | c.1901delA | p.Lys634SerfsTer28 | p.K634Sfs*28 | Q9NZC9 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| SMARCAL1 | SNV | Missense_Mutation | novel | c.148A>G | p.Lys50Glu | p.K50E | Q9NZC9 | protein_coding | tolerated_low_confidence(0.12) | benign(0.026) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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