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Gene: SALL1 |
Gene summary for SALL1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SALL1 | Gene ID | 6299 |
| Gene name | spalt like transcription factor 1 | |
| Gene Alias | HEL-S-89 | |
| Cytomap | 16q12.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9NSC2 |
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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 |
| 6299 | SALL1 | HCC1_Meng | Human | Liver | HCC | 1.34e-11 | -4.88e-02 | 0.0246 |
| 6299 | SALL1 | HCC1 | Human | Liver | HCC | 4.44e-08 | 3.27e+00 | 0.5336 |
| 6299 | SALL1 | HCC2 | Human | Liver | HCC | 3.32e-04 | 1.50e+00 | 0.5341 |
| 6299 | SALL1 | S014 | Human | Liver | HCC | 1.37e-06 | 3.18e-01 | 0.2254 |
| 6299 | SALL1 | S015 | Human | Liver | HCC | 7.80e-06 | 3.92e-01 | 0.2375 |
| 6299 | SALL1 | S016 | Human | Liver | HCC | 4.71e-04 | 2.47e-01 | 0.2243 |
| 6299 | SALL1 | S028 | Human | Liver | HCC | 2.23e-04 | 2.83e-01 | 0.2503 |
| 6299 | SALL1 | S029 | Human | Liver | HCC | 9.56e-05 | 3.96e-01 | 0.2581 |
| 6299 | SALL1 | male-WTA | Human | Thyroid | PTC | 2.65e-21 | 1.68e-01 | 0.1037 |
| 6299 | SALL1 | PTC01 | Human | Thyroid | PTC | 4.61e-04 | 5.06e-02 | 0.1899 |
| 6299 | SALL1 | PTC03 | Human | Thyroid | PTC | 6.68e-03 | -3.81e-02 | 0.1784 |
| 6299 | SALL1 | PTC05 | Human | Thyroid | PTC | 2.61e-16 | 5.13e-01 | 0.2065 |
| 6299 | SALL1 | PTC06 | Human | Thyroid | PTC | 9.04e-16 | 1.97e-01 | 0.2057 |
| 6299 | SALL1 | PTC07 | Human | Thyroid | PTC | 7.46e-11 | 1.87e-01 | 0.2044 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:019873821 | Liver | HCC | cell-cell signaling by wnt | 247/7958 | 446/18723 | 2.11e-08 | 4.96e-07 | 247 |
| GO:004873222 | Liver | HCC | gland development | 242/7958 | 436/18723 | 2.26e-08 | 5.28e-07 | 242 |
| GO:001605521 | Liver | HCC | Wnt signaling pathway | 245/7958 | 444/18723 | 3.68e-08 | 8.09e-07 | 245 |
| GO:003011121 | Liver | HCC | regulation of Wnt signaling pathway | 180/7958 | 328/18723 | 3.62e-06 | 4.72e-05 | 180 |
| GO:003017721 | Liver | HCC | positive regulation of Wnt signaling pathway | 81/7958 | 140/18723 | 1.73e-04 | 1.36e-03 | 81 |
| GO:006056011 | Liver | HCC | developmental growth involved in morphogenesis | 124/7958 | 234/18723 | 7.37e-04 | 4.47e-03 | 124 |
| GO:00016553 | Liver | HCC | urogenital system development | 170/7958 | 338/18723 | 2.15e-03 | 1.08e-02 | 170 |
| GO:00018222 | Liver | HCC | kidney development | 148/7958 | 293/18723 | 3.25e-03 | 1.49e-02 | 148 |
| GO:00720012 | Liver | HCC | renal system development | 152/7958 | 302/18723 | 3.45e-03 | 1.56e-02 | 152 |
| GO:006145811 | Liver | HCC | reproductive system development | 205/7958 | 427/18723 | 1.16e-02 | 4.27e-02 | 205 |
| GO:0016055110 | Thyroid | PTC | Wnt signaling pathway | 217/5968 | 444/18723 | 3.71e-14 | 2.30e-12 | 217 |
| GO:0198738110 | Thyroid | PTC | cell-cell signaling by wnt | 217/5968 | 446/18723 | 6.68e-14 | 3.73e-12 | 217 |
| GO:0030111110 | Thyroid | PTC | regulation of Wnt signaling pathway | 163/5968 | 328/18723 | 1.05e-11 | 4.29e-10 | 163 |
| GO:0048732113 | Thyroid | PTC | gland development | 193/5968 | 436/18723 | 2.88e-08 | 6.42e-07 | 193 |
| GO:000182215 | Thyroid | PTC | kidney development | 133/5968 | 293/18723 | 7.57e-07 | 1.18e-05 | 133 |
| GO:003017719 | Thyroid | PTC | positive regulation of Wnt signaling pathway | 72/5968 | 140/18723 | 1.16e-06 | 1.69e-05 | 72 |
| GO:000165517 | Thyroid | PTC | urogenital system development | 149/5968 | 338/18723 | 1.41e-06 | 2.01e-05 | 149 |
| GO:007200114 | Thyroid | PTC | renal system development | 135/5968 | 302/18723 | 1.76e-06 | 2.43e-05 | 135 |
| GO:006056219 | Thyroid | PTC | epithelial tube morphogenesis | 141/5968 | 325/18723 | 7.52e-06 | 8.73e-05 | 141 |
| GO:00032794 | Thyroid | PTC | cardiac septum development | 54/5968 | 103/18723 | 1.17e-05 | 1.29e-04 | 54 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| SALL1 | SNV | Missense_Mutation | novel | c.2707N>C | p.Ser903Pro | p.S903P | Q9NSC2 | protein_coding | deleterious(0.01) | probably_damaging(0.939) | TCGA-A2-A04P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | PD |
| SALL1 | SNV | Missense_Mutation | rs750514153 | c.1192N>A | p.Ala398Thr | p.A398T | Q9NSC2 | protein_coding | tolerated(0.09) | benign(0.026) | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD |
| SALL1 | SNV | Missense_Mutation | c.356T>A | p.Leu119His | p.L119H | Q9NSC2 | protein_coding | tolerated(0.21) | benign(0.371) | TCGA-A8-A07L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | CR | ||
| SALL1 | SNV | Missense_Mutation | c.3080G>A | p.Arg1027Lys | p.R1027K | Q9NSC2 | protein_coding | tolerated(0.4) | probably_damaging(0.924) | TCGA-AC-A62X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SALL1 | SNV | Missense_Mutation | c.2487N>A | p.Met829Ile | p.M829I | Q9NSC2 | protein_coding | tolerated(0.17) | benign(0.04) | TCGA-AR-A0TP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| SALL1 | SNV | Missense_Mutation | c.2440N>A | p.Asp814Asn | p.D814N | Q9NSC2 | protein_coding | tolerated(0.1) | possibly_damaging(0.728) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| SALL1 | SNV | Missense_Mutation | c.2869G>T | p.Ala957Ser | p.A957S | Q9NSC2 | protein_coding | tolerated(0.64) | benign(0.003) | TCGA-BH-A1F0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SALL1 | SNV | Missense_Mutation | rs766578948 | c.3719N>T | p.Ala1240Val | p.A1240V | Q9NSC2 | protein_coding | tolerated(0.12) | probably_damaging(0.994) | TCGA-E9-A1NE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| SALL1 | SNV | Missense_Mutation | c.1406N>A | p.Arg469His | p.R469H | Q9NSC2 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E9-A1NF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | |
| SALL1 | SNV | Missense_Mutation | c.343G>C | p.Glu115Gln | p.E115Q | Q9NSC2 | protein_coding | deleterious(0.01) | benign(0.005) | TCGA-EW-A1PB-01 | Breast | breast invasive carcinoma | Female | >=65 | 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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