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Gene: SIX1 |
Gene summary for SIX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SIX1 | Gene ID | 6495 |
| Gene name | SIX homeobox 1 | |
| Gene Alias | BOS3 | |
| Cytomap | 14q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q15475 |
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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 |
| 6495 | SIX1 | LZE20T | Human | Esophagus | ESCC | 1.97e-04 | 1.72e-01 | 0.0662 |
| 6495 | SIX1 | LZE22D1 | Human | Esophagus | HGIN | 8.03e-04 | 1.98e-01 | 0.0595 |
| 6495 | SIX1 | LZE22T | Human | Esophagus | ESCC | 6.43e-20 | 1.03e+00 | 0.068 |
| 6495 | SIX1 | LZE24T | Human | Esophagus | ESCC | 2.33e-28 | 8.74e-01 | 0.0596 |
| 6495 | SIX1 | LZE21T | Human | Esophagus | ESCC | 9.73e-05 | 3.63e-01 | 0.0655 |
| 6495 | SIX1 | P1T-E | Human | Esophagus | ESCC | 2.44e-06 | 3.28e-01 | 0.0875 |
| 6495 | SIX1 | P2T-E | Human | Esophagus | ESCC | 1.02e-31 | 5.16e-01 | 0.1177 |
| 6495 | SIX1 | P4T-E | Human | Esophagus | ESCC | 5.16e-10 | 2.76e-01 | 0.1323 |
| 6495 | SIX1 | P5T-E | Human | Esophagus | ESCC | 7.90e-03 | 1.11e-01 | 0.1327 |
| 6495 | SIX1 | P8T-E | Human | Esophagus | ESCC | 2.06e-58 | 1.03e+00 | 0.0889 |
| 6495 | SIX1 | P9T-E | Human | Esophagus | ESCC | 1.88e-05 | 1.93e-01 | 0.1131 |
| 6495 | SIX1 | P10T-E | Human | Esophagus | ESCC | 1.05e-72 | 1.17e+00 | 0.116 |
| 6495 | SIX1 | P11T-E | Human | Esophagus | ESCC | 1.20e-09 | 3.46e-01 | 0.1426 |
| 6495 | SIX1 | P12T-E | Human | Esophagus | ESCC | 6.31e-57 | 1.03e+00 | 0.1122 |
| 6495 | SIX1 | P15T-E | Human | Esophagus | ESCC | 9.35e-52 | 9.78e-01 | 0.1149 |
| 6495 | SIX1 | P16T-E | Human | Esophagus | ESCC | 1.75e-25 | 4.16e-01 | 0.1153 |
| 6495 | SIX1 | P20T-E | Human | Esophagus | ESCC | 2.32e-06 | 2.11e-01 | 0.1124 |
| 6495 | SIX1 | P22T-E | Human | Esophagus | ESCC | 2.27e-21 | 3.79e-01 | 0.1236 |
| 6495 | SIX1 | P23T-E | Human | Esophagus | ESCC | 3.88e-04 | 1.61e-01 | 0.108 |
| 6495 | SIX1 | P24T-E | Human | Esophagus | ESCC | 1.62e-13 | 2.76e-01 | 0.1287 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:007099714 | Breast | IDC | neuron death | 57/1434 | 361/18723 | 1.31e-07 | 7.38e-06 | 57 |
| GO:004873214 | Breast | IDC | gland development | 64/1434 | 436/18723 | 3.47e-07 | 1.74e-05 | 64 |
| GO:005140213 | Breast | IDC | neuron apoptotic process | 42/1434 | 246/18723 | 7.21e-07 | 3.35e-05 | 42 |
| GO:190121414 | Breast | IDC | regulation of neuron death | 48/1434 | 319/18723 | 5.01e-06 | 1.69e-04 | 48 |
| GO:005067313 | Breast | IDC | epithelial cell proliferation | 60/1434 | 437/18723 | 7.13e-06 | 2.15e-04 | 60 |
| GO:005067812 | Breast | IDC | regulation of epithelial cell proliferation | 54/1434 | 381/18723 | 8.07e-06 | 2.39e-04 | 54 |
| GO:004352313 | Breast | IDC | regulation of neuron apoptotic process | 35/1434 | 212/18723 | 1.26e-05 | 3.29e-04 | 35 |
| GO:006056212 | Breast | IDC | epithelial tube morphogenesis | 44/1434 | 325/18723 | 1.58e-04 | 2.73e-03 | 44 |
| GO:00611383 | Breast | IDC | morphogenesis of a branching epithelium | 28/1434 | 182/18723 | 3.05e-04 | 4.60e-03 | 28 |
| GO:19053301 | Breast | IDC | regulation of morphogenesis of an epithelium | 14/1434 | 65/18723 | 3.35e-04 | 4.98e-03 | 14 |
| GO:00605412 | Breast | IDC | respiratory system development | 30/1434 | 203/18723 | 3.85e-04 | 5.40e-03 | 30 |
| GO:00017635 | Breast | IDC | morphogenesis of a branching structure | 29/1434 | 196/18723 | 4.68e-04 | 6.26e-03 | 29 |
| GO:006053711 | Breast | IDC | muscle tissue development | 50/1434 | 403/18723 | 4.91e-04 | 6.45e-03 | 50 |
| GO:0001656 | Breast | IDC | metanephros development | 16/1434 | 85/18723 | 6.49e-04 | 8.04e-03 | 16 |
| GO:004352411 | Breast | IDC | negative regulation of neuron apoptotic process | 23/1434 | 145/18723 | 6.58e-04 | 8.11e-03 | 23 |
| GO:003514812 | Breast | IDC | tube formation | 23/1434 | 148/18723 | 8.79e-04 | 1.02e-02 | 23 |
| GO:00104644 | Breast | IDC | regulation of mesenchymal cell proliferation | 8/1434 | 28/18723 | 9.00e-04 | 1.04e-02 | 8 |
| GO:190121513 | Breast | IDC | negative regulation of neuron death | 29/1434 | 208/18723 | 1.23e-03 | 1.32e-02 | 29 |
| GO:00359141 | Breast | IDC | skeletal muscle cell differentiation | 13/1434 | 67/18723 | 1.52e-03 | 1.52e-02 | 13 |
| GO:1905332 | Breast | IDC | positive regulation of morphogenesis of an epithelium | 9/1434 | 37/18723 | 1.54e-03 | 1.54e-02 | 9 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa052028 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| hsa0520213 | Esophagus | ESCC | Transcriptional misregulation in cancer | 116/4205 | 193/8465 | 2.08e-03 | 5.95e-03 | 3.05e-03 | 116 |
| 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 |
| SIX1 | STM | Breast | IDC | UQCRH,LMO4,CDKN2A, etc. | 2.20e-01 |  |
| SIX1 | COL | Cervix | Healthy | C3,THSD4,SLC34A2, etc. | 3.03e-01 |  |
| SIX1 | STM | Oral cavity | ADJ | KRTCAP3,SIX4,ZNF703, etc. | 7.44e-01 |  |
| SIX1 | INCAF | Oral cavity | NEOLP | CD14,OMD,HHIP, etc. | 7.79e-01 |  |
| ∗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 |
| SIX1 | SNV | Missense_Mutation | c.731N>T | p.Ser244Leu | p.S244L | Q15475 | protein_coding | tolerated_low_confidence(0.39) | benign(0) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SIX1 | SNV | Missense_Mutation | novel | c.208N>A | p.Leu70Met | p.L70M | Q15475 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SIX1 | SNV | Missense_Mutation | c.775N>A | p.Gly259Ser | p.G259S | Q15475 | protein_coding | tolerated_low_confidence(0.95) | benign(0) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| SIX1 | SNV | Missense_Mutation | novel | c.340N>C | p.Lys114Gln | p.K114Q | Q15475 | protein_coding | deleterious(0) | possibly_damaging(0.867) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SIX1 | insertion | In_Frame_Ins | novel | c.10_11insCACAGT | p.Met3_Leu4insProGln | p.M3_L4insPQ | Q15475 | protein_coding | TCGA-DS-A1OA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD | ||
| SIX1 | SNV | Missense_Mutation | c.554A>C | p.Lys185Thr | p.K185T | Q15475 | protein_coding | tolerated(0.08) | probably_damaging(0.954) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SIX1 | SNV | Missense_Mutation | c.603N>A | p.Asn201Lys | p.N201K | Q15475 | protein_coding | tolerated(0.81) | benign(0.015) | TCGA-AA-3875-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SIX1 | SNV | Missense_Mutation | c.775N>A | p.Gly259Ser | p.G259S | Q15475 | protein_coding | tolerated_low_confidence(0.95) | benign(0) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SIX1 | SNV | Missense_Mutation | novel | c.98N>C | p.Phe33Ser | p.F33S | Q15475 | protein_coding | deleterious(0) | possibly_damaging(0.844) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SIX1 | SNV | Missense_Mutation | c.181N>A | p.Gly61Ser | p.G61S | Q15475 | protein_coding | deleterious(0) | benign(0.327) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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