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Gene: SNX6 |
Gene summary for SNX6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNX6 | Gene ID | 58533 |
| Gene name | sorting nexin 6 | |
| Gene Alias | MSTP010 | |
| Cytomap | 14q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0001932 | UniProtAcc | Q9UNH7 |
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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 |
| 58533 | SNX6 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.54e-02 | -2.73e-01 | 0.0155 |
| 58533 | SNX6 | HTA11_347_2000001011 | Human | Colorectum | AD | 7.36e-04 | 4.03e-01 | -0.1954 |
| 58533 | SNX6 | F007 | Human | Colorectum | FAP | 2.24e-02 | -3.17e-01 | 0.1176 |
| 58533 | SNX6 | A002-C-010 | Human | Colorectum | FAP | 3.65e-02 | -2.91e-01 | 0.242 |
| 58533 | SNX6 | A001-C-207 | Human | Colorectum | FAP | 1.65e-02 | -2.20e-01 | 0.1278 |
| 58533 | SNX6 | A015-C-203 | Human | Colorectum | FAP | 2.74e-23 | -2.57e-01 | -0.1294 |
| 58533 | SNX6 | A015-C-204 | Human | Colorectum | FAP | 1.91e-04 | -2.34e-01 | -0.0228 |
| 58533 | SNX6 | A014-C-040 | Human | Colorectum | FAP | 4.45e-03 | -2.75e-01 | -0.1184 |
| 58533 | SNX6 | A002-C-201 | Human | Colorectum | FAP | 2.04e-12 | -3.26e-01 | 0.0324 |
| 58533 | SNX6 | A002-C-203 | Human | Colorectum | FAP | 2.33e-04 | -1.85e-01 | 0.2786 |
| 58533 | SNX6 | A001-C-108 | Human | Colorectum | FAP | 1.66e-10 | -1.67e-01 | -0.0272 |
| 58533 | SNX6 | A002-C-205 | Human | Colorectum | FAP | 6.47e-16 | -1.55e-01 | -0.1236 |
| 58533 | SNX6 | A015-C-006 | Human | Colorectum | FAP | 1.06e-11 | -2.66e-01 | -0.0994 |
| 58533 | SNX6 | A015-C-106 | Human | Colorectum | FAP | 3.48e-09 | -1.78e-01 | -0.0511 |
| 58533 | SNX6 | A002-C-114 | Human | Colorectum | FAP | 5.25e-13 | -2.48e-01 | -0.1561 |
| 58533 | SNX6 | A015-C-104 | Human | Colorectum | FAP | 3.97e-29 | -1.18e-01 | -0.1899 |
| 58533 | SNX6 | A001-C-014 | Human | Colorectum | FAP | 2.94e-11 | -2.97e-01 | 0.0135 |
| 58533 | SNX6 | A002-C-016 | Human | Colorectum | FAP | 1.56e-15 | -2.21e-01 | 0.0521 |
| 58533 | SNX6 | A015-C-002 | Human | Colorectum | FAP | 6.37e-08 | -1.60e-01 | -0.0763 |
| 58533 | SNX6 | A001-C-203 | Human | Colorectum | FAP | 3.54e-07 | -1.14e-01 | -0.0481 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:007156019 | Thyroid | PTC | cellular response to transforming growth factor beta stimulus | 126/5968 | 250/18723 | 7.34e-10 | 2.19e-08 | 126 |
| GO:1901653111 | Thyroid | PTC | cellular response to peptide | 169/5968 | 359/18723 | 9.81e-10 | 2.89e-08 | 169 |
| GO:000717919 | Thyroid | PTC | transforming growth factor beta receptor signaling pathway | 104/5968 | 198/18723 | 1.20e-09 | 3.47e-08 | 104 |
| GO:1901214113 | Thyroid | PTC | regulation of neuron death | 151/5968 | 319/18723 | 4.74e-09 | 1.24e-07 | 151 |
| GO:0006469111 | Thyroid | PTC | negative regulation of protein kinase activity | 107/5968 | 212/18723 | 1.24e-08 | 2.96e-07 | 107 |
| GO:0033673111 | Thyroid | PTC | negative regulation of kinase activity | 115/5968 | 237/18723 | 5.98e-08 | 1.26e-06 | 115 |
| GO:0051402112 | Thyroid | PTC | neuron apoptotic process | 118/5968 | 246/18723 | 8.99e-08 | 1.81e-06 | 118 |
| GO:001701515 | Thyroid | PTC | regulation of transforming growth factor beta receptor signaling pathway | 69/5968 | 128/18723 | 1.92e-07 | 3.51e-06 | 69 |
| GO:003812720 | Thyroid | PTC | ERBB signaling pathway | 66/5968 | 121/18723 | 1.97e-07 | 3.54e-06 | 66 |
| GO:190384415 | Thyroid | PTC | regulation of cellular response to transforming growth factor beta stimulus | 70/5968 | 131/18723 | 2.47e-07 | 4.31e-06 | 70 |
| GO:0043523110 | Thyroid | PTC | regulation of neuron apoptotic process | 102/5968 | 212/18723 | 5.45e-07 | 8.76e-06 | 102 |
| GO:000717320 | Thyroid | PTC | epidermal growth factor receptor signaling pathway | 59/5968 | 108/18723 | 8.00e-07 | 1.23e-05 | 59 |
| GO:000717819 | Thyroid | PTC | transmembrane receptor protein serine/threonine kinase signaling pathway | 156/5968 | 355/18723 | 1.02e-06 | 1.51e-05 | 156 |
| GO:0070849111 | Thyroid | PTC | response to epidermal growth factor | 32/5968 | 49/18723 | 1.56e-06 | 2.19e-05 | 32 |
| GO:0071364111 | Thyroid | PTC | cellular response to epidermal growth factor stimulus | 29/5968 | 45/18723 | 7.13e-06 | 8.38e-05 | 29 |
| GO:190121518 | Thyroid | PTC | negative regulation of neuron death | 95/5968 | 208/18723 | 2.01e-05 | 2.04e-04 | 95 |
| GO:004205915 | Thyroid | PTC | negative regulation of epidermal growth factor receptor signaling pathway | 20/5968 | 28/18723 | 2.01e-05 | 2.04e-04 | 20 |
| GO:190118514 | Thyroid | PTC | negative regulation of ERBB signaling pathway | 22/5968 | 32/18723 | 2.03e-05 | 2.05e-04 | 22 |
| GO:00421479 | Thyroid | PTC | retrograde transport, endosome to Golgi | 48/5968 | 91/18723 | 2.86e-05 | 2.78e-04 | 48 |
| GO:190118410 | Thyroid | PTC | regulation of ERBB signaling pathway | 41/5968 | 79/18723 | 1.70e-04 | 1.31e-03 | 41 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04144 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
| hsa041441 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
| hsa041446 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
| hsa041447 | Colorectum | FAP | Endocytosis | 78/1404 | 251/8465 | 6.20e-09 | 2.96e-07 | 1.80e-07 | 78 |
| hsa041448 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
| hsa041449 | Colorectum | CRC | Endocytosis | 65/1091 | 251/8465 | 1.27e-08 | 1.06e-06 | 7.19e-07 | 65 |
| hsa0414429 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
| hsa04144113 | Esophagus | HGIN | Endocytosis | 76/1383 | 251/8465 | 1.74e-08 | 3.34e-07 | 2.65e-07 | 76 |
| hsa04144210 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0414437 | Esophagus | ESCC | Endocytosis | 186/4205 | 251/8465 | 9.74e-16 | 4.66e-14 | 2.39e-14 | 186 |
| hsa0414412 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| hsa0414413 | Liver | Cirrhotic | Endocytosis | 119/2530 | 251/8465 | 2.33e-09 | 4.56e-08 | 2.81e-08 | 119 |
| hsa0414422 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
| hsa0414432 | Liver | HCC | Endocytosis | 178/4020 | 251/8465 | 2.03e-14 | 5.22e-13 | 2.91e-13 | 178 |
| hsa0414427 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
| hsa04144112 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
| hsa0414428 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
| hsa0414436 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
| hsa0414442 | Oral cavity | EOLP | Endocytosis | 71/1218 | 251/8465 | 5.28e-09 | 8.97e-08 | 5.29e-08 | 71 |
| hsa0414452 | Oral cavity | EOLP | Endocytosis | 71/1218 | 251/8465 | 5.28e-09 | 8.97e-08 | 5.29e-08 | 71 |
| Page: 1 2 |
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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 |
| SNX6 | SNV | Missense_Mutation | novel | c.685N>A | p.Leu229Ile | p.L229I | protein_coding | deleterious(0.03) | benign(0.401) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SNX6 | SNV | Missense_Mutation | c.230C>T | p.Ser77Leu | p.S77L | protein_coding | tolerated(0.1) | benign(0.251) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR | ||
| SNX6 | SNV | Missense_Mutation | c.1234G>T | p.Ala412Ser | p.A412S | protein_coding | tolerated(0.61) | benign(0.007) | TCGA-E2-A1LH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| SNX6 | insertion | Frame_Shift_Ins | novel | c.972_973insTGTAATTCCAGTTC | p.Arg325CysfsTer10 | p.R325Cfs*10 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| SNX6 | SNV | Missense_Mutation | rs745343835 | c.634N>A | p.Val212Ile | p.V212I | protein_coding | tolerated(0.41) | benign(0.072) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| SNX6 | SNV | Missense_Mutation | novel | c.1180G>C | p.Glu394Gln | p.E394Q | protein_coding | tolerated(0.08) | probably_damaging(0.999) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| SNX6 | deletion | Frame_Shift_Del | c.1037delA | p.Asn346IlefsTer30 | p.N346Ifs*30 | protein_coding | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||||
| SNX6 | insertion | Frame_Shift_Ins | novel | c.61_62insTTCCCCACAGGAAGGCCTGGACGACGGCC | p.Pro21LeufsTer24 | p.P21Lfs*24 | protein_coding | TCGA-AZ-5403-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |||
| SNX6 | SNV | Missense_Mutation | novel | c.1045G>A | p.Val349Ile | p.V349I | protein_coding | tolerated(0.27) | probably_damaging(0.997) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SNX6 | SNV | Missense_Mutation | novel | c.82G>A | p.Asp28Asn | p.D28N | protein_coding | tolerated(0.29) | benign(0.171) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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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