|
Gene: SOX9 |
Gene summary for SOX9 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SOX9 | Gene ID | 6662 |
Gene name | SRY-box transcription factor 9 | |
Gene Alias | CMD1 | |
Cytomap | 17q24.3 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P48436 |
Top |
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 |
6662 | SOX9 | GSM4909280 | Human | Breast | Precancer | 8.81e-06 | 5.75e-01 | 0.0305 |
6662 | SOX9 | GSM4909282 | Human | Breast | IDC | 4.00e-24 | 6.87e-01 | -0.0288 |
6662 | SOX9 | GSM4909285 | Human | Breast | IDC | 2.14e-04 | 2.36e-01 | 0.21 |
6662 | SOX9 | GSM4909286 | Human | Breast | IDC | 2.55e-04 | 1.64e-01 | 0.1081 |
6662 | SOX9 | GSM4909287 | Human | Breast | IDC | 9.55e-05 | 3.29e-01 | 0.2057 |
6662 | SOX9 | GSM4909295 | Human | Breast | IDC | 7.27e-10 | 5.86e-01 | 0.0898 |
6662 | SOX9 | GSM4909296 | Human | Breast | IDC | 1.79e-05 | -2.39e-01 | 0.1524 |
6662 | SOX9 | GSM4909297 | Human | Breast | IDC | 1.59e-07 | -3.16e-01 | 0.1517 |
6662 | SOX9 | GSM4909298 | Human | Breast | IDC | 1.34e-24 | 6.51e-01 | 0.1551 |
6662 | SOX9 | GSM4909299 | Human | Breast | IDC | 6.81e-06 | 4.30e-01 | 0.035 |
6662 | SOX9 | GSM4909300 | Human | Breast | IDC | 1.22e-02 | 4.14e-01 | 0.0334 |
6662 | SOX9 | GSM4909301 | Human | Breast | IDC | 1.64e-02 | -2.69e-01 | 0.1577 |
6662 | SOX9 | GSM4909311 | Human | Breast | IDC | 4.78e-16 | -2.44e-01 | 0.1534 |
6662 | SOX9 | GSM4909312 | Human | Breast | IDC | 1.84e-04 | -1.48e-01 | 0.1552 |
6662 | SOX9 | GSM4909313 | Human | Breast | IDC | 1.41e-02 | 2.76e-01 | 0.0391 |
6662 | SOX9 | GSM4909319 | Human | Breast | IDC | 3.49e-23 | -3.80e-01 | 0.1563 |
6662 | SOX9 | GSM4909320 | Human | Breast | IDC | 9.99e-07 | -4.23e-01 | 0.1575 |
6662 | SOX9 | GSM4909321 | Human | Breast | IDC | 1.51e-16 | -3.69e-01 | 0.1559 |
6662 | SOX9 | NCCBC14 | Human | Breast | DCIS | 9.01e-07 | 1.76e-01 | 0.2021 |
6662 | SOX9 | NCCBC5 | Human | Breast | DCIS | 2.85e-10 | -3.52e-01 | 0.2046 |
Page: 1 2 3 4 5 6 7 8 |
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. |
Top |
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:006056212 | Breast | IDC | epithelial tube morphogenesis | 44/1434 | 325/18723 | 1.58e-04 | 2.73e-03 | 44 |
GO:00303244 | Breast | IDC | lung development | 28/1434 | 177/18723 | 1.90e-04 | 3.15e-03 | 28 |
GO:00303234 | Breast | IDC | respiratory tube development | 28/1434 | 181/18723 | 2.78e-04 | 4.26e-03 | 28 |
GO:003087911 | Breast | IDC | mammary gland development | 23/1434 | 137/18723 | 2.87e-04 | 4.37e-03 | 23 |
GO:00611383 | Breast | IDC | morphogenesis of a branching epithelium | 28/1434 | 182/18723 | 3.05e-04 | 4.60e-03 | 28 |
GO:000188913 | Breast | IDC | liver development | 24/1434 | 147/18723 | 3.29e-04 | 4.92e-03 | 24 |
GO:19053301 | Breast | IDC | regulation of morphogenesis of an epithelium | 14/1434 | 65/18723 | 3.35e-04 | 4.98e-03 | 14 |
GO:0008406 | Breast | IDC | gonad development | 32/1434 | 221/18723 | 3.64e-04 | 5.23e-03 | 32 |
GO:00605412 | Breast | IDC | respiratory system development | 30/1434 | 203/18723 | 3.85e-04 | 5.40e-03 | 30 |
GO:00703713 | Breast | IDC | ERK1 and ERK2 cascade | 43/1434 | 330/18723 | 4.28e-04 | 5.84e-03 | 43 |
GO:006100813 | Breast | IDC | hepaticobiliary system development | 24/1434 | 150/18723 | 4.46e-04 | 6.04e-03 | 24 |
GO:007136413 | Breast | IDC | cellular response to epidermal growth factor stimulus | 11/1434 | 45/18723 | 4.57e-04 | 6.13e-03 | 11 |
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:0045137 | Breast | IDC | development of primary sexual characteristics | 32/1434 | 227/18723 | 5.85e-04 | 7.44e-03 | 32 |
GO:00226127 | Breast | IDC | gland morphogenesis | 20/1434 | 118/18723 | 6.13e-04 | 7.69e-03 | 20 |
GO:0001656 | Breast | IDC | metanephros development | 16/1434 | 85/18723 | 6.49e-04 | 8.04e-03 | 16 |
GO:000150311 | Breast | IDC | ossification | 50/1434 | 408/18723 | 6.51e-04 | 8.04e-03 | 50 |
GO:004206311 | Breast | IDC | gliogenesis | 39/1434 | 301/18723 | 8.63e-04 | 1.00e-02 | 39 |
GO:003514812 | Breast | IDC | tube formation | 23/1434 | 148/18723 | 8.79e-04 | 1.02e-02 | 23 |
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 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 |
Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04024 | Colorectum | FAP | cAMP signaling pathway | 51/1404 | 225/8465 | 1.02e-02 | 3.68e-02 | 2.24e-02 | 51 |
hsa040241 | Colorectum | FAP | cAMP signaling pathway | 51/1404 | 225/8465 | 1.02e-02 | 3.68e-02 | 2.24e-02 | 51 |
hsa040242 | Colorectum | CRC | cAMP signaling pathway | 47/1091 | 225/8465 | 4.57e-04 | 4.77e-03 | 3.23e-03 | 47 |
hsa040243 | Colorectum | CRC | cAMP signaling pathway | 47/1091 | 225/8465 | 4.57e-04 | 4.77e-03 | 3.23e-03 | 47 |
Page: 1 |
Top |
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 |
Top |
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 |
∗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 2 3 4 |
Top |
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 |
SOX9 | SNV | Missense_Mutation | c.223N>A | p.Glu75Lys | p.E75K | P48436 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SOX9 | insertion | Frame_Shift_Ins | novel | c.252_253insG | p.Asp85GlyfsTer167 | p.D85Gfs*167 | P48436 | protein_coding | TCGA-AQ-A7U7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | rituximab | CR | ||
SOX9 | SNV | Missense_Mutation | novel | c.970N>G | p.Thr324Ala | p.T324A | P48436 | protein_coding | tolerated(1) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
SOX9 | SNV | Missense_Mutation | novel | c.423N>T | p.Lys141Asn | p.K141N | P48436 | protein_coding | deleterious(0.01) | possibly_damaging(0.691) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
SOX9 | SNV | Missense_Mutation | novel | c.841N>A | p.Asp281Asn | p.D281N | P48436 | protein_coding | deleterious(0) | benign(0.125) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
SOX9 | SNV | Missense_Mutation | c.810N>A | p.Phe270Leu | p.F270L | P48436 | protein_coding | deleterious(0) | benign(0.079) | TCGA-A6-2680-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SOX9 | SNV | Missense_Mutation | c.358N>T | p.Arg120Cys | p.R120C | P48436 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SOX9 | SNV | Missense_Mutation | c.810N>A | p.Phe270Leu | p.F270L | P48436 | protein_coding | deleterious(0) | benign(0.079) | TCGA-A6-4105-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
SOX9 | SNV | Missense_Mutation | rs761747688 | c.838N>G | p.Ser280Gly | p.S280G | P48436 | protein_coding | deleterious(0.01) | possibly_damaging(0.621) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
SOX9 | SNV | Missense_Mutation | c.329N>G | p.Asn110Ser | p.N110S | P48436 | protein_coding | deleterious(0) | possibly_damaging(0.652) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
Top |
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 |