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Gene: SCGB2A2 |
Gene summary for SCGB2A2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SCGB2A2 | Gene ID | 4250 |
Gene name | secretoglobin family 2A member 2 | |
Gene Alias | MGB1 | |
Cytomap | 11q12.3 | |
Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | Q13296 |
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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 |
4250 | SCGB2A2 | GSM4909281 | Human | Breast | IDC | 1.42e-17 | -5.89e-01 | 0.21 |
4250 | SCGB2A2 | GSM4909282 | Human | Breast | IDC | 1.51e-18 | -6.04e-01 | -0.0288 |
4250 | SCGB2A2 | GSM4909285 | Human | Breast | IDC | 2.03e-16 | -5.94e-01 | 0.21 |
4250 | SCGB2A2 | GSM4909286 | Human | Breast | IDC | 6.58e-19 | -6.09e-01 | 0.1081 |
4250 | SCGB2A2 | GSM4909287 | Human | Breast | IDC | 3.19e-08 | -5.02e-01 | 0.2057 |
4250 | SCGB2A2 | GSM4909290 | Human | Breast | IDC | 1.98e-96 | 1.90e+00 | 0.2096 |
4250 | SCGB2A2 | GSM4909291 | Human | Breast | IDC | 4.05e-12 | -6.09e-01 | 0.1753 |
4250 | SCGB2A2 | GSM4909293 | Human | Breast | IDC | 4.28e-03 | -1.13e-01 | 0.1581 |
4250 | SCGB2A2 | GSM4909296 | Human | Breast | IDC | 2.88e-25 | 1.01e+00 | 0.1524 |
4250 | SCGB2A2 | GSM4909297 | Human | Breast | IDC | 7.77e-56 | 1.49e+00 | 0.1517 |
4250 | SCGB2A2 | GSM4909298 | Human | Breast | IDC | 2.45e-124 | 1.90e+00 | 0.1551 |
4250 | SCGB2A2 | GSM4909299 | Human | Breast | IDC | 1.10e-102 | 1.76e+00 | 0.035 |
4250 | SCGB2A2 | GSM4909300 | Human | Breast | IDC | 7.97e-13 | 1.05e+00 | 0.0334 |
4250 | SCGB2A2 | GSM4909301 | Human | Breast | IDC | 5.08e-15 | -6.02e-01 | 0.1577 |
4250 | SCGB2A2 | GSM4909302 | Human | Breast | IDC | 7.23e-08 | -4.18e-01 | 0.1545 |
4250 | SCGB2A2 | GSM4909304 | Human | Breast | IDC | 6.58e-19 | -6.09e-01 | 0.1636 |
4250 | SCGB2A2 | GSM4909305 | Human | Breast | IDC | 6.87e-27 | 1.12e+00 | 0.0436 |
4250 | SCGB2A2 | GSM4909306 | Human | Breast | IDC | 5.49e-79 | 1.36e+00 | 0.1564 |
4250 | SCGB2A2 | GSM4909308 | Human | Breast | IDC | 1.51e-07 | -5.15e-01 | 0.158 |
4250 | SCGB2A2 | GSM4909309 | Human | Breast | IDC | 6.00e-44 | 1.42e+00 | 0.0483 |
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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 |
∗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:00485459 | Breast | Precancer | response to steroid hormone | 53/1080 | 339/18723 | 3.07e-11 | 3.66e-09 | 53 |
GO:00713838 | Breast | Precancer | cellular response to steroid hormone stimulus | 28/1080 | 204/18723 | 1.78e-05 | 4.26e-04 | 28 |
GO:00305217 | Breast | Precancer | androgen receptor signaling pathway | 10/1080 | 44/18723 | 1.61e-04 | 2.69e-03 | 10 |
GO:00305187 | Breast | Precancer | intracellular steroid hormone receptor signaling pathway | 16/1080 | 116/18723 | 1.01e-03 | 1.13e-02 | 16 |
GO:00305228 | Breast | Precancer | intracellular receptor signaling pathway | 27/1080 | 265/18723 | 2.99e-03 | 2.57e-02 | 27 |
GO:00434018 | Breast | Precancer | steroid hormone mediated signaling pathway | 16/1080 | 136/18723 | 5.21e-03 | 3.88e-02 | 16 |
GO:004854514 | Breast | IDC | response to steroid hormone | 70/1434 | 339/18723 | 1.34e-14 | 4.23e-12 | 70 |
GO:007138314 | Breast | IDC | cellular response to steroid hormone stimulus | 35/1434 | 204/18723 | 5.29e-06 | 1.75e-04 | 35 |
GO:003051813 | Breast | IDC | intracellular steroid hormone receptor signaling pathway | 22/1434 | 116/18723 | 6.16e-05 | 1.28e-03 | 22 |
GO:003052113 | Breast | IDC | androgen receptor signaling pathway | 12/1434 | 44/18723 | 8.17e-05 | 1.60e-03 | 12 |
GO:003052214 | Breast | IDC | intracellular receptor signaling pathway | 37/1434 | 265/18723 | 2.77e-04 | 4.26e-03 | 37 |
GO:004340113 | Breast | IDC | steroid hormone mediated signaling pathway | 22/1434 | 136/18723 | 6.51e-04 | 8.04e-03 | 22 |
GO:004854524 | Breast | DCIS | response to steroid hormone | 67/1390 | 339/18723 | 1.02e-13 | 2.76e-11 | 67 |
GO:007138324 | Breast | DCIS | cellular response to steroid hormone stimulus | 34/1390 | 204/18723 | 7.04e-06 | 1.95e-04 | 34 |
GO:003051823 | Breast | DCIS | intracellular steroid hormone receptor signaling pathway | 21/1390 | 116/18723 | 1.16e-04 | 2.03e-03 | 21 |
GO:003052122 | Breast | DCIS | androgen receptor signaling pathway | 11/1390 | 44/18723 | 2.83e-04 | 4.19e-03 | 11 |
GO:003052224 | Breast | DCIS | intracellular receptor signaling pathway | 35/1390 | 265/18723 | 6.38e-04 | 7.92e-03 | 35 |
GO:004340122 | Breast | DCIS | steroid hormone mediated signaling pathway | 21/1390 | 136/18723 | 1.06e-03 | 1.16e-02 | 21 |
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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 |
SCGB2A2 | SNV | Missense_Mutation | novel | c.121G>A | p.Glu41Lys | p.E41K | Q13296 | protein_coding | deleterious(0.05) | benign(0.052) | TCGA-LL-A740-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
SCGB2A2 | insertion | Nonsense_Mutation | novel | c.98_99insTCTCCTGCCTCAGCCTCCTGAGTAGCTTGGACTA | p.Asn34LeufsTer8 | p.N34Lfs*8 | Q13296 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
SCGB2A2 | insertion | In_Frame_Ins | novel | c.245_246insATTAATATATGACAGCAGTCTTTGTGATTT | p.Ile84_Tyr85insTyrAspSerSerLeuCysAspLeuLeuIle | p.I84_Y85insYDSSLCDLLI | Q13296 | protein_coding | TCGA-AH-6549-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | ||
SCGB2A2 | SNV | Missense_Mutation | rs769782640 | c.199N>A | p.Leu67Ile | p.L67I | Q13296 | protein_coding | deleterious(0.01) | probably_damaging(0.977) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
SCGB2A2 | SNV | Missense_Mutation | novel | c.41A>T | p.Gln14Leu | p.Q14L | Q13296 | protein_coding | tolerated(1) | benign(0) | TCGA-73-A9RS-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | PD |
SCGB2A2 | SNV | Missense_Mutation | rs372833801 | c.160N>A | p.Ala54Thr | p.A54T | Q13296 | protein_coding | tolerated(0.64) | benign(0.14) | TCGA-33-4532-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SCGB2A2 | SNV | Missense_Mutation | c.161N>T | p.Ala54Val | p.A54V | Q13296 | protein_coding | tolerated(0.41) | benign(0.005) | TCGA-33-4532-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SCGB2A2 | SNV | Missense_Mutation | novel | c.205C>A | p.Gln69Lys | p.Q69K | Q13296 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-77-8140-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SCGB2A2 | SNV | Missense_Mutation | c.35N>A | p.Leu12His | p.L12H | Q13296 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-D7-8570-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | plfe | 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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