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Gene: SYNPO2 |
Gene summary for SYNPO2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYNPO2 | Gene ID | 171024 |
| Gene name | synaptopodin 2 | |
| Gene Alias | SYNPO2 | |
| Cytomap | 4q26 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | Q9UMS6 |
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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 |
| 171024 | SYNPO2 | CA_HPV_3 | Human | Cervix | CC | 1.09e-03 | 9.88e-02 | 0.0414 |
| 171024 | SYNPO2 | CCI_3 | Human | Cervix | CC | 1.75e-05 | 6.58e-01 | 0.516 |
| 171024 | SYNPO2 | P2T-E | Human | Esophagus | ESCC | 3.60e-39 | 7.50e-01 | 0.1177 |
| 171024 | SYNPO2 | P4T-E | Human | Esophagus | ESCC | 7.58e-11 | 2.29e-01 | 0.1323 |
| 171024 | SYNPO2 | P8T-E | Human | Esophagus | ESCC | 3.91e-05 | 1.61e-01 | 0.0889 |
| 171024 | SYNPO2 | P16T-E | Human | Esophagus | ESCC | 8.65e-16 | 4.15e-01 | 0.1153 |
| 171024 | SYNPO2 | P22T-E | Human | Esophagus | ESCC | 1.38e-02 | 2.25e-03 | 0.1236 |
| 171024 | SYNPO2 | P26T-E | Human | Esophagus | ESCC | 1.81e-20 | 4.50e-01 | 0.1276 |
| 171024 | SYNPO2 | P27T-E | Human | Esophagus | ESCC | 1.52e-04 | 1.59e-01 | 0.1055 |
| 171024 | SYNPO2 | P36T-E | Human | Esophagus | ESCC | 1.72e-03 | 1.02e-01 | 0.1187 |
| 171024 | SYNPO2 | P49T-E | Human | Esophagus | ESCC | 2.12e-02 | 1.60e-01 | 0.1768 |
| 171024 | SYNPO2 | P56T-E | Human | Esophagus | ESCC | 2.89e-05 | 1.36e+00 | 0.1613 |
| 171024 | SYNPO2 | P62T-E | Human | Esophagus | ESCC | 1.50e-13 | 3.60e-01 | 0.1302 |
| 171024 | SYNPO2 | P65T-E | Human | Esophagus | ESCC | 1.10e-02 | 1.29e-02 | 0.0978 |
| 171024 | SYNPO2 | P79T-E | Human | Esophagus | ESCC | 7.70e-11 | 3.06e-01 | 0.1154 |
| 171024 | SYNPO2 | P130T-E | Human | Esophagus | ESCC | 9.03e-10 | 2.68e-01 | 0.1676 |
| 171024 | SYNPO2 | C21 | Human | Oral cavity | OSCC | 3.23e-06 | -4.94e-01 | 0.2678 |
| 171024 | SYNPO2 | C38 | Human | Oral cavity | OSCC | 2.32e-02 | 7.35e-01 | 0.172 |
| 171024 | SYNPO2 | C43 | Human | Oral cavity | OSCC | 2.29e-06 | 3.76e-01 | 0.1704 |
| 171024 | SYNPO2 | C46 | Human | Oral cavity | OSCC | 2.16e-13 | 6.61e-01 | 0.1673 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| 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:003103222 | Liver | HCC | actomyosin structure organization | 109/7958 | 196/18723 | 1.39e-04 | 1.13e-03 | 109 |
| GO:000726621 | Liver | HCC | Rho protein signal transduction | 76/7958 | 137/18723 | 1.46e-03 | 7.75e-03 | 76 |
| GO:003003822 | Liver | HCC | contractile actin filament bundle assembly | 60/7958 | 106/18723 | 2.34e-03 | 1.16e-02 | 60 |
| GO:004314922 | Liver | HCC | stress fiber assembly | 60/7958 | 106/18723 | 2.34e-03 | 1.16e-02 | 60 |
| GO:004657811 | Liver | HCC | regulation of Ras protein signal transduction | 100/7958 | 189/18723 | 2.42e-03 | 1.18e-02 | 100 |
| GO:003223312 | Liver | HCC | positive regulation of actin filament bundle assembly | 38/7958 | 63/18723 | 3.27e-03 | 1.50e-02 | 38 |
| GO:003223122 | Liver | HCC | regulation of actin filament bundle assembly | 57/7958 | 105/18723 | 9.73e-03 | 3.66e-02 | 57 |
| GO:011002022 | Liver | HCC | regulation of actomyosin structure organization | 54/7958 | 100/18723 | 1.33e-02 | 4.76e-02 | 54 |
| GO:001623610 | Oral cavity | OSCC | macroautophagy | 192/7305 | 291/18723 | 7.01e-21 | 1.14e-18 | 192 |
| GO:190290520 | Oral cavity | OSCC | positive regulation of supramolecular fiber organization | 131/7305 | 209/18723 | 3.18e-12 | 1.27e-10 | 131 |
| GO:00070335 | Oral cavity | OSCC | vacuole organization | 115/7305 | 180/18723 | 1.11e-11 | 4.00e-10 | 115 |
| GO:190290320 | Oral cavity | OSCC | regulation of supramolecular fiber organization | 211/7305 | 383/18723 | 9.45e-11 | 2.88e-09 | 211 |
| GO:005149518 | Oral cavity | OSCC | positive regulation of cytoskeleton organization | 135/7305 | 226/18723 | 1.98e-10 | 5.66e-09 | 135 |
| GO:000701520 | Oral cavity | OSCC | actin filament organization | 230/7305 | 442/18723 | 1.37e-08 | 2.77e-07 | 230 |
| GO:003297020 | Oral cavity | OSCC | regulation of actin filament-based process | 209/7305 | 397/18723 | 1.89e-08 | 3.72e-07 | 209 |
| GO:003295620 | Oral cavity | OSCC | regulation of actin cytoskeleton organization | 189/7305 | 358/18723 | 6.81e-08 | 1.21e-06 | 189 |
| GO:011005320 | Oral cavity | OSCC | regulation of actin filament organization | 150/7305 | 278/18723 | 2.68e-07 | 4.15e-06 | 150 |
| GO:19050374 | Oral cavity | OSCC | autophagosome organization | 63/7305 | 103/18723 | 4.30e-06 | 4.98e-05 | 63 |
| GO:00000454 | Oral cavity | OSCC | autophagosome assembly | 60/7305 | 99/18723 | 1.09e-05 | 1.14e-04 | 60 |
| GO:005101720 | Oral cavity | OSCC | actin filament bundle assembly | 86/7305 | 157/18723 | 4.28e-05 | 3.70e-04 | 86 |
| 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 |
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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. |
| 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 |
| SYNPO2 | SNV | Missense_Mutation | c.3222N>G | p.Phe1074Leu | p.F1074L | Q9UMS6 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| SYNPO2 | SNV | Missense_Mutation | rs778638880 | c.532G>A | p.Val178Met | p.V178M | Q9UMS6 | protein_coding | tolerated(0.23) | benign(0.001) | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| SYNPO2 | SNV | Missense_Mutation | c.1988C>T | p.Ser663Leu | p.S663L | Q9UMS6 | protein_coding | deleterious(0.02) | benign(0.084) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNPO2 | SNV | Missense_Mutation | c.1372N>A | p.Gln458Lys | p.Q458K | Q9UMS6 | protein_coding | tolerated(0.55) | benign(0.012) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | |
| SYNPO2 | SNV | Missense_Mutation | novel | c.1342G>A | p.Glu448Lys | p.E448K | Q9UMS6 | protein_coding | deleterious(0.02) | possibly_damaging(0.6) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| SYNPO2 | SNV | Missense_Mutation | c.2069G>A | p.Arg690Lys | p.R690K | Q9UMS6 | protein_coding | tolerated(0.2) | probably_damaging(0.996) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNPO2 | insertion | Frame_Shift_Ins | novel | c.2573_2574insCAGCAAGATAATCCAG | p.Val859SerfsTer11 | p.V859Sfs*11 | Q9UMS6 | protein_coding | TCGA-AO-A03R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| SYNPO2 | deletion | Frame_Shift_Del | novel | c.1869delN | p.Ala624GlnfsTer44 | p.A624Qfs*44 | Q9UMS6 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| SYNPO2 | deletion | Frame_Shift_Del | novel | c.1332delN | p.Val445TrpfsTer16 | p.V445Wfs*16 | Q9UMS6 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| SYNPO2 | SNV | Missense_Mutation | novel | c.3305N>A | p.Ser1102Tyr | p.S1102Y | Q9UMS6 | protein_coding | tolerated(0.08) | possibly_damaging(0.9) | TCGA-C5-A1MJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
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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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