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Gene: SEMA3F |
Gene summary for SEMA3F |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SEMA3F | Gene ID | 6405 |
| Gene name | semaphorin 3F | |
| Gene Alias | SEMA-IV | |
| Cytomap | 3p21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | C9JPG5 |
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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 |
| 6405 | SEMA3F | C30 | Human | Oral cavity | OSCC | 7.67e-17 | 7.28e-01 | 0.3055 |
| 6405 | SEMA3F | C43 | Human | Oral cavity | OSCC | 7.33e-09 | 1.14e-01 | 0.1704 |
| 6405 | SEMA3F | C46 | Human | Oral cavity | OSCC | 1.17e-08 | 1.55e-01 | 0.1673 |
| 6405 | SEMA3F | C51 | Human | Oral cavity | OSCC | 7.80e-17 | 7.39e-01 | 0.2674 |
| 6405 | SEMA3F | C57 | Human | Oral cavity | OSCC | 7.75e-05 | 1.71e-01 | 0.1679 |
| 6405 | SEMA3F | C07 | Human | Oral cavity | OSCC | 1.30e-02 | 7.72e-01 | 0.2491 |
| 6405 | SEMA3F | LN46 | Human | Oral cavity | OSCC | 1.49e-03 | 1.98e-01 | 0.1666 |
| 6405 | SEMA3F | SYSMH1 | Human | Oral cavity | OSCC | 9.27e-15 | 3.37e-01 | 0.1127 |
| 6405 | SEMA3F | SYSMH2 | Human | Oral cavity | OSCC | 4.99e-07 | 2.07e-01 | 0.2326 |
| 6405 | SEMA3F | SYSMH3 | Human | Oral cavity | OSCC | 5.30e-24 | 5.15e-01 | 0.2442 |
| 6405 | SEMA3F | SYSMH4 | Human | Oral cavity | OSCC | 2.87e-05 | 7.42e-02 | 0.1226 |
| 6405 | SEMA3F | SYSMH5 | Human | Oral cavity | OSCC | 2.42e-04 | 9.38e-02 | 0.0647 |
| 6405 | SEMA3F | SYSMH6 | Human | Oral cavity | OSCC | 2.79e-04 | 9.29e-02 | 0.1275 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:001604917 | Oral cavity | OSCC | cell growth | 268/7305 | 482/18723 | 6.55e-14 | 3.51e-12 | 268 |
| GO:000155816 | Oral cavity | OSCC | regulation of cell growth | 228/7305 | 414/18723 | 1.74e-11 | 6.09e-10 | 228 |
| GO:003253519 | Oral cavity | OSCC | regulation of cellular component size | 201/7305 | 383/18723 | 4.80e-08 | 8.88e-07 | 201 |
| GO:00459266 | Oral cavity | OSCC | negative regulation of growth | 135/7305 | 249/18723 | 7.29e-07 | 1.03e-05 | 135 |
| GO:00303084 | Oral cavity | OSCC | negative regulation of cell growth | 101/7305 | 188/18723 | 2.85e-05 | 2.63e-04 | 101 |
| GO:000166719 | Oral cavity | OSCC | ameboidal-type cell migration | 228/7305 | 475/18723 | 3.46e-05 | 3.10e-04 | 228 |
| GO:00507679 | Oral cavity | OSCC | regulation of neurogenesis | 179/7305 | 364/18723 | 4.49e-05 | 3.84e-04 | 179 |
| GO:001097510 | Oral cavity | OSCC | regulation of neuron projection development | 210/7305 | 445/18723 | 2.35e-04 | 1.52e-03 | 210 |
| GO:00485889 | Oral cavity | OSCC | developmental cell growth | 116/7305 | 234/18723 | 6.20e-04 | 3.50e-03 | 116 |
| GO:00605609 | Oral cavity | OSCC | developmental growth involved in morphogenesis | 116/7305 | 234/18723 | 6.20e-04 | 3.50e-03 | 116 |
| GO:00083618 | Oral cavity | OSCC | regulation of cell size | 92/7305 | 181/18723 | 7.86e-04 | 4.26e-03 | 92 |
| GO:00519605 | Oral cavity | OSCC | regulation of nervous system development | 205/7305 | 443/18723 | 9.80e-04 | 5.11e-03 | 205 |
| GO:19901388 | Oral cavity | OSCC | neuron projection extension | 86/7305 | 172/18723 | 2.13e-03 | 9.80e-03 | 86 |
| GO:00486759 | Oral cavity | OSCC | axon extension | 61/7305 | 120/18723 | 5.52e-03 | 2.14e-02 | 61 |
| GO:00509204 | Oral cavity | OSCC | regulation of chemotaxis | 105/7305 | 223/18723 | 8.27e-03 | 3.01e-02 | 105 |
| GO:00313458 | Oral cavity | OSCC | negative regulation of cell projection organization | 89/7305 | 186/18723 | 8.51e-03 | 3.09e-02 | 89 |
| GO:006156410 | Oral cavity | OSCC | axon development | 207/7305 | 467/18723 | 1.01e-02 | 3.51e-02 | 207 |
| GO:00487627 | Oral cavity | OSCC | mesenchymal cell differentiation | 109/7305 | 236/18723 | 1.43e-02 | 4.69e-02 | 109 |
| GO:00488637 | Oral cavity | OSCC | stem cell differentiation | 96/7305 | 206/18723 | 1.55e-02 | 4.99e-02 | 96 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0436014 | Oral cavity | OSCC | Axon guidance | 97/3704 | 182/8465 | 5.59e-03 | 1.33e-02 | 6.76e-03 | 97 |
| hsa0436015 | Oral cavity | OSCC | Axon guidance | 97/3704 | 182/8465 | 5.59e-03 | 1.33e-02 | 6.76e-03 | 97 |
| 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 |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | Cervix | CC |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | CRC | AD |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | CRC | MSI-H |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | Esophagus | ESCC |
| SEMA3F | NRP2_PLXNA1 | SEMA3F_NRP2_PLXNA1 | SEMA3 | HNSCC | OSCC |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | HNSCC | OSCC |
| SEMA3F | NRP2_PLXNA1 | SEMA3F_NRP2_PLXNA1 | SEMA3 | HNSCC | Precancer |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | HNSCC | Precancer |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | Prostate | Tumor |
| SEMA3F | NRP2_PLXNA1 | SEMA3F_NRP2_PLXNA1 | SEMA3 | THCA | ADJ |
| SEMA3F | NRP2_PLXNA2 | SEMA3F_NRP2_PLXNA2 | SEMA3 | THCA | ADJ |
| SEMA3F | NRP2_PLXNA3 | SEMA3F_NRP2_PLXNA3 | SEMA3 | THCA | ADJ |
| SEMA3F | NRP2_PLXNA1 | SEMA3F_NRP2_PLXNA1 | SEMA3 | THCA | Cancer |
| SEMA3F | NRP2_PLXNA3 | SEMA3F_NRP2_PLXNA3 | SEMA3 | THCA | Cancer |
| 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 |
| SEMA3F | insertion | Frame_Shift_Ins | novel | c.1014_1015insGG | p.Leu339GlyfsTer13 | p.L339Gfs*13 | Q13275 | protein_coding | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD | ||
| SEMA3F | insertion | Frame_Shift_Ins | novel | c.1016_1017insGAACGGTAAGCGCAGCCCCAGGAGCCCTT | p.Gln340AsnfsTer21 | p.Q340Nfs*21 | Q13275 | protein_coding | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD | ||
| SEMA3F | insertion | In_Frame_Ins | novel | c.1351_1352insACA | p.Arg450_Arg451insHis | p.R450_R451insH | Q13275 | protein_coding | TCGA-AO-A03P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | PD | ||
| SEMA3F | insertion | Nonsense_Mutation | novel | c.1352_1353insTTGAGCCATTCCACCTGTGCCATGTGAAGCAGAAATGAACCA | p.Arg451_Pro452insTer | p.R451_P452ins* | Q13275 | protein_coding | TCGA-AO-A03P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | PD | ||
| SEMA3F | insertion | Frame_Shift_Ins | novel | c.1903_1904insCAGAAGTCCACGCAGCCCACGAAGCTGC | p.Val635AlafsTer11 | p.V635Afs*11 | Q13275 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SEMA3F | SNV | Missense_Mutation | c.853N>A | p.Glu285Lys | p.E285K | Q13275 | protein_coding | deleterious(0) | benign(0.285) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| SEMA3F | SNV | Missense_Mutation | rs753830480 | c.2204N>T | p.Ala735Val | p.A735V | Q13275 | protein_coding | deleterious(0.03) | benign(0.079) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SEMA3F | SNV | Missense_Mutation | c.1259N>A | p.Ser420Tyr | p.S420Y | Q13275 | protein_coding | tolerated(0.87) | probably_damaging(0.914) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SEMA3F | SNV | Missense_Mutation | c.451N>A | p.Ala151Thr | p.A151T | Q13275 | protein_coding | tolerated(0.27) | possibly_damaging(0.474) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| SEMA3F | SNV | Missense_Mutation | c.1748N>A | p.Arg583Gln | p.R583Q | Q13275 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 |
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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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