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Gene: SEMA3D |
Gene summary for SEMA3D |
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Gene information | Species | Human | Gene symbol | SEMA3D | Gene ID | 223117 |
Gene name | semaphorin 3D | |
Gene Alias | Sema-Z2 | |
Cytomap | 7q21.11 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O95025 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
223117 | SEMA3D | Adj_PTCwithHT_6 | Human | Thyroid | HT | 1.01e-02 | -3.92e-01 | 0.02 |
223117 | SEMA3D | PTCwithHT_6 | Human | Thyroid | HT | 2.69e-04 | -3.94e-01 | 0.02 |
223117 | SEMA3D | PTCwithHT_8 | Human | Thyroid | HT | 5.67e-05 | -3.96e-01 | 0.0351 |
223117 | SEMA3D | PTCwithoutHT_2 | Human | Thyroid | PTC | 1.28e-06 | -3.96e-01 | 0.0419 |
223117 | SEMA3D | male-WTA | Human | Thyroid | PTC | 3.68e-05 | -2.48e-01 | 0.1037 |
223117 | SEMA3D | PTC01 | Human | Thyroid | PTC | 1.49e-05 | -3.79e-01 | 0.1899 |
223117 | SEMA3D | PTC04 | Human | Thyroid | PTC | 6.91e-04 | -3.73e-01 | 0.1927 |
223117 | SEMA3D | PTC06 | Human | Thyroid | PTC | 3.90e-03 | -3.56e-01 | 0.2057 |
223117 | SEMA3D | PTC07 | Human | Thyroid | PTC | 1.12e-05 | -3.70e-01 | 0.2044 |
223117 | SEMA3D | ATC12 | Human | Thyroid | ATC | 2.66e-05 | -3.96e-01 | 0.34 |
223117 | SEMA3D | ATC13 | Human | Thyroid | ATC | 1.23e-02 | -2.07e-01 | 0.34 |
223117 | SEMA3D | ATC2 | Human | Thyroid | ATC | 1.80e-02 | -1.02e-01 | 0.34 |
223117 | SEMA3D | ATC4 | Human | Thyroid | ATC | 1.90e-05 | -3.96e-01 | 0.34 |
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Tissue | Expression Dynamics | Abbreviation |
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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:001604926 | Thyroid | HT | cell growth | 58/1272 | 482/18723 | 1.56e-05 | 3.82e-04 | 58 |
GO:00400138 | Thyroid | HT | negative regulation of locomotion | 46/1272 | 391/18723 | 1.94e-04 | 2.84e-03 | 46 |
GO:001097519 | Thyroid | HT | regulation of neuron projection development | 50/1272 | 445/18723 | 3.18e-04 | 4.18e-03 | 50 |
GO:000155825 | Thyroid | HT | regulation of cell growth | 47/1272 | 414/18723 | 3.77e-04 | 4.76e-03 | 47 |
GO:000166728 | Thyroid | HT | ameboidal-type cell migration | 52/1272 | 475/18723 | 4.54e-04 | 5.53e-03 | 52 |
GO:00459269 | Thyroid | HT | negative regulation of growth | 31/1272 | 249/18723 | 8.02e-04 | 8.75e-03 | 31 |
GO:006156418 | Thyroid | HT | axon development | 50/1272 | 467/18723 | 9.50e-04 | 9.83e-03 | 50 |
GO:004876210 | Thyroid | HT | mesenchymal cell differentiation | 29/1272 | 236/18723 | 1.43e-03 | 1.35e-02 | 29 |
GO:003253525 | Thyroid | HT | regulation of cellular component size | 40/1272 | 383/18723 | 4.50e-03 | 3.22e-02 | 40 |
GO:004858818 | Thyroid | HT | developmental cell growth | 27/1272 | 234/18723 | 4.91e-03 | 3.35e-02 | 27 |
GO:005076715 | Thyroid | HT | regulation of neurogenesis | 38/1272 | 364/18723 | 5.56e-03 | 3.64e-02 | 38 |
GO:000836114 | Thyroid | HT | regulation of cell size | 22/1272 | 181/18723 | 5.74e-03 | 3.72e-02 | 22 |
GO:199013810 | Thyroid | HT | neuron projection extension | 21/1272 | 172/18723 | 6.51e-03 | 4.06e-02 | 21 |
GO:004886310 | Thyroid | HT | stem cell differentiation | 24/1272 | 206/18723 | 6.84e-03 | 4.19e-02 | 24 |
GO:004867516 | Thyroid | HT | axon extension | 16/1272 | 120/18723 | 7.23e-03 | 4.35e-02 | 16 |
GO:00604858 | Thyroid | HT | mesenchyme development | 31/1272 | 291/18723 | 8.69e-03 | 4.92e-02 | 31 |
GO:0016049112 | Thyroid | PTC | cell growth | 225/5968 | 482/18723 | 4.75e-12 | 2.07e-10 | 225 |
GO:0032535112 | Thyroid | PTC | regulation of cellular component size | 181/5968 | 383/18723 | 1.70e-10 | 5.64e-09 | 181 |
GO:0001558111 | Thyroid | PTC | regulation of cell growth | 188/5968 | 414/18723 | 4.13e-09 | 1.09e-07 | 188 |
GO:0010975110 | Thyroid | PTC | regulation of neuron projection development | 194/5968 | 445/18723 | 1.05e-07 | 2.08e-06 | 194 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Breast | ADJ |
SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | Breast | ADJ |
SEMA3D | NRP1_PLXNA4 | SEMA3D_NRP1_PLXNA4 | SEMA3 | Breast | DCIS |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Breast | Healthy |
SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | Breast | Healthy |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Endometrium | ADJ |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Endometrium | AEH |
SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | Endometrium | AEH |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Endometrium | EEC |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Esophagus | ESCC |
SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | Esophagus | ESCC |
SEMA3D | NRP1_PLXNA1 | SEMA3D_NRP1_PLXNA1 | SEMA3 | HNSCC | OSCC |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | HNSCC | OSCC |
SEMA3D | NRP2_PLXNA1 | SEMA3D_NRP2_PLXNA1 | SEMA3 | HNSCC | OSCC |
SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | HNSCC | OSCC |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | HNSCC | Precancer |
SEMA3D | NRP2_PLXNA1 | SEMA3D_NRP2_PLXNA1 | SEMA3 | HNSCC | Precancer |
SEMA3D | NRP2_PLXNA2 | SEMA3D_NRP2_PLXNA2 | SEMA3 | HNSCC | Precancer |
SEMA3D | NRP1_PLXNA4 | SEMA3D_NRP1_PLXNA4 | SEMA3 | Lung | ADJ |
SEMA3D | NRP1_PLXNA2 | SEMA3D_NRP1_PLXNA2 | SEMA3 | Lung | AIS |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
SEMA3D | SNV | Missense_Mutation | novel | c.1477G>T | p.Val493Leu | p.V493L | O95025 | protein_coding | tolerated(1) | benign(0.007) | TCGA-CV-A461-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
SEMA3D | SNV | Missense_Mutation | c.2240G>T | p.Gly747Val | p.G747V | O95025 | protein_coding | tolerated(0.28) | benign(0.011) | TCGA-QK-A8Z8-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | PD | |
SEMA3D | insertion | Frame_Shift_Ins | novel | c.1198_1199insCATTACATCGTACTGGCCATCTTCT | p.Ser400ThrfsTer13 | p.S400Tfs*13 | O95025 | protein_coding | TCGA-H7-8502-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | unknown | SD | ||
SEMA3D | SNV | Missense_Mutation | rs757282057 | c.2279G>A | p.Arg760Gln | p.R760Q | O95025 | protein_coding | tolerated(0.05) | probably_damaging(0.998) | TCGA-G9-7519-01 | Prostate | prostate adenocarcinoma | Male | <65 | 7 | Unknown | Unknown | SD |
SEMA3D | SNV | Missense_Mutation | c.2128N>T | p.Arg710Trp | p.R710W | O95025 | protein_coding | deleterious(0) | benign(0.328) | TCGA-HC-7740-01 | Prostate | prostate adenocarcinoma | Male | <65 | 7 | Unknown | Unknown | SD | |
SEMA3D | SNV | Missense_Mutation | novel | c.2222N>T | p.Arg741Ile | p.R741I | O95025 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
SEMA3D | SNV | Missense_Mutation | c.2128C>T | p.Arg710Trp | p.R710W | O95025 | protein_coding | deleterious(0) | benign(0.328) | TCGA-B7-5816-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SEMA3D | SNV | Missense_Mutation | novel | c.1127N>G | p.Lys376Arg | p.K376R | O95025 | protein_coding | tolerated(0.42) | probably_damaging(0.999) | TCGA-BR-7704-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SEMA3D | SNV | Missense_Mutation | c.284T>A | p.Leu95Gln | p.L95Q | O95025 | protein_coding | deleterious(0) | probably_damaging(0.934) | TCGA-BR-7901-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
SEMA3D | SNV | Missense_Mutation | rs150646719 | c.1715N>A | p.Arg572His | p.R572H | O95025 | protein_coding | deleterious(0) | probably_damaging(0.974) | TCGA-BR-8372-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | etoposide | CR |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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