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Gene: SEMA6D |
Gene summary for SEMA6D |
Gene summary. |
Gene information | Species | Human | Gene symbol | SEMA6D | Gene ID | 80031 |
Gene name | semaphorin 6D | |
Gene Alias | SEMA6D | |
Cytomap | 15q21.1 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q8NFY4 |
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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 |
80031 | SEMA6D | HTA11_347_2000001011 | Human | Colorectum | AD | 1.20e-06 | 4.24e-01 | -0.1954 |
80031 | SEMA6D | A002-C-205 | Human | Colorectum | FAP | 4.85e-02 | -1.16e-01 | -0.1236 |
80031 | SEMA6D | A002-C-116 | Human | Colorectum | FAP | 3.82e-02 | -9.41e-02 | -0.0452 |
80031 | SEMA6D | LZE4T | Human | Esophagus | ESCC | 1.20e-04 | 1.93e-01 | 0.0811 |
80031 | SEMA6D | P2T-E | Human | Esophagus | ESCC | 8.40e-04 | 1.18e-01 | 0.1177 |
80031 | SEMA6D | P9T-E | Human | Esophagus | ESCC | 4.01e-04 | 1.49e-01 | 0.1131 |
80031 | SEMA6D | P10T-E | Human | Esophagus | ESCC | 2.02e-06 | 1.75e-01 | 0.116 |
80031 | SEMA6D | P11T-E | Human | Esophagus | ESCC | 1.20e-09 | 4.28e-01 | 0.1426 |
80031 | SEMA6D | P12T-E | Human | Esophagus | ESCC | 5.00e-17 | 3.93e-01 | 0.1122 |
80031 | SEMA6D | P15T-E | Human | Esophagus | ESCC | 4.01e-11 | 3.00e-01 | 0.1149 |
80031 | SEMA6D | P16T-E | Human | Esophagus | ESCC | 4.17e-05 | 1.62e-01 | 0.1153 |
80031 | SEMA6D | P19T-E | Human | Esophagus | ESCC | 1.65e-10 | 6.23e-01 | 0.1662 |
80031 | SEMA6D | P22T-E | Human | Esophagus | ESCC | 2.02e-06 | 1.53e-01 | 0.1236 |
80031 | SEMA6D | P23T-E | Human | Esophagus | ESCC | 2.89e-02 | 1.11e-01 | 0.108 |
80031 | SEMA6D | P26T-E | Human | Esophagus | ESCC | 1.85e-18 | 3.75e-01 | 0.1276 |
80031 | SEMA6D | P27T-E | Human | Esophagus | ESCC | 1.78e-03 | 1.15e-01 | 0.1055 |
80031 | SEMA6D | P28T-E | Human | Esophagus | ESCC | 4.40e-09 | 1.86e-01 | 0.1149 |
80031 | SEMA6D | P30T-E | Human | Esophagus | ESCC | 4.41e-11 | 4.61e-01 | 0.137 |
80031 | SEMA6D | P39T-E | Human | Esophagus | ESCC | 9.20e-06 | 1.52e-01 | 0.0894 |
80031 | SEMA6D | P42T-E | Human | Esophagus | ESCC | 9.46e-03 | 1.52e-01 | 0.1175 |
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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. |
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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:0032535 | Colorectum | AD | regulation of cellular component size | 142/3918 | 383/18723 | 1.74e-13 | 3.41e-11 | 142 |
GO:0016049 | Colorectum | AD | cell growth | 143/3918 | 482/18723 | 2.83e-06 | 8.09e-05 | 143 |
GO:0001558 | Colorectum | AD | regulation of cell growth | 124/3918 | 414/18723 | 7.67e-06 | 1.86e-04 | 124 |
GO:0001667 | Colorectum | AD | ameboidal-type cell migration | 137/3918 | 475/18723 | 2.17e-05 | 4.33e-04 | 137 |
GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
GO:0007409 | Colorectum | AD | axonogenesis | 122/3918 | 418/18723 | 3.36e-05 | 6.15e-04 | 122 |
GO:0061564 | Colorectum | AD | axon development | 132/3918 | 467/18723 | 8.40e-05 | 1.31e-03 | 132 |
GO:0031345 | Colorectum | AD | negative regulation of cell projection organization | 58/3918 | 186/18723 | 6.37e-04 | 6.58e-03 | 58 |
GO:0008361 | Colorectum | AD | regulation of cell size | 56/3918 | 181/18723 | 9.61e-04 | 9.07e-03 | 56 |
GO:0050770 | Colorectum | AD | regulation of axonogenesis | 49/3918 | 154/18723 | 9.88e-04 | 9.28e-03 | 49 |
GO:0048638 | Colorectum | AD | regulation of developmental growth | 92/3918 | 330/18723 | 1.48e-03 | 1.25e-02 | 92 |
GO:0050767 | Colorectum | AD | regulation of neurogenesis | 99/3918 | 364/18723 | 2.35e-03 | 1.82e-02 | 99 |
GO:0030516 | Colorectum | AD | regulation of axon extension | 32/3918 | 95/18723 | 2.59e-03 | 1.96e-02 | 32 |
GO:0010977 | Colorectum | AD | negative regulation of neuron projection development | 43/3918 | 137/18723 | 2.60e-03 | 1.97e-02 | 43 |
GO:0048588 | Colorectum | AD | developmental cell growth | 67/3918 | 234/18723 | 3.03e-03 | 2.25e-02 | 67 |
GO:0048675 | Colorectum | AD | axon extension | 38/3918 | 120/18723 | 3.76e-03 | 2.65e-02 | 38 |
GO:0045926 | Colorectum | AD | negative regulation of growth | 70/3918 | 249/18723 | 4.07e-03 | 2.83e-02 | 70 |
GO:0060560 | Colorectum | AD | developmental growth involved in morphogenesis | 66/3918 | 234/18723 | 4.75e-03 | 3.22e-02 | 66 |
GO:0007411 | Colorectum | AD | axon guidance | 64/3918 | 227/18723 | 5.41e-03 | 3.55e-02 | 64 |
GO:0097485 | Colorectum | AD | neuron projection guidance | 64/3918 | 228/18723 | 6.02e-03 | 3.78e-02 | 64 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04360 | Colorectum | AD | Axon guidance | 61/2092 | 182/8465 | 4.36e-03 | 2.17e-02 | 1.38e-02 | 61 |
hsa043601 | Colorectum | AD | Axon guidance | 61/2092 | 182/8465 | 4.36e-03 | 2.17e-02 | 1.38e-02 | 61 |
hsa043604 | Colorectum | FAP | Axon guidance | 47/1404 | 182/8465 | 9.09e-04 | 5.20e-03 | 3.16e-03 | 47 |
hsa043605 | Colorectum | FAP | Axon guidance | 47/1404 | 182/8465 | 9.09e-04 | 5.20e-03 | 3.16e-03 | 47 |
hsa0436016 | Esophagus | ESCC | Axon guidance | 108/4205 | 182/8465 | 5.13e-03 | 1.30e-02 | 6.67e-03 | 108 |
hsa0436017 | Esophagus | ESCC | Axon guidance | 108/4205 | 182/8465 | 5.13e-03 | 1.30e-02 | 6.67e-03 | 108 |
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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 |
SEMA6D | PLXNA1 | SEMA6D_PLXNA1 | SEMA6 | HNSCC | Precancer |
SEMA6D | PLXNA1 | SEMA6D_PLXNA1 | SEMA6 | Lung | AAH |
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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 |
SEMA6D | SNV | Missense_Mutation | novel | c.2879G>T | p.Arg960Ile | p.R960I | Q8NFY4 | protein_coding | tolerated(0.08) | possibly_damaging(0.714) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SEMA6D | SNV | Missense_Mutation | rs199606505 | c.761G>A | p.Arg254His | p.R254H | Q8NFY4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A2K7-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | taxol | SD |
SEMA6D | SNV | Missense_Mutation | novel | c.1966N>G | p.Asn656Asp | p.N656D | Q8NFY4 | protein_coding | tolerated(0.87) | benign(0) | TCGA-AJ-A3BH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
SEMA6D | SNV | Missense_Mutation | rs773168430 | c.95N>A | p.Thr32Asn | p.T32N | Q8NFY4 | protein_coding | deleterious(0) | benign(0.017) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
SEMA6D | SNV | Missense_Mutation | novel | c.727N>A | p.Glu243Lys | p.E243K | Q8NFY4 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SEMA6D | SNV | Missense_Mutation | novel | c.1778N>A | p.Ser593Tyr | p.S593Y | Q8NFY4 | protein_coding | tolerated(0.12) | benign(0.089) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SEMA6D | SNV | Missense_Mutation | rs534298453 | c.1390G>A | p.Val464Ile | p.V464I | Q8NFY4 | protein_coding | tolerated(0.23) | benign(0.015) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SEMA6D | SNV | Missense_Mutation | novel | c.1430G>A | p.Cys477Tyr | p.C477Y | Q8NFY4 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SEMA6D | SNV | Missense_Mutation | c.749N>A | p.Ala250Asp | p.A250D | Q8NFY4 | protein_coding | deleterious(0) | possibly_damaging(0.904) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SEMA6D | SNV | Missense_Mutation | rs145056482 | c.2301G>C | p.Glu767Asp | p.E767D | Q8NFY4 | protein_coding | tolerated(0.53) | benign(0.029) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | 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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