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Gene: PLXND1 |
Gene summary for PLXND1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PLXND1 | Gene ID | 23129 |
| Gene name | plexin D1 | |
| Gene Alias | PLEXD1 | |
| Cytomap | 3q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9Y4D7 |
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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 |
| 23129 | PLXND1 | HCC1_Meng | Human | Liver | HCC | 6.15e-15 | 4.14e-02 | 0.0246 |
| 23129 | PLXND1 | HCC2 | Human | Liver | HCC | 4.00e-18 | 3.03e+00 | 0.5341 |
| 23129 | PLXND1 | Pt13.b | Human | Liver | HCC | 3.18e-04 | 1.37e-01 | 0.0251 |
| 23129 | PLXND1 | Pt14.a | Human | Liver | HCC | 9.82e-05 | 3.44e-01 | 0.0169 |
| 23129 | PLXND1 | Pt14.d | Human | Liver | HCC | 6.59e-11 | 2.90e-01 | 0.0143 |
| 23129 | PLXND1 | S014 | Human | Liver | HCC | 2.93e-23 | 9.61e-01 | 0.2254 |
| 23129 | PLXND1 | S015 | Human | Liver | HCC | 1.29e-30 | 1.25e+00 | 0.2375 |
| 23129 | PLXND1 | S016 | Human | Liver | HCC | 3.38e-35 | 1.21e+00 | 0.2243 |
| 23129 | PLXND1 | S027 | Human | Liver | HCC | 5.50e-13 | 8.93e-01 | 0.2446 |
| 23129 | PLXND1 | S028 | Human | Liver | HCC | 6.91e-30 | 1.02e+00 | 0.2503 |
| 23129 | PLXND1 | S029 | Human | Liver | HCC | 1.75e-18 | 7.53e-01 | 0.2581 |
| 23129 | PLXND1 | male-WTA | Human | Thyroid | PTC | 4.42e-19 | 2.48e-01 | 0.1037 |
| 23129 | PLXND1 | PTC01 | Human | Thyroid | PTC | 1.25e-05 | 1.29e-01 | 0.1899 |
| 23129 | PLXND1 | PTC03 | Human | Thyroid | PTC | 3.54e-03 | 2.95e-01 | 0.1784 |
| 23129 | PLXND1 | PTC04 | Human | Thyroid | PTC | 2.77e-07 | 1.78e-01 | 0.1927 |
| 23129 | PLXND1 | PTC05 | Human | Thyroid | PTC | 5.53e-08 | 2.73e-01 | 0.2065 |
| 23129 | PLXND1 | PTC06 | Human | Thyroid | PTC | 3.45e-18 | 4.01e-01 | 0.2057 |
| 23129 | PLXND1 | PTC07 | Human | Thyroid | PTC | 2.31e-12 | 2.77e-01 | 0.2044 |
| 23129 | PLXND1 | ATC11 | Human | Thyroid | ATC | 2.02e-16 | 7.97e-01 | 0.3386 |
| 23129 | PLXND1 | ATC12 | Human | Thyroid | ATC | 6.38e-17 | 3.54e-01 | 0.34 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:005109822 | Liver | HCC | regulation of binding | 225/7958 | 363/18723 | 3.78e-14 | 2.37e-12 | 225 |
| GO:004339322 | Liver | HCC | regulation of protein binding | 129/7958 | 196/18723 | 3.27e-11 | 1.26e-09 | 129 |
| GO:002260422 | Liver | HCC | regulation of cell morphogenesis | 188/7958 | 309/18723 | 4.84e-11 | 1.82e-09 | 188 |
| GO:004873222 | Liver | HCC | gland development | 242/7958 | 436/18723 | 2.26e-08 | 5.28e-07 | 242 |
| GO:005109922 | Liver | HCC | positive regulation of binding | 108/7958 | 173/18723 | 9.22e-08 | 1.83e-06 | 108 |
| GO:003209221 | Liver | HCC | positive regulation of protein binding | 59/7958 | 85/18723 | 4.66e-07 | 7.61e-06 | 59 |
| GO:003134611 | Liver | HCC | positive regulation of cell projection organization | 193/7958 | 353/18723 | 2.28e-06 | 3.08e-05 | 193 |
| GO:000836022 | Liver | HCC | regulation of cell shape | 92/7958 | 154/18723 | 1.15e-05 | 1.31e-04 | 92 |
| GO:001072011 | Liver | HCC | positive regulation of cell development | 155/7958 | 298/18723 | 5.39e-04 | 3.48e-03 | 155 |
| GO:001097511 | Liver | HCC | regulation of neuron projection development | 220/7958 | 445/18723 | 1.68e-03 | 8.78e-03 | 220 |
| GO:00016553 | Liver | HCC | urogenital system development | 170/7958 | 338/18723 | 2.15e-03 | 1.08e-02 | 170 |
| GO:00507674 | Liver | HCC | regulation of neurogenesis | 181/7958 | 364/18723 | 3.00e-03 | 1.40e-02 | 181 |
| GO:00018222 | Liver | HCC | kidney development | 148/7958 | 293/18723 | 3.25e-03 | 1.49e-02 | 148 |
| GO:00720012 | Liver | HCC | renal system development | 152/7958 | 302/18723 | 3.45e-03 | 1.56e-02 | 152 |
| GO:00507693 | Liver | HCC | positive regulation of neurogenesis | 116/7958 | 225/18723 | 3.67e-03 | 1.63e-02 | 116 |
| GO:000166721 | Liver | HCC | ameboidal-type cell migration | 226/7958 | 475/18723 | 1.35e-02 | 4.81e-02 | 226 |
| GO:0051098113 | Thyroid | PTC | regulation of binding | 195/5968 | 363/18723 | 3.21e-18 | 3.37e-16 | 195 |
| GO:0022604112 | Thyroid | PTC | regulation of cell morphogenesis | 165/5968 | 309/18723 | 2.60e-15 | 1.82e-13 | 165 |
| GO:0051099113 | Thyroid | PTC | positive regulation of binding | 100/5968 | 173/18723 | 1.56e-12 | 6.96e-11 | 100 |
| GO:0031346110 | Thyroid | PTC | positive regulation of cell projection organization | 173/5968 | 353/18723 | 1.09e-11 | 4.40e-10 | 173 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Breast | DCIS |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Breast | Healthy |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Cervix | ADJ |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Cervix | CC |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Cervix | Precancer |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | CRC | AD |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | CRC | CRC |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | CRC | FAP |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | CRC | MSI-H |
| SEMA3E | PLXND1 | SEMA3E_PLXND1 | SEMA3 | CRC | MSI-H |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | CRC | MSS |
| SEMA3E | PLXND1 | SEMA3E_PLXND1 | SEMA3 | CRC | MSS |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | CRC | SER |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Endometrium | ADJ |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Endometrium | AEH |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | Esophagus | ESCC |
| SEMA3E | PLXND1 | SEMA3E_PLXND1 | SEMA3 | Esophagus | ESCC |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | GC | ADJ |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | HNSCC | ADJ |
| SEMA3C | PLXND1 | SEMA3C_PLXND1 | SEMA3 | HNSCC | OSCC |
| 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 |
| PLXND1 | SNV | Missense_Mutation | c.3667N>A | p.Asp1223Asn | p.D1223N | Q9Y4D7 | protein_coding | tolerated(0.4) | benign(0) | TCGA-E2-A14O-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | arimidex | SD | |
| PLXND1 | SNV | Missense_Mutation | c.4069C>T | p.Arg1357Cys | p.R1357C | Q9Y4D7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E9-A1RF-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| PLXND1 | SNV | Missense_Mutation | novel | c.441N>A | p.Phe147Leu | p.F147L | Q9Y4D7 | protein_coding | tolerated(0.38) | benign(0.011) | TCGA-LL-A8F5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| PLXND1 | deletion | In_Frame_Del | c.4453_4461delNNNNNNNNN | p.Arg1485_Glu1487del | p.R1485_E1487del | Q9Y4D7 | protein_coding | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |||
| PLXND1 | SNV | Missense_Mutation | rs748102549 | c.3277C>T | p.Arg1093Cys | p.R1093C | Q9Y4D7 | protein_coding | deleterious(0.02) | probably_damaging(0.938) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PLXND1 | SNV | Missense_Mutation | rs781053507 | c.3725N>T | p.Ala1242Val | p.A1242V | Q9Y4D7 | protein_coding | tolerated(0.22) | benign(0.015) | TCGA-C5-A7X8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PLXND1 | SNV | Missense_Mutation | rs372693427 | c.3278G>A | p.Arg1093His | p.R1093H | Q9Y4D7 | protein_coding | tolerated(0.12) | probably_damaging(0.938) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PLXND1 | SNV | Missense_Mutation | rs377455226 | c.4526N>T | p.Thr1509Met | p.T1509M | Q9Y4D7 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PLXND1 | SNV | Missense_Mutation | c.3901G>A | p.Glu1301Lys | p.E1301K | Q9Y4D7 | protein_coding | deleterious(0.02) | probably_damaging(0.994) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PLXND1 | SNV | Missense_Mutation | novel | c.3431G>T | p.Arg1144Leu | p.R1144L | Q9Y4D7 | protein_coding | tolerated(0.75) | benign(0.001) | TCGA-Q1-A73R-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 18 |
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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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