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Gene: PBX2 |
Gene summary for PBX2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PBX2 | Gene ID | 5089 |
| Gene name | PBX homeobox 2 | |
| Gene Alias | G17 | |
| Cytomap | 6p21.32 | |
| Gene Type | protein-coding | GO ID | GO:0001654 | UniProtAcc | A0A024RCR3 |
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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 |
| 5089 | PBX2 | S014 | Human | Liver | HCC | 2.92e-14 | 5.88e-01 | 0.2254 |
| 5089 | PBX2 | S015 | Human | Liver | HCC | 2.05e-19 | 8.18e-01 | 0.2375 |
| 5089 | PBX2 | S016 | Human | Liver | HCC | 8.70e-19 | 6.07e-01 | 0.2243 |
| 5089 | PBX2 | S027 | Human | Liver | HCC | 2.60e-02 | 3.06e-01 | 0.2446 |
| 5089 | PBX2 | S028 | Human | Liver | HCC | 1.89e-11 | 4.47e-01 | 0.2503 |
| 5089 | PBX2 | S029 | Human | Liver | HCC | 3.22e-06 | 3.74e-01 | 0.2581 |
| 5089 | PBX2 | C04 | Human | Oral cavity | OSCC | 4.09e-09 | 5.60e-01 | 0.2633 |
| 5089 | PBX2 | C21 | Human | Oral cavity | OSCC | 4.67e-11 | 4.17e-01 | 0.2678 |
| 5089 | PBX2 | C30 | Human | Oral cavity | OSCC | 2.74e-44 | 1.54e+00 | 0.3055 |
| 5089 | PBX2 | C38 | Human | Oral cavity | OSCC | 6.48e-08 | 9.46e-01 | 0.172 |
| 5089 | PBX2 | C46 | Human | Oral cavity | OSCC | 2.14e-08 | 2.92e-01 | 0.1673 |
| 5089 | PBX2 | C51 | Human | Oral cavity | OSCC | 4.58e-05 | 2.59e-01 | 0.2674 |
| 5089 | PBX2 | C57 | Human | Oral cavity | OSCC | 1.71e-03 | 2.34e-01 | 0.1679 |
| 5089 | PBX2 | C08 | Human | Oral cavity | OSCC | 3.60e-13 | 3.78e-01 | 0.1919 |
| 5089 | PBX2 | LN46 | Human | Oral cavity | OSCC | 8.11e-03 | 2.40e-01 | 0.1666 |
| 5089 | PBX2 | LP15 | Human | Oral cavity | LP | 2.77e-03 | 6.99e-01 | 0.2174 |
| 5089 | PBX2 | SYSMH2 | Human | Oral cavity | OSCC | 5.61e-10 | 2.86e-01 | 0.2326 |
| 5089 | PBX2 | SYSMH3 | Human | Oral cavity | OSCC | 1.27e-05 | 2.64e-01 | 0.2442 |
| 5089 | PBX2 | SYSMH5 | Human | Oral cavity | OSCC | 8.06e-03 | 1.52e-01 | 0.0647 |
| 5089 | PBX2 | SYSMH6 | Human | Oral cavity | OSCC | 7.64e-03 | 1.21e-01 | 0.1275 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00485687 | Esophagus | ESCC | embryonic organ development | 228/8552 | 427/18723 | 7.28e-04 | 3.79e-03 | 228 |
| GO:00487367 | Esophagus | ESCC | appendage development | 98/8552 | 172/18723 | 1.83e-03 | 8.37e-03 | 98 |
| GO:00601737 | Esophagus | ESCC | limb development | 98/8552 | 172/18723 | 1.83e-03 | 8.37e-03 | 98 |
| GO:00485688 | Thyroid | ATC | embryonic organ development | 172/6293 | 427/18723 | 2.08e-03 | 9.84e-03 | 172 |
| GO:00351074 | Thyroid | ATC | appendage morphogenesis | 63/6293 | 138/18723 | 2.13e-03 | 1.00e-02 | 63 |
| GO:00351084 | Thyroid | ATC | limb morphogenesis | 63/6293 | 138/18723 | 2.13e-03 | 1.00e-02 | 63 |
| GO:00487368 | Thyroid | ATC | appendage development | 76/6293 | 172/18723 | 2.41e-03 | 1.12e-02 | 76 |
| GO:00601738 | Thyroid | ATC | limb development | 76/6293 | 172/18723 | 2.41e-03 | 1.12e-02 | 76 |
| GO:00303262 | Thyroid | ATC | embryonic limb morphogenesis | 52/6293 | 116/18723 | 7.67e-03 | 3.00e-02 | 52 |
| GO:00351132 | Thyroid | ATC | embryonic appendage morphogenesis | 52/6293 | 116/18723 | 7.67e-03 | 3.00e-02 | 52 |
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| 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 |
| 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 |
| PBX2 | MAIT | Liver | Healthy | HACD1,PABPN1,EIF2AK3, etc. | 1.01e-02 |  |
| PBX2 | MON | Liver | Healthy | HACD1,PABPN1,EIF2AK3, etc. | 1.39e-02 | |
| PBX2 | BN | Liver | NAFLD | HACD1,PABPN1,EIF2AK3, etc. | 1.75e-01 |  |
| PBX2 | M1MAC | Oral cavity | ADJ | ASS1,TPD52L1,ASNS, etc. | 2.80e-01 |  |
| PBX2 | CD8TEXINT | Oral cavity | ADJ | ASS1,TPD52L1,ASNS, etc. | 3.84e-03 | |
| PBX2 | M1MAC | Oral cavity | Healthy | ASS1,TPD52L1,ASNS, etc. | 3.14e-01 |  |
| PBX2 | M1MAC | Oral cavity | LP | ASS1,TPD52L1,ASNS, etc. | 2.61e-01 |  |
| PBX2 | MAST | Oral cavity | LP | ASS1,TPD52L1,ASNS, etc. | 1.16e-01 | |
| PBX2 | M1MAC | Oral cavity | OSCC | ASS1,TPD52L1,ASNS, etc. | 1.29e-01 |  |
| PBX2 | NEUT | Pancreas | ADJ | ALAS1,CSF3R,SAP25, etc. | 4.01e-01 |  |
| ∗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 2 |
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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 |
| PBX2 | SNV | Missense_Mutation | c.705G>A | p.Met235Ile | p.M235I | P40425 | protein_coding | tolerated(0.09) | possibly_damaging(0.759) | TCGA-A8-A09N-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PBX2 | SNV | Missense_Mutation | c.1215N>C | p.Trp405Cys | p.W405C | P40425 | protein_coding | deleterious(0) | benign(0.111) | TCGA-E2-A1LS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cyclophosphamide | SD | |
| PBX2 | SNV | Missense_Mutation | novel | c.1037C>G | p.Ser346Cys | p.S346C | P40425 | protein_coding | deleterious(0.03) | probably_damaging(0.971) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| PBX2 | SNV | Missense_Mutation | rs774240386 | c.49N>A | p.Gly17Ser | p.G17S | P40425 | protein_coding | tolerated_low_confidence(0.17) | benign(0.003) | TCGA-A6-6650-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PBX2 | SNV | Missense_Mutation | c.1253N>T | p.Thr418Met | p.T418M | P40425 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.551) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| PBX2 | SNV | Missense_Mutation | rs763303454 | c.1114N>A | p.Val372Met | p.V372M | P40425 | protein_coding | tolerated_low_confidence(0.07) | benign(0.058) | TCGA-AA-3867-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
| PBX2 | SNV | Missense_Mutation | novel | c.1054N>G | p.Ser352Ala | p.S352A | P40425 | protein_coding | tolerated(0.25) | benign(0.013) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PBX2 | SNV | Missense_Mutation | novel | c.278N>G | p.Glu93Gly | p.E93G | P40425 | protein_coding | deleterious(0) | possibly_damaging(0.756) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| PBX2 | SNV | Missense_Mutation | c.1013N>G | p.Pro338Arg | p.P338R | P40425 | protein_coding | deleterious(0) | possibly_damaging(0.862) | TCGA-NH-A6GC-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | SD | |
| PBX2 | SNV | Missense_Mutation | novel | c.531G>T | p.Glu177Asp | p.E177D | P40425 | protein_coding | deleterious(0.03) | possibly_damaging(0.836) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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