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Gene: XAB2 |
Gene summary for XAB2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | XAB2 | Gene ID | 56949 |
| Gene name | XPA binding protein 2 | |
| Gene Alias | HCNP | |
| Cytomap | 19p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000349 | UniProtAcc | Q9HCS7 |
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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 |
| 56949 | XAB2 | LZE2T | Human | Esophagus | ESCC | 2.55e-04 | 4.71e-01 | 0.082 |
| 56949 | XAB2 | LZE4T | Human | Esophagus | ESCC | 1.63e-04 | 1.44e-01 | 0.0811 |
| 56949 | XAB2 | LZE5T | Human | Esophagus | ESCC | 1.28e-02 | 2.26e-01 | 0.0514 |
| 56949 | XAB2 | LZE7T | Human | Esophagus | ESCC | 3.41e-10 | 3.84e-01 | 0.0667 |
| 56949 | XAB2 | LZE8T | Human | Esophagus | ESCC | 4.57e-04 | 1.08e-01 | 0.067 |
| 56949 | XAB2 | LZE20T | Human | Esophagus | ESCC | 3.94e-04 | 1.25e-01 | 0.0662 |
| 56949 | XAB2 | LZE24T | Human | Esophagus | ESCC | 1.08e-15 | 2.79e-01 | 0.0596 |
| 56949 | XAB2 | LZE21T | Human | Esophagus | ESCC | 2.74e-06 | 2.29e-01 | 0.0655 |
| 56949 | XAB2 | P1T-E | Human | Esophagus | ESCC | 2.38e-10 | 6.52e-01 | 0.0875 |
| 56949 | XAB2 | P2T-E | Human | Esophagus | ESCC | 1.18e-27 | 2.54e-01 | 0.1177 |
| 56949 | XAB2 | P4T-E | Human | Esophagus | ESCC | 3.78e-15 | 2.39e-01 | 0.1323 |
| 56949 | XAB2 | P5T-E | Human | Esophagus | ESCC | 6.36e-19 | 3.12e-01 | 0.1327 |
| 56949 | XAB2 | P8T-E | Human | Esophagus | ESCC | 6.72e-32 | 4.87e-01 | 0.0889 |
| 56949 | XAB2 | P9T-E | Human | Esophagus | ESCC | 5.20e-13 | 3.05e-01 | 0.1131 |
| 56949 | XAB2 | P10T-E | Human | Esophagus | ESCC | 1.59e-24 | 4.18e-01 | 0.116 |
| 56949 | XAB2 | P11T-E | Human | Esophagus | ESCC | 1.85e-11 | 4.71e-01 | 0.1426 |
| 56949 | XAB2 | P12T-E | Human | Esophagus | ESCC | 1.14e-29 | 5.40e-01 | 0.1122 |
| 56949 | XAB2 | P15T-E | Human | Esophagus | ESCC | 1.81e-23 | 4.84e-01 | 0.1149 |
| 56949 | XAB2 | P16T-E | Human | Esophagus | ESCC | 2.19e-21 | 3.15e-01 | 0.1153 |
| 56949 | XAB2 | P17T-E | Human | Esophagus | ESCC | 2.37e-21 | 7.28e-01 | 0.1278 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
| GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
| GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
| GO:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
| GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
| GO:000170119 | Esophagus | ESCC | in utero embryonic development | 243/8552 | 367/18723 | 1.00e-15 | 6.86e-14 | 243 |
| GO:000182412 | Esophagus | ESCC | blastocyst development | 73/8552 | 106/18723 | 1.13e-06 | 1.40e-05 | 73 |
| GO:00062891 | Esophagus | ESCC | nucleotide-excision repair | 42/8552 | 60/18723 | 1.18e-04 | 8.14e-04 | 42 |
| GO:00215436 | Esophagus | ESCC | pallium development | 94/8552 | 169/18723 | 5.79e-03 | 2.14e-02 | 94 |
| GO:002261320 | Oral cavity | OSCC | ribonucleoprotein complex biogenesis | 333/7305 | 463/18723 | 8.28e-48 | 5.24e-44 | 333 |
| GO:000838020 | Oral cavity | OSCC | RNA splicing | 308/7305 | 434/18723 | 2.43e-42 | 7.70e-39 | 308 |
| GO:000037519 | Oral cavity | OSCC | RNA splicing, via transesterification reactions | 225/7305 | 324/18723 | 5.20e-29 | 2.99e-26 | 225 |
| GO:000037719 | Oral cavity | OSCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 221/7305 | 320/18723 | 5.50e-28 | 2.18e-25 | 221 |
| GO:000039819 | Oral cavity | OSCC | mRNA splicing, via spliceosome | 221/7305 | 320/18723 | 5.50e-28 | 2.18e-25 | 221 |
| GO:007182620 | Oral cavity | OSCC | ribonucleoprotein complex subunit organization | 152/7305 | 227/18723 | 1.05e-17 | 1.01e-15 | 152 |
| GO:002261820 | Oral cavity | OSCC | ribonucleoprotein complex assembly | 146/7305 | 220/18723 | 1.53e-16 | 1.23e-14 | 146 |
| GO:000170116 | Oral cavity | OSCC | in utero embryonic development | 207/7305 | 367/18723 | 7.92e-12 | 2.95e-10 | 207 |
| GO:00018243 | Oral cavity | OSCC | blastocyst development | 66/7305 | 106/18723 | 1.04e-06 | 1.40e-05 | 66 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0304016 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| hsa0304017 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| hsa0304026 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
| hsa0304036 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
| hsa0304025 | Prostate | Tumor | Spliceosome | 66/1791 | 217/8465 | 7.53e-04 | 3.59e-03 | 2.23e-03 | 66 |
| hsa0304035 | Prostate | Tumor | Spliceosome | 66/1791 | 217/8465 | 7.53e-04 | 3.59e-03 | 2.23e-03 | 66 |
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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 |
| ∗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 |
| XAB2 | SNV | Missense_Mutation | rs763601327 | c.385N>C | p.Thr129Pro | p.T129P | Q9HCS7 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-A7-A26E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | SD |
| XAB2 | SNV | Missense_Mutation | rs763601327 | c.385A>C | p.Thr129Pro | p.T129P | Q9HCS7 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-AR-A1AY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unspecific | Doxorubicin | SD |
| XAB2 | SNV | Missense_Mutation | c.1550N>G | p.Thr517Arg | p.T517R | Q9HCS7 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| XAB2 | SNV | Missense_Mutation | rs745761079 | c.412N>T | p.Arg138Trp | p.R138W | Q9HCS7 | protein_coding | deleterious(0) | probably_damaging(0.932) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
| XAB2 | SNV | Missense_Mutation | c.2222T>C | p.Met741Thr | p.M741T | Q9HCS7 | protein_coding | tolerated(0.2) | benign(0.015) | TCGA-E2-A1IH-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | aromasin | SD | |
| XAB2 | SNV | Missense_Mutation | rs191550276 | c.623N>A | p.Arg208His | p.R208H | Q9HCS7 | protein_coding | tolerated(0.2) | benign(0.001) | TCGA-E2-A1L9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| XAB2 | SNV | Missense_Mutation | rs763601327 | c.385N>C | p.Thr129Pro | p.T129P | Q9HCS7 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-EW-A1OY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| XAB2 | SNV | Missense_Mutation | rs763601327 | c.385N>C | p.Thr129Pro | p.T129P | Q9HCS7 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-EW-A1PB-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| XAB2 | SNV | Missense_Mutation | rs770164799 | c.2096N>T | p.Thr699Met | p.T699M | Q9HCS7 | protein_coding | deleterious(0.01) | benign(0.018) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| XAB2 | SNV | Missense_Mutation | novel | c.1493N>A | p.Gly498Asp | p.G498D | Q9HCS7 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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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