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Gene: HLA-DPA1 |
Gene summary for HLA-DPA1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | HLA-DPA1 | Gene ID | 3113 |
Gene name | major histocompatibility complex, class II, DP alpha 1 | |
Gene Alias | DP(W3) | |
Cytomap | 6p21.32 | |
Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | P20036 |
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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 |
3113 | HLA-DPA1 | GSM4909287 | Human | Breast | IDC | 6.52e-27 | 7.47e-01 | 0.2057 |
3113 | HLA-DPA1 | GSM4909290 | Human | Breast | IDC | 1.56e-05 | 2.71e-01 | 0.2096 |
3113 | HLA-DPA1 | GSM4909293 | Human | Breast | IDC | 9.07e-08 | 2.27e-01 | 0.1581 |
3113 | HLA-DPA1 | GSM4909305 | Human | Breast | IDC | 2.63e-02 | 2.19e-01 | 0.0436 |
3113 | HLA-DPA1 | GSM4909317 | Human | Breast | IDC | 8.08e-06 | 2.80e-01 | 0.1355 |
3113 | HLA-DPA1 | M1 | Human | Breast | IDC | 1.37e-17 | 5.64e-01 | 0.1577 |
3113 | HLA-DPA1 | M2 | Human | Breast | IDC | 1.83e-05 | 6.44e-01 | 0.21 |
3113 | HLA-DPA1 | NCCBC11 | Human | Breast | DCIS | 3.90e-09 | 8.54e-01 | 0.1232 |
3113 | HLA-DPA1 | NCCBC14 | Human | Breast | DCIS | 2.42e-07 | 4.77e-01 | 0.2021 |
3113 | HLA-DPA1 | NCCBC3 | Human | Breast | DCIS | 1.57e-73 | 1.47e+00 | 0.1198 |
3113 | HLA-DPA1 | NCCBC5 | Human | Breast | DCIS | 5.80e-28 | 9.67e-01 | 0.2046 |
3113 | HLA-DPA1 | P2 | Human | Breast | IDC | 4.77e-26 | 9.60e-01 | 0.21 |
3113 | HLA-DPA1 | DCIS2 | Human | Breast | DCIS | 1.03e-02 | 4.32e-02 | 0.0085 |
3113 | HLA-DPA1 | CA_HPV_1 | Human | Cervix | CC | 5.76e-10 | 6.60e-01 | 0.0264 |
3113 | HLA-DPA1 | CA_HPV_3 | Human | Cervix | CC | 4.76e-02 | -4.65e-01 | 0.0414 |
3113 | HLA-DPA1 | N_HPV_1 | Human | Cervix | N_HPV | 3.00e-05 | 2.45e-01 | 0.0079 |
3113 | HLA-DPA1 | CCI_1 | Human | Cervix | CC | 6.16e-10 | -1.04e+00 | 0.528 |
3113 | HLA-DPA1 | CCI_3 | Human | Cervix | CC | 9.65e-08 | -9.64e-01 | 0.516 |
3113 | HLA-DPA1 | CCII_1 | Human | Cervix | CC | 1.70e-18 | -1.04e+00 | 0.3249 |
3113 | HLA-DPA1 | Tumor | Human | Cervix | CC | 1.26e-17 | -5.58e-01 | 0.1241 |
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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:004800213 | Breast | IDC | antigen processing and presentation of peptide antigen | 18/1434 | 62/18723 | 5.28e-07 | 2.59e-05 | 18 |
GO:004578514 | Breast | IDC | positive regulation of cell adhesion | 62/1434 | 437/18723 | 1.70e-06 | 7.16e-05 | 62 |
GO:000250112 | Breast | IDC | peptide antigen assembly with MHC protein complex | 9/1434 | 18/18723 | 2.28e-06 | 9.05e-05 | 9 |
GO:000247813 | Breast | IDC | antigen processing and presentation of exogenous peptide antigen | 13/1434 | 38/18723 | 2.60e-06 | 1.01e-04 | 13 |
GO:000239612 | Breast | IDC | MHC protein complex assembly | 9/1434 | 19/18723 | 4.03e-06 | 1.43e-04 | 9 |
GO:00023997 | Breast | IDC | MHC class II protein complex assembly | 8/1434 | 16/18723 | 8.56e-06 | 2.47e-04 | 8 |
GO:00025037 | Breast | IDC | peptide antigen assembly with MHC class II protein complex | 8/1434 | 16/18723 | 8.56e-06 | 2.47e-04 | 8 |
GO:004211012 | Breast | IDC | T cell activation | 64/1434 | 487/18723 | 1.49e-05 | 3.77e-04 | 64 |
GO:005086311 | Breast | IDC | regulation of T cell activation | 47/1434 | 329/18723 | 2.49e-05 | 5.91e-04 | 47 |
GO:000181911 | Breast | IDC | positive regulation of cytokine production | 61/1434 | 467/18723 | 2.81e-05 | 6.58e-04 | 61 |
GO:00024957 | Breast | IDC | antigen processing and presentation of peptide antigen via MHC class II | 11/1434 | 34/18723 | 2.81e-05 | 6.58e-04 | 11 |
GO:001988413 | Breast | IDC | antigen processing and presentation of exogenous antigen | 13/1434 | 47/18723 | 3.53e-05 | 8.08e-04 | 13 |
GO:005087011 | Breast | IDC | positive regulation of T cell activation | 34/1434 | 216/18723 | 4.59e-05 | 1.03e-03 | 34 |
GO:001988613 | Breast | IDC | antigen processing and presentation of exogenous peptide antigen via MHC class II | 10/1434 | 30/18723 | 4.87e-05 | 1.07e-03 | 10 |
GO:00025047 | Breast | IDC | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 11/1434 | 36/18723 | 5.13e-05 | 1.10e-03 | 11 |
GO:000715912 | Breast | IDC | leukocyte cell-cell adhesion | 49/1434 | 371/18723 | 1.27e-04 | 2.33e-03 | 49 |
GO:00198829 | Breast | IDC | antigen processing and presentation | 20/1434 | 106/18723 | 1.41e-04 | 2.49e-03 | 20 |
GO:190303911 | Breast | IDC | positive regulation of leukocyte cell-cell adhesion | 35/1434 | 239/18723 | 1.58e-04 | 2.73e-03 | 35 |
GO:190303711 | Breast | IDC | regulation of leukocyte cell-cell adhesion | 45/1434 | 336/18723 | 1.72e-04 | 2.92e-03 | 45 |
GO:002240712 | Breast | IDC | regulation of cell-cell adhesion | 55/1434 | 448/18723 | 3.43e-04 | 5.07e-03 | 55 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0514533 | Prostate | Tumor | Toxoplasmosis | 40/1791 | 112/8465 | 2.55e-04 | 1.43e-03 | 8.87e-04 | 40 |
hsa0541636 | Prostate | Tumor | Viral myocarditis | 24/1791 | 60/8465 | 6.83e-04 | 3.33e-03 | 2.06e-03 | 24 |
hsa0461236 | Prostate | Tumor | Antigen processing and presentation | 28/1791 | 78/8465 | 1.88e-03 | 7.76e-03 | 4.81e-03 | 28 |
hsa0465932 | Prostate | Tumor | Th17 cell differentiation | 36/1791 | 108/8465 | 2.11e-03 | 8.42e-03 | 5.22e-03 | 36 |
hsa0516433 | Prostate | Tumor | Influenza A | 49/1791 | 171/8465 | 1.18e-02 | 3.64e-02 | 2.26e-02 | 49 |
hsa0514033 | Prostate | Tumor | Leishmaniasis | 25/1791 | 77/8465 | 1.35e-02 | 4.10e-02 | 2.54e-02 | 25 |
hsa0461212 | Stomach | GC | Antigen processing and presentation | 28/708 | 78/8465 | 8.70e-12 | 2.53e-10 | 1.78e-10 | 28 |
hsa0541612 | Stomach | GC | Viral myocarditis | 21/708 | 60/8465 | 6.11e-09 | 1.22e-07 | 8.61e-08 | 21 |
hsa0516612 | Stomach | GC | Human T-cell leukemia virus 1 infection | 41/708 | 222/8465 | 9.06e-07 | 1.71e-05 | 1.20e-05 | 41 |
hsa04940 | Stomach | GC | Type I diabetes mellitus | 13/708 | 43/8465 | 3.03e-05 | 3.88e-04 | 2.73e-04 | 13 |
hsa05330 | Stomach | GC | Allograft rejection | 12/708 | 38/8465 | 3.77e-05 | 4.47e-04 | 3.15e-04 | 12 |
hsa05332 | Stomach | GC | Graft-versus-host disease | 12/708 | 42/8465 | 1.13e-04 | 1.16e-03 | 8.19e-04 | 12 |
hsa05145 | Stomach | GC | Toxoplasmosis | 22/708 | 112/8465 | 1.22e-04 | 1.22e-03 | 8.56e-04 | 22 |
hsa0516912 | Stomach | GC | Epstein-Barr virus infection | 33/708 | 202/8465 | 1.35e-04 | 1.31e-03 | 9.22e-04 | 33 |
hsa05140 | Stomach | GC | Leishmaniasis | 16/708 | 77/8465 | 5.21e-04 | 4.63e-03 | 3.26e-03 | 16 |
hsa05323 | Stomach | GC | Rheumatoid arthritis | 18/708 | 93/8465 | 5.93e-04 | 5.13e-03 | 3.61e-03 | 18 |
hsa05164 | Stomach | GC | Influenza A | 27/708 | 171/8465 | 9.20e-04 | 7.01e-03 | 4.94e-03 | 27 |
hsa05320 | Stomach | GC | Autoimmune thyroid disease | 12/708 | 53/8465 | 1.16e-03 | 7.72e-03 | 5.43e-03 | 12 |
hsa04514 | Stomach | GC | Cell adhesion molecules | 24/708 | 157/8465 | 2.70e-03 | 1.69e-02 | 1.19e-02 | 24 |
hsa0414512 | Stomach | GC | Phagosome | 23/708 | 152/8465 | 3.73e-03 | 2.17e-02 | 1.53e-02 | 23 |
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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 |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Breast | DCIS |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Breast | Healthy |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Breast | IDC |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Cervix | ADJ |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Cervix | CC |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Cervix | Healthy |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Cervix | Precancer |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | CRC | AD |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | CRC | ADJ |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | CRC | MSI-H |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | CRC | MSS |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | CRC | SER |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Endometrium | ADJ |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Endometrium | AEH |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Endometrium | EEC |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | Endometrium | Healthy |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | HNSCC | ADJ |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | HNSCC | Healthy |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | HNSCC | OSCC |
HLA-DPA1 | CD4 | HLA-DPA1_CD4 | MHC-II | HNSCC | Precancer |
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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 |
HLA-DPA1 | SNV | Missense_Mutation | c.397C>T | p.Pro133Ser | p.P133S | P20036 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A2-A0CT-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD | |
HLA-DPA1 | SNV | Missense_Mutation | novel | c.325N>G | p.Asn109Asp | p.N109D | P20036 | protein_coding | deleterious(0.01) | probably_damaging(0.989) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HLA-DPA1 | SNV | Missense_Mutation | rs770307009 | c.746N>A | p.Arg249His | p.R249H | P20036 | protein_coding | tolerated(0.21) | benign(0.005) | TCGA-CM-4747-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | fluorouracil | SD |
HLA-DPA1 | SNV | Missense_Mutation | rs371532700 | c.137C>T | p.Thr46Met | p.T46M | P20036 | protein_coding | deleterious(0.04) | possibly_damaging(0.895) | TCGA-G4-6295-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
HLA-DPA1 | SNV | Missense_Mutation | c.100N>A | p.Ala34Thr | p.A34T | P20036 | protein_coding | deleterious(0.03) | benign(0.106) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD | |
HLA-DPA1 | SNV | Missense_Mutation | c.484G>T | p.Gly162Cys | p.G162C | P20036 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
HLA-DPA1 | SNV | Missense_Mutation | rs751649425 | c.724N>A | p.Val242Ile | p.V242I | P20036 | protein_coding | tolerated(1) | benign(0) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HLA-DPA1 | SNV | Missense_Mutation | novel | c.446N>G | p.Asn149Ser | p.N149S | P20036 | protein_coding | tolerated(0.18) | benign(0.033) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HLA-DPA1 | SNV | Missense_Mutation | rs761093053 | c.5N>A | p.Arg2His | p.R2H | P20036 | protein_coding | tolerated_low_confidence(0.56) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
HLA-DPA1 | SNV | Missense_Mutation | novel | c.718G>A | p.Gly240Ser | p.G240S | P20036 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
3113 | HLA-DPA1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME, CELL SURFACE | peginterferon alfa-2b | 26387494 |
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