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Gene: B2M |
Gene summary for B2M |
Gene summary. |
Gene information | Species | Human | Gene symbol | B2M | Gene ID | 567 |
Gene name | beta-2-microglobulin | |
Gene Alias | IMD43 | |
Cytomap | 15q21.1 | |
Gene Type | protein-coding | GO ID | GO:0000041 | UniProtAcc | P61769 |
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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 |
567 | B2M | GSM4909282 | Human | Breast | IDC | 4.65e-17 | 2.48e-01 | -0.0288 |
567 | B2M | GSM4909285 | Human | Breast | IDC | 6.83e-38 | -4.84e-01 | 0.21 |
567 | B2M | GSM4909286 | Human | Breast | IDC | 1.01e-107 | -1.68e+00 | 0.1081 |
567 | B2M | GSM4909290 | Human | Breast | IDC | 3.00e-02 | 2.15e-01 | 0.2096 |
567 | B2M | GSM4909291 | Human | Breast | IDC | 3.14e-18 | -4.32e-01 | 0.1753 |
567 | B2M | GSM4909292 | Human | Breast | IDC | 9.03e-03 | -4.29e-01 | 0.1236 |
567 | B2M | GSM4909294 | Human | Breast | IDC | 3.18e-20 | -6.69e-01 | 0.2022 |
567 | B2M | GSM4909298 | Human | Breast | IDC | 1.59e-23 | -4.86e-01 | 0.1551 |
567 | B2M | GSM4909299 | Human | Breast | IDC | 6.75e-06 | 1.66e-01 | 0.035 |
567 | B2M | GSM4909300 | Human | Breast | IDC | 8.22e-05 | 2.80e-01 | 0.0334 |
567 | B2M | GSM4909301 | Human | Breast | IDC | 1.50e-37 | -6.45e-01 | 0.1577 |
567 | B2M | GSM4909303 | Human | Breast | IDC | 3.70e-02 | -3.12e-01 | 0.0438 |
567 | B2M | GSM4909304 | Human | Breast | IDC | 5.17e-52 | -6.58e-01 | 0.1636 |
567 | B2M | GSM4909306 | Human | Breast | IDC | 2.55e-09 | -1.52e-01 | 0.1564 |
567 | B2M | GSM4909307 | Human | Breast | IDC | 3.26e-15 | 2.34e-01 | 0.1569 |
567 | B2M | GSM4909308 | Human | Breast | IDC | 4.74e-18 | 3.16e-01 | 0.158 |
567 | B2M | GSM4909309 | Human | Breast | IDC | 5.35e-16 | 3.20e-01 | 0.0483 |
567 | B2M | GSM4909311 | Human | Breast | IDC | 1.91e-41 | -9.88e-01 | 0.1534 |
567 | B2M | GSM4909312 | Human | Breast | IDC | 2.90e-57 | -1.10e+00 | 0.1552 |
567 | B2M | GSM4909315 | Human | Breast | IDC | 1.42e-29 | -6.90e-01 | 0.21 |
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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:00064578 | Breast | Precancer | protein folding | 43/1080 | 212/18723 | 3.48e-13 | 7.45e-11 | 43 |
GO:00420268 | Breast | Precancer | protein refolding | 10/1080 | 23/18723 | 2.25e-07 | 1.13e-05 | 10 |
GO:00022629 | Breast | Precancer | myeloid cell homeostasis | 27/1080 | 157/18723 | 3.10e-07 | 1.49e-05 | 27 |
GO:00100389 | Breast | Precancer | response to metal ion | 47/1080 | 373/18723 | 3.88e-07 | 1.79e-05 | 47 |
GO:00457859 | Breast | Precancer | positive regulation of cell adhesion | 52/1080 | 437/18723 | 5.74e-07 | 2.49e-05 | 52 |
GO:00341019 | Breast | Precancer | erythrocyte homeostasis | 23/1080 | 129/18723 | 1.20e-06 | 4.60e-05 | 23 |
GO:00510989 | Breast | Precancer | regulation of binding | 44/1080 | 363/18723 | 2.59e-06 | 8.65e-05 | 44 |
GO:00300999 | Breast | Precancer | myeloid cell differentiation | 45/1080 | 381/18723 | 4.00e-06 | 1.25e-04 | 45 |
GO:00018196 | Breast | Precancer | positive regulation of cytokine production | 52/1080 | 467/18723 | 4.18e-06 | 1.29e-04 | 52 |
GO:00024839 | Breast | Precancer | antigen processing and presentation of endogenous peptide antigen | 8/1080 | 19/18723 | 5.10e-06 | 1.53e-04 | 8 |
GO:00075688 | Breast | Precancer | aging | 41/1080 | 339/18723 | 5.95e-06 | 1.71e-04 | 41 |
GO:00022378 | Breast | Precancer | response to molecule of bacterial origin | 43/1080 | 363/18723 | 6.05e-06 | 1.72e-04 | 43 |
GO:00198839 | Breast | Precancer | antigen processing and presentation of endogenous antigen | 9/1080 | 26/18723 | 8.75e-06 | 2.34e-04 | 9 |
GO:00421107 | Breast | Precancer | T cell activation | 52/1080 | 487/18723 | 1.37e-05 | 3.42e-04 | 52 |
GO:00508707 | Breast | Precancer | positive regulation of T cell activation | 29/1080 | 216/18723 | 1.94e-05 | 4.58e-04 | 29 |
GO:00466868 | Breast | Precancer | response to cadmium ion | 14/1080 | 68/18723 | 2.74e-05 | 6.21e-04 | 14 |
GO:00456379 | Breast | Precancer | regulation of myeloid cell differentiation | 28/1080 | 210/18723 | 3.05e-05 | 6.72e-04 | 28 |
GO:19037069 | Breast | Precancer | regulation of hemopoiesis | 41/1080 | 367/18723 | 3.95e-05 | 8.52e-04 | 41 |
GO:19030396 | Breast | Precancer | positive regulation of leukocyte cell-cell adhesion | 30/1080 | 239/18723 | 5.13e-05 | 1.07e-03 | 30 |
GO:00506736 | Breast | Precancer | epithelial cell proliferation | 46/1080 | 437/18723 | 6.02e-05 | 1.23e-03 | 46 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0461218 | Breast | Precancer | Antigen processing and presentation | 19/684 | 78/8465 | 9.61e-06 | 1.12e-04 | 8.62e-05 | 19 |
hsa0516918 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
hsa0516618 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
hsa0516316 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
hsa0461219 | Breast | Precancer | Antigen processing and presentation | 19/684 | 78/8465 | 9.61e-06 | 1.12e-04 | 8.62e-05 | 19 |
hsa0516919 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
hsa0516619 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
hsa0516317 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
hsa0516922 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
hsa0461223 | Breast | IDC | Antigen processing and presentation | 24/867 | 78/8465 | 4.61e-07 | 8.33e-06 | 6.23e-06 | 24 |
hsa0516624 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
hsa0516324 | Breast | IDC | Human cytomegalovirus infection | 39/867 | 225/8465 | 6.66e-04 | 5.41e-03 | 4.05e-03 | 39 |
hsa0517014 | Breast | IDC | Human immunodeficiency virus 1 infection | 33/867 | 212/8465 | 9.28e-03 | 4.37e-02 | 3.27e-02 | 33 |
hsa0516932 | Breast | IDC | Epstein-Barr virus infection | 45/867 | 202/8465 | 3.16e-07 | 6.05e-06 | 4.52e-06 | 45 |
hsa0461233 | Breast | IDC | Antigen processing and presentation | 24/867 | 78/8465 | 4.61e-07 | 8.33e-06 | 6.23e-06 | 24 |
hsa0516634 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
hsa0516334 | Breast | IDC | Human cytomegalovirus infection | 39/867 | 225/8465 | 6.66e-04 | 5.41e-03 | 4.05e-03 | 39 |
hsa0517015 | Breast | IDC | Human immunodeficiency virus 1 infection | 33/867 | 212/8465 | 9.28e-03 | 4.37e-02 | 3.27e-02 | 33 |
hsa0516642 | Breast | DCIS | Human T-cell leukemia virus 1 infection | 41/846 | 222/8465 | 7.03e-05 | 6.88e-04 | 5.07e-04 | 41 |
hsa0516344 | Breast | DCIS | Human cytomegalovirus infection | 38/846 | 225/8465 | 8.11e-04 | 5.95e-03 | 4.38e-03 | 38 |
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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 |
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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 |
B2M | SNV | Missense_Mutation | c.192G>C | p.Glu64Asp | p.E64D | P61769 | protein_coding | tolerated(0.1) | benign(0.009) | TCGA-QK-A6II-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD | |
B2M | SNV | Missense_Mutation | c.289N>A | p.Glu97Lys | p.E97K | P61769 | protein_coding | tolerated(0.52) | benign(0.006) | TCGA-T2-A6X2-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
B2M | SNV | Missense_Mutation | c.289G>A | p.Glu97Lys | p.E97K | P61769 | protein_coding | tolerated(0.52) | benign(0.006) | TCGA-T3-A92M-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
B2M | insertion | Frame_Shift_Ins | novel | c.78_79insA | p.Ile27AsnfsTer30 | p.I27Nfs*30 | P61769 | protein_coding | TCGA-CV-7099-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
B2M | deletion | Frame_Shift_Del | novel | c.221delT | p.Leu74CysfsTer29 | p.L74Cfs*29 | P61769 | protein_coding | TCGA-H7-A76A-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
B2M | deletion | Frame_Shift_Del | novel | c.285delA | p.Asp96MetfsTer7 | p.D96Mfs*7 | P61769 | protein_coding | TCGA-BR-8382-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
B2M | insertion | Frame_Shift_Ins | novel | c.285dupA | p.Asp96ArgfsTer2 | p.D96Rfs*2 | P61769 | protein_coding | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
B2M | deletion | Frame_Shift_Del | novel | c.194_198delNNNNN | p.Ile66LysfsTer22 | p.I66Kfs*22 | P61769 | protein_coding | TCGA-D7-8570-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | plfe | SD | ||
B2M | deletion | Frame_Shift_Del | c.200delN | p.Val69TrpfsTer34 | p.V69Wfs*34 | P61769 | protein_coding | TCGA-D7-A6EY-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |||
B2M | deletion | Frame_Shift_Del | novel | c.318_319delNN | p.Leu107ValfsTer7 | p.L107Vfs*7 | P61769 | protein_coding | TCGA-FP-A4BE-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
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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 |
567 | B2M | CLINICALLY ACTIONABLE, DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUG RESISTANCE | AMIKACIN | AMIKACIN | 7672871 | |
567 | B2M | CLINICALLY ACTIONABLE, DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUG RESISTANCE | PEMBROLIZUMAB | PEMBROLIZUMAB | 27433843 | |
567 | B2M | CLINICALLY ACTIONABLE, DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, DRUG RESISTANCE | THYROGLOBULIN | THYROGLOBULIN | 9609129 |
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