|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: ARPC1B |
Gene summary for ARPC1B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARPC1B | Gene ID | 10095 |
| Gene name | actin related protein 2/3 complex subunit 1B | |
| Gene Alias | ARC41 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | A4D275 |
Top |
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 |
| 10095 | ARPC1B | GSM4909282 | Human | Breast | IDC | 4.07e-02 | 2.68e-01 | -0.0288 |
| 10095 | ARPC1B | GSM4909288 | Human | Breast | IDC | 1.87e-03 | 2.42e-02 | 0.0988 |
| 10095 | ARPC1B | GSM4909290 | Human | Breast | IDC | 3.77e-02 | -2.72e-01 | 0.2096 |
| 10095 | ARPC1B | GSM4909294 | Human | Breast | IDC | 3.46e-02 | -2.24e-01 | 0.2022 |
| 10095 | ARPC1B | GSM4909296 | Human | Breast | IDC | 1.47e-04 | 1.78e-01 | 0.1524 |
| 10095 | ARPC1B | GSM4909297 | Human | Breast | IDC | 8.70e-07 | -1.32e-01 | 0.1517 |
| 10095 | ARPC1B | GSM4909304 | Human | Breast | IDC | 5.11e-07 | 3.55e-01 | 0.1636 |
| 10095 | ARPC1B | GSM4909311 | Human | Breast | IDC | 1.12e-19 | -8.78e-02 | 0.1534 |
| 10095 | ARPC1B | GSM4909312 | Human | Breast | IDC | 1.24e-06 | -1.04e-01 | 0.1552 |
| 10095 | ARPC1B | GSM4909319 | Human | Breast | IDC | 1.43e-30 | 8.70e-02 | 0.1563 |
| 10095 | ARPC1B | GSM4909320 | Human | Breast | IDC | 2.22e-03 | -2.12e-01 | 0.1575 |
| 10095 | ARPC1B | GSM4909321 | Human | Breast | IDC | 3.23e-06 | 2.24e-02 | 0.1559 |
| 10095 | ARPC1B | brca1 | Human | Breast | Precancer | 3.44e-10 | 5.09e-01 | -0.0338 |
| 10095 | ARPC1B | brca2 | Human | Breast | Precancer | 7.42e-22 | 5.19e-01 | -0.024 |
| 10095 | ARPC1B | brca3 | Human | Breast | Precancer | 4.08e-10 | 2.94e-01 | -0.0263 |
| 10095 | ARPC1B | M2 | Human | Breast | IDC | 9.90e-06 | 3.51e-01 | 0.21 |
| 10095 | ARPC1B | NCCBC11 | Human | Breast | DCIS | 1.13e-03 | 3.41e-01 | 0.1232 |
| 10095 | ARPC1B | NCCBC14 | Human | Breast | DCIS | 2.88e-09 | 3.11e-01 | 0.2021 |
| 10095 | ARPC1B | NCCBC2 | Human | Breast | DCIS | 3.23e-03 | 2.42e-01 | 0.1554 |
| 10095 | ARPC1B | NCCBC3 | Human | Breast | DCIS | 4.16e-04 | 1.33e-01 | 0.1198 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 | ||
| 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. |
Top |
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:00432549 | Breast | Precancer | regulation of protein-containing complex assembly | 50/1080 | 428/18723 | 1.63e-06 | 5.97e-05 | 50 |
| GO:00313349 | Breast | Precancer | positive regulation of protein-containing complex assembly | 33/1080 | 237/18723 | 2.39e-06 | 8.21e-05 | 33 |
| GO:00436273 | Breast | Precancer | response to estrogen | 15/1080 | 75/18723 | 2.06e-05 | 4.83e-04 | 15 |
| GO:19029059 | Breast | Precancer | positive regulation of supramolecular fiber organization | 28/1080 | 209/18723 | 2.79e-05 | 6.28e-04 | 28 |
| GO:19029039 | Breast | Precancer | regulation of supramolecular fiber organization | 42/1080 | 383/18723 | 4.92e-05 | 1.04e-03 | 42 |
| GO:00329709 | Breast | Precancer | regulation of actin filament-based process | 42/1080 | 397/18723 | 1.11e-04 | 2.01e-03 | 42 |
| GO:00514959 | Breast | Precancer | positive regulation of cytoskeleton organization | 28/1080 | 226/18723 | 1.13e-04 | 2.04e-03 | 28 |
| GO:00070159 | Breast | Precancer | actin filament organization | 44/1080 | 442/18723 | 3.02e-04 | 4.35e-03 | 44 |
| GO:00323555 | Breast | Precancer | response to estradiol | 19/1080 | 141/18723 | 4.81e-04 | 6.31e-03 | 19 |
| GO:00329569 | Breast | Precancer | regulation of actin cytoskeleton organization | 36/1080 | 358/18723 | 8.56e-04 | 9.88e-03 | 36 |
| GO:00322739 | Breast | Precancer | positive regulation of protein polymerization | 18/1080 | 138/18723 | 9.85e-04 | 1.11e-02 | 18 |
| GO:01100539 | Breast | Precancer | regulation of actin filament organization | 29/1080 | 278/18723 | 1.50e-03 | 1.55e-02 | 29 |
| GO:00343146 | Breast | Precancer | Arp2/3 complex-mediated actin nucleation | 7/1080 | 39/18723 | 6.32e-03 | 4.43e-02 | 7 |
| GO:190290514 | Breast | IDC | positive regulation of supramolecular fiber organization | 37/1434 | 209/18723 | 1.33e-06 | 5.75e-05 | 37 |
| GO:004325414 | Breast | IDC | regulation of protein-containing complex assembly | 61/1434 | 428/18723 | 1.77e-06 | 7.31e-05 | 61 |
| GO:003133414 | Breast | IDC | positive regulation of protein-containing complex assembly | 40/1434 | 237/18723 | 1.77e-06 | 7.31e-05 | 40 |
| GO:003297014 | Breast | IDC | regulation of actin filament-based process | 56/1434 | 397/18723 | 6.37e-06 | 1.99e-04 | 56 |
| GO:003235512 | Breast | IDC | response to estradiol | 27/1434 | 141/18723 | 7.87e-06 | 2.35e-04 | 27 |
| GO:190290314 | Breast | IDC | regulation of supramolecular fiber organization | 54/1434 | 383/18723 | 9.40e-06 | 2.66e-04 | 54 |
| GO:004362711 | Breast | IDC | response to estrogen | 17/1434 | 75/18723 | 4.05e-05 | 9.25e-04 | 17 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513028 | Prostate | BPH | Pathogenic Escherichia coli infection | 77/1718 | 197/8465 | 7.09e-10 | 1.11e-08 | 6.89e-09 | 77 |
| hsa0453028 | Prostate | BPH | Tight junction | 68/1718 | 169/8465 | 1.70e-09 | 2.55e-08 | 1.58e-08 | 68 |
| hsa0414425 | Prostate | BPH | Endocytosis | 89/1718 | 251/8465 | 1.06e-08 | 1.29e-07 | 7.99e-08 | 89 |
| hsa0481020 | Prostate | BPH | Regulation of actin cytoskeleton | 80/1718 | 229/8465 | 1.23e-07 | 1.31e-06 | 8.10e-07 | 80 |
| hsa0510028 | Prostate | BPH | Bacterial invasion of epithelial cells | 35/1718 | 77/8465 | 5.15e-07 | 4.86e-06 | 3.00e-06 | 35 |
| hsa0513518 | Prostate | BPH | Yersinia infection | 49/1718 | 137/8465 | 1.65e-05 | 1.27e-04 | 7.86e-05 | 49 |
| hsa0466616 | Prostate | BPH | Fc gamma R-mediated phagocytosis | 31/1718 | 97/8465 | 4.40e-03 | 1.53e-02 | 9.45e-03 | 31 |
| hsa05132113 | Prostate | BPH | Salmonella infection | 99/1718 | 249/8465 | 7.26e-13 | 1.50e-11 | 9.27e-12 | 99 |
| hsa05131112 | Prostate | BPH | Shigellosis | 94/1718 | 247/8465 | 5.19e-11 | 9.51e-10 | 5.89e-10 | 94 |
| hsa05130113 | Prostate | BPH | Pathogenic Escherichia coli infection | 77/1718 | 197/8465 | 7.09e-10 | 1.11e-08 | 6.89e-09 | 77 |
| hsa04530113 | Prostate | BPH | Tight junction | 68/1718 | 169/8465 | 1.70e-09 | 2.55e-08 | 1.58e-08 | 68 |
| hsa04144111 | Prostate | BPH | Endocytosis | 89/1718 | 251/8465 | 1.06e-08 | 1.29e-07 | 7.99e-08 | 89 |
| hsa04810110 | Prostate | BPH | Regulation of actin cytoskeleton | 80/1718 | 229/8465 | 1.23e-07 | 1.31e-06 | 8.10e-07 | 80 |
| hsa05100112 | Prostate | BPH | Bacterial invasion of epithelial cells | 35/1718 | 77/8465 | 5.15e-07 | 4.86e-06 | 3.00e-06 | 35 |
| hsa0513519 | Prostate | BPH | Yersinia infection | 49/1718 | 137/8465 | 1.65e-05 | 1.27e-04 | 7.86e-05 | 49 |
| hsa0466617 | Prostate | BPH | Fc gamma R-mediated phagocytosis | 31/1718 | 97/8465 | 4.40e-03 | 1.53e-02 | 9.45e-03 | 31 |
| hsa0513229 | Prostate | Tumor | Salmonella infection | 98/1791 | 249/8465 | 2.55e-11 | 5.28e-10 | 3.27e-10 | 98 |
| hsa0513129 | Prostate | Tumor | Shigellosis | 94/1791 | 247/8465 | 5.56e-10 | 9.69e-09 | 6.01e-09 | 94 |
| hsa0453029 | Prostate | Tumor | Tight junction | 69/1791 | 169/8465 | 3.92e-09 | 6.18e-08 | 3.83e-08 | 69 |
| hsa0513029 | Prostate | Tumor | Pathogenic Escherichia coli infection | 77/1791 | 197/8465 | 5.20e-09 | 7.77e-08 | 4.82e-08 | 77 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
Top |
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 |
Top |
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 |
Top |
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 |
| ARPC1B | SNV | Missense_Mutation | c.33N>G | p.Ile11Met | p.I11M | O15143 | protein_coding | deleterious(0) | probably_damaging(0.957) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| ARPC1B | SNV | Missense_Mutation | c.1072N>A | p.Asp358Asn | p.D358N | O15143 | protein_coding | tolerated(0.15) | probably_damaging(0.953) | TCGA-E2-A1LG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| ARPC1B | insertion | In_Frame_Ins | novel | c.429_430insTGGGCAGAT | p.Ser143_Thr144insTrpAlaAsp | p.S143_T144insWAD | O15143 | protein_coding | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| ARPC1B | insertion | Frame_Shift_Ins | novel | c.431_432insAG | p.Val145AlafsTer51 | p.V145Afs*51 | O15143 | protein_coding | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| ARPC1B | SNV | Missense_Mutation | c.232N>A | p.Val78Met | p.V78M | O15143 | protein_coding | deleterious(0.03) | possibly_damaging(0.751) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ARPC1B | SNV | Missense_Mutation | c.932N>T | p.Ser311Phe | p.S311F | O15143 | protein_coding | deleterious(0.01) | possibly_damaging(0.472) | TCGA-AZ-6599-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| ARPC1B | SNV | Missense_Mutation | c.92N>G | p.Glu31Gly | p.E31G | O15143 | protein_coding | deleterious(0.01) | possibly_damaging(0.761) | TCGA-CK-5916-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ARPC1B | SNV | Missense_Mutation | novel | c.245N>T | p.Lys82Met | p.K82M | O15143 | protein_coding | deleterious(0.02) | possibly_damaging(0.735) | TCGA-AG-A00Y-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| ARPC1B | SNV | Missense_Mutation | novel | c.132G>T | p.Lys44Asn | p.K44N | O15143 | protein_coding | tolerated(0.45) | possibly_damaging(0.794) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| ARPC1B | SNV | Missense_Mutation | rs369966813 | c.713N>T | p.Ala238Val | p.A238V | O15143 | protein_coding | tolerated(0.51) | benign(0.017) | TCGA-AJ-A3NE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |