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Gene: ARPC1A |
Gene summary for ARPC1A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARPC1A | Gene ID | 10552 |
| Gene name | actin related protein 2/3 complex subunit 1A | |
| Gene Alias | Arc40 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | Q92747 |
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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 |
| 10552 | ARPC1A | GSM4909282 | Human | Breast | IDC | 6.25e-18 | 5.35e-01 | -0.0288 |
| 10552 | ARPC1A | GSM4909285 | Human | Breast | IDC | 3.81e-03 | 2.55e-01 | 0.21 |
| 10552 | ARPC1A | GSM4909286 | Human | Breast | IDC | 1.90e-33 | 7.26e-01 | 0.1081 |
| 10552 | ARPC1A | GSM4909288 | Human | Breast | IDC | 2.81e-05 | 1.76e-01 | 0.0988 |
| 10552 | ARPC1A | GSM4909296 | Human | Breast | IDC | 2.79e-05 | -1.36e-02 | 0.1524 |
| 10552 | ARPC1A | GSM4909297 | Human | Breast | IDC | 4.54e-08 | -1.21e-01 | 0.1517 |
| 10552 | ARPC1A | GSM4909298 | Human | Breast | IDC | 9.32e-04 | 2.83e-01 | 0.1551 |
| 10552 | ARPC1A | GSM4909301 | Human | Breast | IDC | 3.69e-03 | -1.67e-01 | 0.1577 |
| 10552 | ARPC1A | GSM4909302 | Human | Breast | IDC | 1.43e-05 | 2.29e-01 | 0.1545 |
| 10552 | ARPC1A | GSM4909304 | Human | Breast | IDC | 4.31e-03 | 3.08e-01 | 0.1636 |
| 10552 | ARPC1A | GSM4909308 | Human | Breast | IDC | 7.33e-18 | 4.66e-01 | 0.158 |
| 10552 | ARPC1A | GSM4909311 | Human | Breast | IDC | 8.21e-20 | -2.53e-01 | 0.1534 |
| 10552 | ARPC1A | GSM4909312 | Human | Breast | IDC | 4.65e-09 | 1.70e-01 | 0.1552 |
| 10552 | ARPC1A | GSM4909313 | Human | Breast | IDC | 3.61e-02 | 1.43e-01 | 0.0391 |
| 10552 | ARPC1A | GSM4909318 | Human | Breast | IDC | 6.44e-07 | 2.42e-01 | 0.2031 |
| 10552 | ARPC1A | GSM4909319 | Human | Breast | IDC | 6.45e-34 | -1.04e-01 | 0.1563 |
| 10552 | ARPC1A | GSM4909320 | Human | Breast | IDC | 3.83e-06 | -2.31e-01 | 0.1575 |
| 10552 | ARPC1A | GSM4909321 | Human | Breast | IDC | 1.73e-11 | -5.60e-02 | 0.1559 |
| 10552 | ARPC1A | brca2 | Human | Breast | Precancer | 9.24e-04 | 2.28e-01 | -0.024 |
| 10552 | ARPC1A | brca3 | Human | Breast | Precancer | 9.31e-05 | 2.25e-01 | -0.0263 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| 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 | ||
| 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 | ||
| 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. |
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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: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: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: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:190290314 | Breast | IDC | regulation of supramolecular fiber organization | 54/1434 | 383/18723 | 9.40e-06 | 2.66e-04 | 54 |
| GO:003227314 | Breast | IDC | positive regulation of protein polymerization | 25/1434 | 138/18723 | 4.46e-05 | 1.01e-03 | 25 |
| GO:005149513 | Breast | IDC | positive regulation of cytoskeleton organization | 35/1434 | 226/18723 | 5.04e-05 | 1.09e-03 | 35 |
| GO:003295614 | Breast | IDC | regulation of actin cytoskeleton organization | 48/1434 | 358/18723 | 1.03e-04 | 1.96e-03 | 48 |
| GO:000701514 | Breast | IDC | actin filament organization | 55/1434 | 442/18723 | 2.45e-04 | 3.84e-03 | 55 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513218 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
| hsa0513018 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
| hsa0513118 | Breast | Precancer | Shigellosis | 44/684 | 247/8465 | 3.91e-07 | 6.86e-06 | 5.26e-06 | 44 |
| hsa0453018 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
| hsa0510018 | Breast | Precancer | Bacterial invasion of epithelial cells | 16/684 | 77/8465 | 3.55e-04 | 2.80e-03 | 2.15e-03 | 16 |
| hsa0513219 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
| hsa0513019 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
| hsa0513119 | Breast | Precancer | Shigellosis | 44/684 | 247/8465 | 3.91e-07 | 6.86e-06 | 5.26e-06 | 44 |
| hsa0453019 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
| hsa0510019 | Breast | Precancer | Bacterial invasion of epithelial cells | 16/684 | 77/8465 | 3.55e-04 | 2.80e-03 | 2.15e-03 | 16 |
| hsa0513224 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
| hsa0453024 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
| hsa0513024 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
| hsa0513124 | Breast | IDC | Shigellosis | 47/867 | 247/8465 | 1.78e-05 | 2.00e-04 | 1.49e-04 | 47 |
| hsa0510024 | Breast | IDC | Bacterial invasion of epithelial cells | 17/867 | 77/8465 | 1.69e-03 | 1.19e-02 | 8.93e-03 | 17 |
| hsa0481014 | Breast | IDC | Regulation of actin cytoskeleton | 36/867 | 229/8465 | 5.79e-03 | 3.13e-02 | 2.34e-02 | 36 |
| hsa0513234 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
| hsa0453034 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
| hsa0513034 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
| hsa0513134 | Breast | IDC | Shigellosis | 47/867 | 247/8465 | 1.78e-05 | 2.00e-04 | 1.49e-04 | 47 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
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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 |
| ARPC1A | SNV | Missense_Mutation | c.322N>C | p.Glu108Gln | p.E108Q | Q92747 | protein_coding | deleterious(0) | probably_damaging(0.97) | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| ARPC1A | SNV | Missense_Mutation | c.875N>A | p.Ser292Asn | p.S292N | Q92747 | protein_coding | tolerated(0.26) | probably_damaging(0.979) | TCGA-D8-A1XV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ARPC1A | SNV | Missense_Mutation | novel | c.43N>T | p.Ala15Ser | p.A15S | Q92747 | protein_coding | tolerated(0.23) | probably_damaging(0.971) | TCGA-OL-A5RU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
| ARPC1A | insertion | Nonsense_Mutation | novel | c.365_366insGTTAAATGAGTCATGGTGAATTTTGCTC | p.Cys123LeufsTer6 | p.C123Lfs*6 | Q92747 | protein_coding | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| ARPC1A | SNV | Missense_Mutation | rs760596520 | c.682G>A | p.Val228Met | p.V228M | Q92747 | protein_coding | deleterious(0.01) | benign(0.04) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ARPC1A | SNV | Missense_Mutation | rs773348651 | c.944N>A | p.Arg315His | p.R315H | Q92747 | protein_coding | tolerated(0.14) | benign(0.007) | TCGA-C5-A7CO-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
| ARPC1A | SNV | Missense_Mutation | c.638N>G | p.Ser213Cys | p.S213C | Q92747 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-C5-A7UC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| ARPC1A | SNV | Missense_Mutation | c.313N>C | p.Ser105Pro | p.S105P | Q92747 | protein_coding | deleterious(0) | probably_damaging(0.939) | TCGA-C5-A905-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| ARPC1A | SNV | Missense_Mutation | c.589G>C | p.Glu197Gln | p.E197Q | Q92747 | protein_coding | deleterious(0) | benign(0.108) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| ARPC1A | SNV | Missense_Mutation | c.548N>T | p.Thr183Met | p.T183M | Q92747 | protein_coding | deleterious(0.01) | possibly_damaging(0.533) | TCGA-AA-3856-01 | Colorectum | colon 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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