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Gene: ARPC5 |
Gene summary for ARPC5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARPC5 | Gene ID | 10092 |
| Gene name | actin related protein 2/3 complex subunit 5 | |
| Gene Alias | ARC16 | |
| Cytomap | 1q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0006928 | UniProtAcc | O15511 |
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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 |
| 10092 | ARPC5 | GSM4909281 | Human | Breast | IDC | 3.79e-18 | 5.84e-01 | 0.21 |
| 10092 | ARPC5 | GSM4909282 | Human | Breast | IDC | 1.36e-32 | 7.36e-01 | -0.0288 |
| 10092 | ARPC5 | GSM4909285 | Human | Breast | IDC | 6.99e-28 | 6.27e-01 | 0.21 |
| 10092 | ARPC5 | GSM4909286 | Human | Breast | IDC | 4.86e-03 | -1.55e-01 | 0.1081 |
| 10092 | ARPC5 | GSM4909287 | Human | Breast | IDC | 1.67e-07 | 4.06e-01 | 0.2057 |
| 10092 | ARPC5 | GSM4909288 | Human | Breast | IDC | 1.15e-04 | 2.53e-01 | 0.0988 |
| 10092 | ARPC5 | GSM4909293 | Human | Breast | IDC | 7.94e-05 | 2.84e-01 | 0.1581 |
| 10092 | ARPC5 | GSM4909296 | Human | Breast | IDC | 4.94e-14 | -3.39e-01 | 0.1524 |
| 10092 | ARPC5 | GSM4909297 | Human | Breast | IDC | 6.03e-11 | -1.86e-01 | 0.1517 |
| 10092 | ARPC5 | GSM4909301 | Human | Breast | IDC | 7.39e-19 | 5.52e-01 | 0.1577 |
| 10092 | ARPC5 | GSM4909308 | Human | Breast | IDC | 1.95e-06 | 3.17e-01 | 0.158 |
| 10092 | ARPC5 | GSM4909309 | Human | Breast | IDC | 1.82e-03 | -2.07e-01 | 0.0483 |
| 10092 | ARPC5 | GSM4909311 | Human | Breast | IDC | 4.23e-33 | -3.61e-01 | 0.1534 |
| 10092 | ARPC5 | GSM4909312 | Human | Breast | IDC | 5.33e-08 | -1.73e-02 | 0.1552 |
| 10092 | ARPC5 | GSM4909317 | Human | Breast | IDC | 1.61e-05 | 3.34e-01 | 0.1355 |
| 10092 | ARPC5 | GSM4909319 | Human | Breast | IDC | 5.22e-34 | -3.43e-01 | 0.1563 |
| 10092 | ARPC5 | GSM4909320 | Human | Breast | IDC | 4.96e-07 | -4.97e-01 | 0.1575 |
| 10092 | ARPC5 | GSM4909321 | Human | Breast | IDC | 3.40e-14 | 1.96e-01 | 0.1559 |
| 10092 | ARPC5 | brca1 | Human | Breast | Precancer | 1.49e-06 | 4.21e-01 | -0.0338 |
| 10092 | ARPC5 | brca2 | Human | Breast | Precancer | 2.83e-02 | 2.32e-01 | -0.024 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| 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:003297022 | Liver | HCC | regulation of actin filament-based process | 222/7958 | 397/18723 | 3.81e-08 | 8.30e-07 | 222 |
| GO:003227322 | Liver | HCC | positive regulation of protein polymerization | 90/7958 | 138/18723 | 5.73e-08 | 1.21e-06 | 90 |
| GO:003295622 | Liver | HCC | regulation of actin cytoskeleton organization | 202/7958 | 358/18723 | 6.18e-08 | 1.29e-06 | 202 |
| GO:000815422 | Liver | HCC | actin polymerization or depolymerization | 130/7958 | 218/18723 | 2.31e-07 | 4.14e-06 | 130 |
| GO:003004122 | Liver | HCC | actin filament polymerization | 116/7958 | 191/18723 | 2.66e-07 | 4.68e-06 | 116 |
| GO:011005322 | Liver | HCC | regulation of actin filament organization | 158/7958 | 278/18723 | 9.01e-07 | 1.37e-05 | 158 |
| GO:003083212 | Liver | HCC | regulation of actin filament length | 113/7958 | 189/18723 | 1.16e-06 | 1.71e-05 | 113 |
| GO:003083322 | Liver | HCC | regulation of actin filament polymerization | 104/7958 | 172/18723 | 1.46e-06 | 2.08e-05 | 104 |
| GO:000806412 | Liver | HCC | regulation of actin polymerization or depolymerization | 112/7958 | 188/18723 | 1.65e-06 | 2.31e-05 | 112 |
| GO:003431421 | Liver | HCC | Arp2/3 complex-mediated actin nucleation | 30/7958 | 39/18723 | 1.28e-05 | 1.43e-04 | 30 |
| GO:003083812 | Liver | HCC | positive regulation of actin filament polymerization | 63/7958 | 99/18723 | 1.76e-05 | 1.89e-04 | 63 |
| GO:009758121 | Liver | HCC | lamellipodium organization | 58/7958 | 90/18723 | 2.16e-05 | 2.30e-04 | 58 |
| GO:004501011 | Liver | HCC | actin nucleation | 35/7958 | 52/18723 | 2.63e-04 | 1.94e-03 | 35 |
| GO:000716331 | Liver | Cyst | establishment or maintenance of cell polarity | 17/496 | 218/18723 | 7.45e-05 | 3.66e-03 | 17 |
| GO:190290332 | Liver | Cyst | regulation of supramolecular fiber organization | 22/496 | 383/18723 | 6.04e-04 | 1.73e-02 | 22 |
| GO:000701532 | Liver | Cyst | actin filament organization | 24/496 | 442/18723 | 7.70e-04 | 2.07e-02 | 24 |
| GO:003227332 | Liver | Cyst | positive regulation of protein polymerization | 11/496 | 138/18723 | 1.13e-03 | 2.87e-02 | 11 |
| GO:190290532 | Liver | Cyst | positive regulation of supramolecular fiber organization | 14/496 | 209/18723 | 1.41e-03 | 3.41e-02 | 14 |
| GO:005125832 | Liver | Cyst | protein polymerization | 17/496 | 297/18723 | 2.53e-03 | 4.87e-02 | 17 |
| GO:004325420 | Oral cavity | OSCC | regulation of protein-containing complex assembly | 255/7305 | 428/18723 | 2.94e-18 | 3.15e-16 | 255 |
| 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 |
| 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 15 16 |
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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 |
| ARPC5 | SNV | Missense_Mutation | c.79G>A | p.Glu27Lys | p.E27K | O15511 | protein_coding | deleterious(0.05) | benign(0.387) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ARPC5 | insertion | Nonsense_Mutation | novel | c.404_405insTCTAAAACAAACCACCTGACCAAGAGG | p.Leu136_Ala137insLysGlnThrThrTerProArgGlyLeu | p.L136_A137insKQTT*PRGL | O15511 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| ARPC5 | insertion | Nonsense_Mutation | novel | c.403-1_403insTTATAAATATCGAGTA | p.Ala135LeufsTer2 | p.A135Lfs*2 | O15511 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| ARPC5 | SNV | Missense_Mutation | c.115N>A | p.Glu39Lys | p.E39K | O15511 | protein_coding | tolerated(0.08) | possibly_damaging(0.55) | TCGA-DS-A0VN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| ARPC5 | SNV | Missense_Mutation | novel | c.259N>G | p.Ile87Val | p.I87V | O15511 | protein_coding | tolerated(0.44) | benign(0.005) | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| ARPC5 | SNV | Missense_Mutation | c.197N>A | p.Pro66His | p.P66H | O15511 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ARPC5 | SNV | Missense_Mutation | novel | c.288N>T | p.Lys96Asn | p.K96N | O15511 | protein_coding | tolerated(0.21) | possibly_damaging(0.524) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ARPC5 | SNV | Missense_Mutation | novel | c.305N>G | p.Asp102Gly | p.D102G | O15511 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARPC5 | SNV | Missense_Mutation | c.452G>T | p.Arg151Ile | p.R151I | O15511 | protein_coding | deleterious(0) | probably_damaging(0.956) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| ARPC5 | SNV | Missense_Mutation | novel | c.299N>T | p.Ser100Phe | p.S100F | O15511 | protein_coding | deleterious(0) | possibly_damaging(0.905) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 |
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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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