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Gene: NAP1L1 |
Gene summary for NAP1L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NAP1L1 | Gene ID | 4673 |
| Gene name | nucleosome assembly protein 1 like 1 | |
| Gene Alias | NAP1 | |
| Cytomap | 12q21.2 | |
| Gene Type | protein-coding | GO ID | GO:0006260 | UniProtAcc | B7Z2V4 |
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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 |
| 4673 | NAP1L1 | GSM4909285 | Human | Breast | IDC | 5.35e-04 | 3.32e-01 | 0.21 |
| 4673 | NAP1L1 | GSM4909286 | Human | Breast | IDC | 1.54e-06 | 3.70e-01 | 0.1081 |
| 4673 | NAP1L1 | GSM4909287 | Human | Breast | IDC | 1.75e-02 | -2.54e-01 | 0.2057 |
| 4673 | NAP1L1 | GSM4909294 | Human | Breast | IDC | 6.66e-07 | -1.18e-01 | 0.2022 |
| 4673 | NAP1L1 | GSM4909296 | Human | Breast | IDC | 2.49e-16 | -3.69e-01 | 0.1524 |
| 4673 | NAP1L1 | GSM4909297 | Human | Breast | IDC | 1.55e-30 | -1.74e-01 | 0.1517 |
| 4673 | NAP1L1 | GSM4909302 | Human | Breast | IDC | 4.84e-03 | -9.75e-02 | 0.1545 |
| 4673 | NAP1L1 | GSM4909304 | Human | Breast | IDC | 2.07e-05 | -1.88e-01 | 0.1636 |
| 4673 | NAP1L1 | GSM4909309 | Human | Breast | IDC | 8.34e-05 | -2.27e-01 | 0.0483 |
| 4673 | NAP1L1 | GSM4909311 | Human | Breast | IDC | 3.33e-61 | -6.52e-01 | 0.1534 |
| 4673 | NAP1L1 | GSM4909312 | Human | Breast | IDC | 5.53e-30 | -5.92e-01 | 0.1552 |
| 4673 | NAP1L1 | GSM4909313 | Human | Breast | IDC | 4.72e-05 | -2.40e-01 | 0.0391 |
| 4673 | NAP1L1 | GSM4909316 | Human | Breast | IDC | 1.58e-04 | -2.99e-01 | 0.21 |
| 4673 | NAP1L1 | GSM4909319 | Human | Breast | IDC | 2.14e-71 | -6.40e-01 | 0.1563 |
| 4673 | NAP1L1 | GSM4909320 | Human | Breast | IDC | 2.44e-20 | -7.23e-01 | 0.1575 |
| 4673 | NAP1L1 | GSM4909321 | Human | Breast | IDC | 3.60e-21 | -4.28e-01 | 0.1559 |
| 4673 | NAP1L1 | brca1 | Human | Breast | Precancer | 2.68e-07 | -2.40e-01 | -0.0338 |
| 4673 | NAP1L1 | brca2 | Human | Breast | Precancer | 6.98e-11 | -2.12e-01 | -0.024 |
| 4673 | NAP1L1 | brca3 | Human | Breast | Precancer | 7.87e-04 | -3.76e-02 | -0.0263 |
| 4673 | NAP1L1 | M2 | Human | Breast | IDC | 1.55e-06 | 1.41e-01 | 0.21 |
| 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 | ||
| 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:005196211 | Prostate | Tumor | positive regulation of nervous system development | 69/3246 | 272/18723 | 4.99e-04 | 3.67e-03 | 69 |
| GO:005196011 | Prostate | Tumor | regulation of nervous system development | 102/3246 | 443/18723 | 1.20e-03 | 7.60e-03 | 102 |
| GO:000633811 | Prostate | Tumor | chromatin remodeling | 63/3246 | 255/18723 | 1.73e-03 | 1.02e-02 | 63 |
| GO:000626012 | Skin | cSCC | DNA replication | 106/4864 | 260/18723 | 1.18e-07 | 2.77e-06 | 106 |
| GO:000632519 | Skin | cSCC | chromatin organization | 147/4864 | 409/18723 | 4.41e-06 | 6.52e-05 | 147 |
| GO:000633812 | Skin | cSCC | chromatin remodeling | 94/4864 | 255/18723 | 7.58e-05 | 7.26e-04 | 94 |
| GO:001072016 | Skin | cSCC | positive regulation of cell development | 105/4864 | 298/18723 | 2.30e-04 | 1.89e-03 | 105 |
| GO:00718241 | Skin | cSCC | protein-DNA complex subunit organization | 87/4864 | 241/18723 | 3.09e-04 | 2.47e-03 | 87 |
| GO:005076913 | Skin | cSCC | positive regulation of neurogenesis | 80/4864 | 225/18723 | 8.85e-04 | 6.07e-03 | 80 |
| GO:005076722 | Skin | cSCC | regulation of neurogenesis | 118/4864 | 364/18723 | 3.32e-03 | 1.81e-02 | 118 |
| GO:00711031 | Skin | cSCC | DNA conformation change | 96/4864 | 290/18723 | 3.87e-03 | 2.07e-02 | 96 |
| GO:005196213 | Skin | cSCC | positive regulation of nervous system development | 88/4864 | 272/18723 | 1.07e-02 | 4.66e-02 | 88 |
| GO:001072017 | Thyroid | HT | positive regulation of cell development | 40/1272 | 298/18723 | 2.85e-05 | 6.14e-04 | 40 |
| GO:00507699 | Thyroid | HT | positive regulation of neurogenesis | 29/1272 | 225/18723 | 6.69e-04 | 7.61e-03 | 29 |
| GO:00519627 | Thyroid | HT | positive regulation of nervous system development | 31/1272 | 272/18723 | 3.27e-03 | 2.58e-02 | 31 |
| GO:005076715 | Thyroid | HT | regulation of neurogenesis | 38/1272 | 364/18723 | 5.56e-03 | 3.64e-02 | 38 |
| GO:000632520 | Thyroid | PTC | chromatin organization | 183/5968 | 409/18723 | 2.55e-08 | 5.70e-07 | 183 |
| GO:001072018 | Thyroid | PTC | positive regulation of cell development | 138/5968 | 298/18723 | 1.13e-07 | 2.22e-06 | 138 |
| GO:005076914 | Thyroid | PTC | positive regulation of neurogenesis | 105/5968 | 225/18723 | 2.28e-06 | 3.05e-05 | 105 |
| GO:005076716 | Thyroid | PTC | regulation of neurogenesis | 156/5968 | 364/18723 | 5.86e-06 | 7.05e-05 | 156 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| NAP1L1 | SNV | Missense_Mutation | c.374N>T | p.Tyr125Phe | p.Y125F | P55209 | protein_coding | tolerated(0.09) | possibly_damaging(0.666) | TCGA-AO-A0J6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| NAP1L1 | SNV | Missense_Mutation | novel | c.85G>A | p.Glu29Lys | p.E29K | P55209 | protein_coding | tolerated(0.26) | possibly_damaging(0.899) | TCGA-AR-A2LN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | letrozole | SD |
| NAP1L1 | SNV | Missense_Mutation | c.37N>C | p.Asp13His | p.D13H | P55209 | protein_coding | deleterious(0.01) | probably_damaging(0.99) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NAP1L1 | SNV | Missense_Mutation | c.428N>T | p.Ser143Leu | p.S143L | P55209 | protein_coding | tolerated(0.15) | benign(0.009) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NAP1L1 | SNV | Missense_Mutation | c.898N>G | p.Phe300Val | p.F300V | P55209 | protein_coding | deleterious(0.01) | probably_damaging(0.967) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NAP1L1 | SNV | Missense_Mutation | novel | c.755N>G | p.Ile252Ser | p.I252S | P55209 | protein_coding | deleterious(0.03) | probably_damaging(0.992) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NAP1L1 | SNV | Missense_Mutation | novel | c.286N>G | p.Tyr96Asp | p.Y96D | P55209 | protein_coding | deleterious(0) | benign(0.053) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NAP1L1 | SNV | Missense_Mutation | c.952N>T | p.Ala318Ser | p.A318S | P55209 | protein_coding | tolerated(0.47) | benign(0.026) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| NAP1L1 | SNV | Missense_Mutation | c.1097N>G | p.Glu366Gly | p.E366G | P55209 | protein_coding | tolerated(0.14) | probably_damaging(0.954) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NAP1L1 | SNV | Missense_Mutation | novel | c.835N>T | p.His279Tyr | p.H279Y | P55209 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <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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