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Gene: LUC7L3 |
Gene summary for LUC7L3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LUC7L3 | Gene ID | 51747 |
| Gene name | LUC7 like 3 pre-mRNA splicing factor | |
| Gene Alias | CRA | |
| Cytomap | 17q21.33 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | J3KPP4 |
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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 |
| 51747 | LUC7L3 | GSM4909286 | Human | Breast | IDC | 1.41e-18 | 4.26e-01 | 0.1081 |
| 51747 | LUC7L3 | GSM4909294 | Human | Breast | IDC | 2.75e-06 | -2.44e-01 | 0.2022 |
| 51747 | LUC7L3 | GSM4909296 | Human | Breast | IDC | 6.56e-26 | -4.71e-01 | 0.1524 |
| 51747 | LUC7L3 | GSM4909297 | Human | Breast | IDC | 2.23e-21 | -2.05e-01 | 0.1517 |
| 51747 | LUC7L3 | GSM4909298 | Human | Breast | IDC | 2.91e-12 | 4.28e-01 | 0.1551 |
| 51747 | LUC7L3 | GSM4909301 | Human | Breast | IDC | 1.67e-02 | -1.50e-02 | 0.1577 |
| 51747 | LUC7L3 | GSM4909304 | Human | Breast | IDC | 1.00e-03 | -3.05e-01 | 0.1636 |
| 51747 | LUC7L3 | GSM4909309 | Human | Breast | IDC | 1.10e-02 | -1.62e-02 | 0.0483 |
| 51747 | LUC7L3 | GSM4909311 | Human | Breast | IDC | 5.39e-40 | -5.67e-01 | 0.1534 |
| 51747 | LUC7L3 | GSM4909312 | Human | Breast | IDC | 6.79e-18 | -3.04e-01 | 0.1552 |
| 51747 | LUC7L3 | GSM4909313 | Human | Breast | IDC | 1.17e-03 | -2.65e-01 | 0.0391 |
| 51747 | LUC7L3 | GSM4909315 | Human | Breast | IDC | 7.25e-07 | -3.16e-01 | 0.21 |
| 51747 | LUC7L3 | GSM4909316 | Human | Breast | IDC | 1.38e-03 | -4.08e-01 | 0.21 |
| 51747 | LUC7L3 | GSM4909317 | Human | Breast | IDC | 5.22e-03 | 2.80e-01 | 0.1355 |
| 51747 | LUC7L3 | GSM4909319 | Human | Breast | IDC | 1.58e-53 | -2.88e-01 | 0.1563 |
| 51747 | LUC7L3 | GSM4909320 | Human | Breast | IDC | 8.07e-08 | -4.95e-01 | 0.1575 |
| 51747 | LUC7L3 | GSM4909321 | Human | Breast | IDC | 4.72e-27 | -3.42e-01 | 0.1559 |
| 51747 | LUC7L3 | brca10 | Human | Breast | Precancer | 3.62e-03 | -3.71e-01 | -0.0029 |
| 51747 | LUC7L3 | M1 | Human | Breast | IDC | 4.13e-17 | 6.13e-01 | 0.1577 |
| 51747 | LUC7L3 | M2 | Human | Breast | IDC | 3.29e-02 | -1.88e-02 | 0.21 |
| 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 | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
| GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
| GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
| GO:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
| GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
| GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:002261314 | Breast | IDC | ribonucleoprotein complex biogenesis | 83/1434 | 463/18723 | 2.01e-13 | 5.20e-11 | 83 |
| GO:007182614 | Breast | IDC | ribonucleoprotein complex subunit organization | 52/1434 | 227/18723 | 5.18e-13 | 1.21e-10 | 52 |
| GO:002261814 | Breast | IDC | ribonucleoprotein complex assembly | 51/1434 | 220/18723 | 5.32e-13 | 1.21e-10 | 51 |
| GO:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
| GO:000037514 | Breast | IDC | RNA splicing, via transesterification reactions | 58/1434 | 324/18723 | 9.44e-10 | 9.58e-08 | 58 |
| GO:000037714 | Breast | IDC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:000039814 | Breast | IDC | mRNA splicing, via spliceosome | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:002261324 | Breast | DCIS | ribonucleoprotein complex biogenesis | 83/1390 | 463/18723 | 3.65e-14 | 1.09e-11 | 83 |
| GO:007182624 | Breast | DCIS | ribonucleoprotein complex subunit organization | 52/1390 | 227/18723 | 1.54e-13 | 3.95e-11 | 52 |
| GO:002261824 | Breast | DCIS | ribonucleoprotein complex assembly | 51/1390 | 220/18723 | 1.60e-13 | 3.95e-11 | 51 |
| GO:000838024 | Breast | DCIS | RNA splicing | 73/1390 | 434/18723 | 3.05e-11 | 5.08e-09 | 73 |
| GO:000037524 | Breast | DCIS | RNA splicing, via transesterification reactions | 58/1390 | 324/18723 | 2.89e-10 | 3.34e-08 | 58 |
| GO:000037724 | Breast | DCIS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1390 | 320/18723 | 5.01e-10 | 5.35e-08 | 57 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 |
| LUC7L3 | SNV | Missense_Mutation | c.685N>C | p.Glu229Gln | p.E229Q | protein_coding | tolerated(0.06) | benign(0.293) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| LUC7L3 | SNV | Missense_Mutation | novel | c.1178N>T | p.Ser393Phe | p.S393F | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LUC7L3 | SNV | Missense_Mutation | c.620G>A | p.Arg207Gln | p.R207Q | protein_coding | deleterious(0.04) | probably_damaging(0.979) | TCGA-BH-A0DS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| LUC7L3 | deletion | Frame_Shift_Del | c.228delC | p.Phe76LeufsTer2 | p.F76Lfs*2 | protein_coding | TCGA-E9-A248-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||||
| LUC7L3 | SNV | Missense_Mutation | novel | c.1361N>A | p.Ser454Asn | p.S454N | protein_coding | tolerated_low_confidence(0.18) | probably_damaging(0.995) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LUC7L3 | SNV | Missense_Mutation | c.607G>A | p.Asp203Asn | p.D203N | protein_coding | deleterious(0) | benign(0.019) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LUC7L3 | SNV | Missense_Mutation | c.781N>T | p.Arg261Trp | p.R261W | protein_coding | deleterious(0) | possibly_damaging(0.645) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| LUC7L3 | SNV | Missense_Mutation | c.781C>T | p.Arg261Trp | p.R261W | protein_coding | deleterious(0) | possibly_damaging(0.645) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
| LUC7L3 | SNV | Missense_Mutation | novel | c.107N>C | p.Lys36Thr | p.K36T | protein_coding | tolerated(0.31) | possibly_damaging(0.482) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| LUC7L3 | SNV | Missense_Mutation | c.530N>T | p.Ser177Leu | p.S177L | protein_coding | tolerated(0.13) | probably_damaging(0.979) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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