|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: LCN6 |
Gene summary for LCN6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LCN6 | Gene ID | 158062 |
| Gene name | lipocalin 6 | |
| Gene Alias | LCN5 | |
| Cytomap | 9q34.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A024R8I9 |
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 |
| 158062 | LCN6 | PTC01 | Human | Thyroid | PTC | 1.72e-28 | 9.98e-01 | 0.1899 |
| 158062 | LCN6 | PTC06 | Human | Thyroid | PTC | 2.51e-21 | 1.40e+00 | 0.2057 |
| 158062 | LCN6 | PTC07 | Human | Thyroid | PTC | 4.25e-14 | 4.13e-01 | 0.2044 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:003253520 | Esophagus | ESCC | regulation of cellular component size | 227/8552 | 383/18723 | 4.77e-08 | 8.60e-07 | 227 |
| GO:00083619 | Esophagus | ESCC | regulation of cell size | 107/8552 | 181/18723 | 1.81e-04 | 1.16e-03 | 107 |
| GO:000961216 | Esophagus | ESCC | response to mechanical stimulus | 124/8552 | 216/18723 | 3.30e-04 | 1.94e-03 | 124 |
| GO:003253522 | Liver | HCC | regulation of cellular component size | 217/7958 | 383/18723 | 1.28e-08 | 3.14e-07 | 217 |
| GO:00096124 | Liver | HCC | response to mechanical stimulus | 113/7958 | 216/18723 | 2.20e-03 | 1.10e-02 | 113 |
| GO:00083614 | Liver | HCC | regulation of cell size | 95/7958 | 181/18723 | 4.15e-03 | 1.81e-02 | 95 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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 |
| LCN6 | SNV | Missense_Mutation | rs776575106 | c.127C>T | p.Arg43Trp | p.R43W | P62502 | protein_coding | tolerated(0.18) | benign(0.009) | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD |
| LCN6 | insertion | Frame_Shift_Ins | novel | c.125_126insGT | p.Arg43SerfsTer12 | p.R43Sfs*12 | P62502 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| LCN6 | insertion | Frame_Shift_Ins | novel | c.124_125insGGGGGCTTCCCACGGCCCCTCTGCACCCC | p.Ser42TrpfsTer22 | p.S42Wfs*22 | P62502 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| LCN6 | SNV | Missense_Mutation | novel | c.307N>A | p.Gly103Ser | p.G103S | P62502 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LCN6 | SNV | Missense_Mutation | rs777381668 | c.169N>A | p.Val57Met | p.V57M | P62502 | protein_coding | deleterious(0.01) | benign(0.139) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LCN6 | SNV | Missense_Mutation | c.398C>T | p.Thr133Ile | p.T133I | P62502 | protein_coding | tolerated(0.07) | probably_damaging(0.966) | TCGA-AF-A56N-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
| LCN6 | SNV | Missense_Mutation | rs770143346 | c.272N>A | p.Arg91Gln | p.R91Q | P62502 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LCN6 | SNV | Missense_Mutation | c.332N>T | p.Ala111Val | p.A111V | P62502 | protein_coding | deleterious(0) | benign(0.171) | TCGA-A5-A0VP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LCN6 | SNV | Missense_Mutation | novel | c.155N>G | p.Asp52Gly | p.D52G | P62502 | protein_coding | tolerated(0.1) | benign(0.22) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LCN6 | SNV | Missense_Mutation | rs770143346 | c.272N>A | p.Arg91Gln | p.R91Q | P62502 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-BK-A6W3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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 |