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Gene: LARGE2 |
Gene summary for LARGE2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LARGE2 | Gene ID | 120071 |
Gene name | LARGE xylosyl- and glucuronyltransferase 2 | |
Gene Alias | GYLTL1B | |
Cytomap | 11p11.2 | |
Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q8N3Y3 |
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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 |
120071 | LARGE2 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.01e-07 | 2.06e-01 | 0.096 |
120071 | LARGE2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.11e-09 | 2.73e-01 | 0.0674 |
120071 | LARGE2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.53e-19 | 4.00e-01 | 0.294 |
120071 | LARGE2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.00e-24 | 6.02e-01 | 0.3859 |
120071 | LARGE2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.19e-14 | 5.41e-01 | 0.2585 |
120071 | LARGE2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.98e-27 | 5.90e-01 | 0.3005 |
120071 | LARGE2 | S014 | Human | Liver | HCC | 1.24e-36 | 1.08e+00 | 0.2254 |
120071 | LARGE2 | S015 | Human | Liver | HCC | 1.81e-34 | 1.29e+00 | 0.2375 |
120071 | LARGE2 | S016 | Human | Liver | HCC | 1.32e-57 | 1.70e+00 | 0.2243 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0060249 | Colorectum | AD | anatomical structure homeostasis | 94/3918 | 314/18723 | 9.37e-05 | 1.42e-03 | 94 |
GO:0006486 | Colorectum | AD | protein glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
GO:0043413 | Colorectum | AD | macromolecule glycosylation | 64/3918 | 226/18723 | 4.86e-03 | 3.27e-02 | 64 |
GO:0070085 | Colorectum | AD | glycosylation | 67/3918 | 240/18723 | 5.78e-03 | 3.67e-02 | 67 |
GO:00602492 | Colorectum | MSS | anatomical structure homeostasis | 84/3467 | 314/18723 | 1.87e-04 | 2.64e-03 | 84 |
GO:0046716 | Colorectum | MSS | muscle cell cellular homeostasis | 9/3467 | 19/18723 | 3.88e-03 | 2.83e-02 | 9 |
GO:00064862 | Liver | HCC | protein glycosylation | 122/7958 | 226/18723 | 3.11e-04 | 2.21e-03 | 122 |
GO:00434132 | Liver | HCC | macromolecule glycosylation | 122/7958 | 226/18723 | 3.11e-04 | 2.21e-03 | 122 |
GO:00700852 | Liver | HCC | glycosylation | 128/7958 | 240/18723 | 4.35e-04 | 2.92e-03 | 128 |
GO:0009100 | Liver | HCC | glycoprotein metabolic process | 193/7958 | 387/18723 | 1.89e-03 | 9.62e-03 | 193 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
LARGE2 | SNV | Missense_Mutation | c.1592N>G | p.Tyr531Cys | p.Y531C | Q8N3Y3 | protein_coding | deleterious(0) | benign(0.18) | TCGA-CD-A4MJ-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | CR | |
LARGE2 | SNV | Missense_Mutation | c.997N>C | p.Ser333Pro | p.S333P | Q8N3Y3 | protein_coding | deleterious(0.03) | benign(0.078) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
LARGE2 | SNV | Missense_Mutation | novel | c.1489N>G | p.Pro497Ala | p.P497A | Q8N3Y3 | protein_coding | tolerated(0.69) | benign(0) | TCGA-HF-A5NB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | SD |
LARGE2 | SNV | Missense_Mutation | novel | c.1221G>T | p.Gln407His | p.Q407H | Q8N3Y3 | protein_coding | tolerated(0.15) | benign(0.017) | TCGA-VQ-A8P2-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unspecific | Complete Response | |
LARGE2 | SNV | Missense_Mutation | rs200132116 | c.929N>A | p.Arg310His | p.R310H | Q8N3Y3 | protein_coding | tolerated(0.09) | possibly_damaging(0.738) | TCGA-VQ-A91D-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
LARGE2 | SNV | Missense_Mutation | rs576172696 | c.1684N>T | p.Arg562Cys | p.R562C | Q8N3Y3 | protein_coding | deleterious(0) | probably_damaging(0.93) | TCGA-VQ-A91K-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | CR |
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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 |
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