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Gene: KRT2 |
Gene summary for KRT2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | KRT2 | Gene ID | 3849 |
Gene name | keratin 2 | |
Gene Alias | CK-2e | |
Cytomap | 12q13.13 | |
Gene Type | protein-coding | GO ID | GO:0001667 | UniProtAcc | P35908 |
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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 |
3849 | KRT2 | P4_S8_cSCC | Human | Skin | cSCC | 1.75e-20 | 3.71e-01 | -0.3095 |
3849 | KRT2 | cSCC_p11 | Human | Skin | cSCC | 8.41e-11 | 2.91e-01 | -0.2102 |
3849 | KRT2 | cSCC_p3 | Human | Skin | cSCC | 5.59e-19 | 6.90e-01 | -0.2085 |
3849 | KRT2 | cSCC_p7 | Human | Skin | cSCC | 1.05e-04 | 3.65e-01 | -0.2332 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Skin | AK: Actinic keratosis | |
cSCC: Cutaneous squamous cell carcinoma | ||
SCCIS:squamous cell carcinoma in situ |
∗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:0031667 | Colorectum | AD | response to nutrient levels | 138/3918 | 474/18723 | 1.22e-05 | 2.68e-04 | 138 |
GO:0050708 | Colorectum | AD | regulation of protein secretion | 83/3918 | 268/18723 | 6.59e-05 | 1.07e-03 | 83 |
GO:0009306 | Colorectum | AD | protein secretion | 105/3918 | 359/18723 | 1.05e-04 | 1.57e-03 | 105 |
GO:0035592 | Colorectum | AD | establishment of protein localization to extracellular region | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
GO:0042594 | Colorectum | AD | response to starvation | 63/3918 | 197/18723 | 1.77e-04 | 2.38e-03 | 63 |
GO:0071692 | Colorectum | AD | protein localization to extracellular region | 106/3918 | 368/18723 | 1.86e-04 | 2.49e-03 | 106 |
GO:0071496 | Colorectum | AD | cellular response to external stimulus | 94/3918 | 320/18723 | 1.98e-04 | 2.64e-03 | 94 |
GO:0009267 | Colorectum | AD | cellular response to starvation | 51/3918 | 156/18723 | 3.90e-04 | 4.44e-03 | 51 |
GO:0031668 | Colorectum | AD | cellular response to extracellular stimulus | 71/3918 | 246/18723 | 1.86e-03 | 1.52e-02 | 71 |
GO:0031669 | Colorectum | AD | cellular response to nutrient levels | 63/3918 | 215/18723 | 2.19e-03 | 1.73e-02 | 63 |
GO:00316671 | Colorectum | SER | response to nutrient levels | 106/2897 | 474/18723 | 3.94e-05 | 1.00e-03 | 106 |
GO:00507081 | Colorectum | SER | regulation of protein secretion | 63/2897 | 268/18723 | 3.42e-04 | 5.39e-03 | 63 |
GO:00093061 | Colorectum | SER | protein secretion | 79/2897 | 359/18723 | 5.99e-04 | 8.19e-03 | 79 |
GO:00355921 | Colorectum | SER | establishment of protein localization to extracellular region | 79/2897 | 360/18723 | 6.54e-04 | 8.77e-03 | 79 |
GO:00716921 | Colorectum | SER | protein localization to extracellular region | 80/2897 | 368/18723 | 8.13e-04 | 1.01e-02 | 80 |
GO:00425941 | Colorectum | SER | response to starvation | 47/2897 | 197/18723 | 1.31e-03 | 1.45e-02 | 47 |
GO:00714961 | Colorectum | SER | cellular response to external stimulus | 70/2897 | 320/18723 | 1.40e-03 | 1.53e-02 | 70 |
GO:00092671 | Colorectum | SER | cellular response to starvation | 38/2897 | 156/18723 | 2.45e-03 | 2.32e-02 | 38 |
GO:00316681 | Colorectum | SER | cellular response to extracellular stimulus | 54/2897 | 246/18723 | 4.26e-03 | 3.45e-02 | 54 |
GO:00316691 | Colorectum | SER | cellular response to nutrient levels | 48/2897 | 215/18723 | 4.82e-03 | 3.78e-02 | 48 |
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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 |
KRT2 | SNV | Missense_Mutation | c.1882N>C | p.Glu628Gln | p.E628Q | P35908 | protein_coding | deleterious_low_confidence(0) | benign(0.003) | TCGA-66-2771-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | CR | |
KRT2 | SNV | Missense_Mutation | c.344G>T | p.Gly115Val | p.G115V | P35908 | protein_coding | tolerated(0.07) | benign(0.311) | TCGA-96-A4JK-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | gemcitabine | CR | |
KRT2 | SNV | Missense_Mutation | novel | c.516G>C | p.Gln172His | p.Q172H | P35908 | protein_coding | deleterious(0.01) | possibly_damaging(0.566) | TCGA-BA-5152-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
KRT2 | SNV | Missense_Mutation | rs567369735 | c.1567N>T | p.Gly523Cys | p.G523C | P35908 | protein_coding | deleterious(0.04) | possibly_damaging(0.754) | TCGA-BA-5153-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unspecific | Xeloda | PD |
KRT2 | SNV | Missense_Mutation | novel | c.1414G>C | p.Ala472Pro | p.A472P | P35908 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-CQ-5327-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
KRT2 | SNV | Missense_Mutation | c.1078G>A | p.Ala360Thr | p.A360T | P35908 | protein_coding | tolerated(0.05) | possibly_damaging(0.752) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD | |
KRT2 | SNV | Missense_Mutation | rs60537449 | c.1427N>T | p.Glu476Val | p.E476V | P35908 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BR-4191-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | docetaxel | SD |
KRT2 | SNV | Missense_Mutation | c.473N>A | p.Ser158Asn | p.S158N | P35908 | protein_coding | tolerated(0.08) | possibly_damaging(0.638) | TCGA-BR-4362-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
KRT2 | SNV | Missense_Mutation | novel | c.1385N>G | p.Asp462Gly | p.D462G | P35908 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
KRT2 | SNV | Missense_Mutation | novel | c.778N>A | p.Leu260Ile | p.L260I | P35908 | protein_coding | deleterious(0.03) | benign(0.241) | TCGA-BR-7704-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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