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Gene: KPNA4 |
Gene summary for KPNA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | KPNA4 | Gene ID | 3840 |
| Gene name | karyopherin subunit alpha 4 | |
| Gene Alias | IPOA3 | |
| Cytomap | 3q25.33 | |
| Gene Type | protein-coding | GO ID | GO:0006606 | UniProtAcc | O00629 |
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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 |
| 3840 | KPNA4 | GSM5353227_PA_PR5199-193K_Pool_1_2_3_S55_L002 | Human | Prostate | Tumor | 3.45e-02 | 8.86e-02 | 0.1602 |
| 3840 | KPNA4 | GSM5353240_PA_PR5254_T1_S15_L001 | Human | Prostate | Tumor | 3.61e-03 | -3.32e-02 | 0.1575 |
| 3840 | KPNA4 | GSM5353243_PA_PR5261_T1_S23_L002 | Human | Prostate | Tumor | 1.47e-05 | -2.37e-01 | 0.1545 |
| 3840 | KPNA4 | GSM5353244_PA_PR5261_T2_S24_L002 | Human | Prostate | Tumor | 5.98e-05 | -1.47e-01 | 0.1569 |
| 3840 | KPNA4 | P1_S1_AK | Human | Skin | AK | 1.48e-17 | 5.70e-01 | -0.3399 |
| 3840 | KPNA4 | P2_S3_AK | Human | Skin | AK | 5.84e-03 | 3.30e-01 | -0.3287 |
| 3840 | KPNA4 | P2_S4_SCCIS | Human | Skin | SCCIS | 8.20e-09 | 4.69e-01 | -0.3043 |
| 3840 | KPNA4 | P3_S6_AK | Human | Skin | AK | 1.70e-08 | 3.89e-01 | -0.3256 |
| 3840 | KPNA4 | P4_S8_cSCC | Human | Skin | cSCC | 2.10e-14 | 4.56e-01 | -0.3095 |
| 3840 | KPNA4 | P5_S10_cSCC | Human | Skin | cSCC | 1.34e-07 | 3.24e-01 | -0.299 |
| 3840 | KPNA4 | P1_cSCC | Human | Skin | cSCC | 5.20e-12 | 5.25e-01 | 0.0292 |
| 3840 | KPNA4 | P2_cSCC | Human | Skin | cSCC | 1.84e-02 | 2.58e-01 | -0.024 |
| 3840 | KPNA4 | P4_cSCC | Human | Skin | cSCC | 7.42e-15 | 6.01e-01 | -0.00290000000000005 |
| 3840 | KPNA4 | P10_cSCC | Human | Skin | cSCC | 6.09e-21 | 7.75e-01 | 0.1017 |
| 3840 | KPNA4 | Adj_PTCwithHT_6 | Human | Thyroid | HT | 1.25e-05 | -2.98e-01 | 0.02 |
| 3840 | KPNA4 | Adj_PTCwithHT_8 | Human | Thyroid | HT | 3.22e-05 | -3.16e-01 | 0.0267 |
| 3840 | KPNA4 | PTCwithHT_6 | Human | Thyroid | HT | 3.56e-02 | -2.82e-01 | 0.02 |
| 3840 | KPNA4 | PTCwithoutHT_2 | Human | Thyroid | PTC | 8.17e-03 | -2.86e-01 | 0.0419 |
| 3840 | KPNA4 | male-WTA | Human | Thyroid | PTC | 9.34e-30 | -1.89e-02 | 0.1037 |
| 3840 | KPNA4 | PTC01 | Human | Thyroid | PTC | 3.05e-13 | -4.48e-02 | 0.1899 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:00725949 | Cervix | CC | establishment of protein localization to organelle | 99/2311 | 422/18723 | 1.23e-10 | 2.11e-08 | 99 |
| GO:00069139 | Cervix | CC | nucleocytoplasmic transport | 71/2311 | 301/18723 | 4.04e-08 | 2.54e-06 | 71 |
| GO:00511699 | Cervix | CC | nuclear transport | 71/2311 | 301/18723 | 4.04e-08 | 2.54e-06 | 71 |
| GO:00345048 | Cervix | CC | protein localization to nucleus | 68/2311 | 290/18723 | 9.91e-08 | 5.25e-06 | 68 |
| GO:00170388 | Cervix | CC | protein import | 48/2311 | 206/18723 | 8.62e-06 | 1.98e-04 | 48 |
| GO:00511707 | Cervix | CC | import into nucleus | 38/2311 | 159/18723 | 3.98e-05 | 6.18e-04 | 38 |
| GO:00066067 | Cervix | CC | protein import into nucleus | 37/2311 | 155/18723 | 5.13e-05 | 7.71e-04 | 37 |
| GO:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0006913 | Colorectum | AD | nucleocytoplasmic transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0051169 | Colorectum | AD | nuclear transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0034504 | Colorectum | AD | protein localization to nucleus | 94/3918 | 290/18723 | 2.83e-06 | 8.09e-05 | 94 |
| GO:0017038 | Colorectum | AD | protein import | 67/3918 | 206/18723 | 6.34e-05 | 1.05e-03 | 67 |
| GO:0051170 | Colorectum | AD | import into nucleus | 53/3918 | 159/18723 | 1.76e-04 | 2.38e-03 | 53 |
| GO:0006606 | Colorectum | AD | protein import into nucleus | 51/3918 | 155/18723 | 3.29e-04 | 3.86e-03 | 51 |
| GO:00725942 | Colorectum | MSS | establishment of protein localization to organelle | 139/3467 | 422/18723 | 5.75e-13 | 1.12e-10 | 139 |
| GO:00069132 | Colorectum | MSS | nucleocytoplasmic transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
| GO:00511692 | Colorectum | MSS | nuclear transport | 99/3467 | 301/18723 | 1.35e-09 | 1.03e-07 | 99 |
| GO:00345042 | Colorectum | MSS | protein localization to nucleus | 92/3467 | 290/18723 | 3.66e-08 | 1.98e-06 | 92 |
| GO:00170382 | Colorectum | MSS | protein import | 65/3467 | 206/18723 | 4.28e-06 | 1.22e-04 | 65 |
| GO:00511702 | Colorectum | MSS | import into nucleus | 52/3467 | 159/18723 | 1.23e-05 | 2.87e-04 | 52 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513220 | Cervix | CC | Salmonella infection | 74/1267 | 249/8465 | 1.33e-09 | 2.54e-08 | 1.50e-08 | 74 |
| hsa05132110 | Cervix | CC | Salmonella infection | 74/1267 | 249/8465 | 1.33e-09 | 2.54e-08 | 1.50e-08 | 74 |
| hsa05132 | Colorectum | AD | Salmonella infection | 102/2092 | 249/8465 | 7.65e-09 | 1.28e-07 | 8.17e-08 | 102 |
| hsa051321 | Colorectum | AD | Salmonella infection | 102/2092 | 249/8465 | 7.65e-09 | 1.28e-07 | 8.17e-08 | 102 |
| hsa051324 | Colorectum | MSS | Salmonella infection | 92/1875 | 249/8465 | 5.23e-08 | 9.74e-07 | 5.97e-07 | 92 |
| hsa051325 | Colorectum | MSS | Salmonella infection | 92/1875 | 249/8465 | 5.23e-08 | 9.74e-07 | 5.97e-07 | 92 |
| hsa051328 | Colorectum | FAP | Salmonella infection | 67/1404 | 249/8465 | 2.04e-05 | 2.52e-04 | 1.53e-04 | 67 |
| hsa051329 | Colorectum | FAP | Salmonella infection | 67/1404 | 249/8465 | 2.04e-05 | 2.52e-04 | 1.53e-04 | 67 |
| hsa0513210 | Colorectum | CRC | Salmonella infection | 48/1091 | 249/8465 | 2.43e-03 | 1.69e-02 | 1.15e-02 | 48 |
| hsa05207 | Colorectum | CRC | Chemical carcinogenesis - receptor activation | 42/1091 | 212/8465 | 2.62e-03 | 1.75e-02 | 1.19e-02 | 42 |
| hsa0513211 | Colorectum | CRC | Salmonella infection | 48/1091 | 249/8465 | 2.43e-03 | 1.69e-02 | 1.15e-02 | 48 |
| hsa052071 | Colorectum | CRC | Chemical carcinogenesis - receptor activation | 42/1091 | 212/8465 | 2.62e-03 | 1.75e-02 | 1.19e-02 | 42 |
| hsa05132211 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa0301321 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
| hsa05132310 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa0301331 | Esophagus | ESCC | Nucleocytoplasmic transport | 89/4205 | 108/8465 | 1.20e-12 | 2.37e-11 | 1.21e-11 | 89 |
| hsa0513222 | Liver | Cirrhotic | Salmonella infection | 121/2530 | 249/8465 | 2.47e-10 | 5.13e-09 | 3.16e-09 | 121 |
| hsa0513232 | Liver | Cirrhotic | Salmonella infection | 121/2530 | 249/8465 | 2.47e-10 | 5.13e-09 | 3.16e-09 | 121 |
| hsa0513242 | Liver | HCC | Salmonella infection | 178/4020 | 249/8465 | 5.90e-15 | 1.98e-13 | 1.10e-13 | 178 |
| hsa03013 | Liver | HCC | Nucleocytoplasmic transport | 81/4020 | 108/8465 | 4.28e-09 | 6.83e-08 | 3.80e-08 | 81 |
| Page: 1 2 |
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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 |
| KPNA4 | SNV | Missense_Mutation | novel | c.1013C>G | p.Pro338Arg | p.P338R | O00629 | protein_coding | deleterious(0.04) | benign(0.012) | TCGA-A2-A0YD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| KPNA4 | SNV | Missense_Mutation | c.1363N>C | p.Glu455Gln | p.E455Q | O00629 | protein_coding | deleterious(0.01) | possibly_damaging(0.601) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| KPNA4 | SNV | Missense_Mutation | novel | c.304N>C | p.Asp102His | p.D102H | O00629 | protein_coding | deleterious(0.05) | probably_damaging(1) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| KPNA4 | SNV | Missense_Mutation | c.335N>C | p.Lys112Thr | p.K112T | O00629 | protein_coding | tolerated(0.12) | benign(0.021) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| KPNA4 | SNV | Missense_Mutation | novel | c.322N>A | p.Asp108Asn | p.D108N | O00629 | protein_coding | tolerated(0.25) | benign(0.429) | TCGA-AA-3872-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
| KPNA4 | SNV | Missense_Mutation | rs765202780 | c.308N>A | p.Arg103Gln | p.R103Q | O00629 | protein_coding | deleterious(0.01) | probably_damaging(0.958) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| KPNA4 | SNV | Missense_Mutation | c.86N>A | p.Arg29Gln | p.R29Q | O00629 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| KPNA4 | SNV | Missense_Mutation | c.1000N>T | p.Leu334Phe | p.L334F | O00629 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| KPNA4 | SNV | Missense_Mutation | novel | c.48N>T | p.Lys16Asn | p.K16N | O00629 | protein_coding | deleterious(0) | probably_damaging(0.939) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| KPNA4 | SNV | Missense_Mutation | c.86N>A | p.Arg29Gln | p.R29Q | O00629 | protein_coding | deleterious(0) | probably_damaging(0.99) | 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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