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Gene: CANX |
Gene summary for CANX |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CANX | Gene ID | 821 |
| Gene name | calnexin | |
| Gene Alias | CNX | |
| Cytomap | 5q35.3 | |
| Gene Type | protein-coding | GO ID | GO:0006457 | UniProtAcc | P27824 |
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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 |
| 821 | CANX | GSM4909280 | Human | Breast | Precancer | 9.60e-03 | -5.07e-01 | 0.0305 |
| 821 | CANX | GSM4909282 | Human | Breast | IDC | 7.98e-06 | -3.57e-01 | -0.0288 |
| 821 | CANX | GSM4909285 | Human | Breast | IDC | 1.11e-02 | -1.36e-01 | 0.21 |
| 821 | CANX | GSM4909286 | Human | Breast | IDC | 2.09e-12 | -4.38e-01 | 0.1081 |
| 821 | CANX | GSM4909287 | Human | Breast | IDC | 4.74e-03 | 4.71e-03 | 0.2057 |
| 821 | CANX | GSM4909291 | Human | Breast | IDC | 4.59e-05 | 2.95e-01 | 0.1753 |
| 821 | CANX | GSM4909294 | Human | Breast | IDC | 6.64e-07 | -3.55e-01 | 0.2022 |
| 821 | CANX | GSM4909296 | Human | Breast | IDC | 6.44e-13 | -2.92e-01 | 0.1524 |
| 821 | CANX | GSM4909297 | Human | Breast | IDC | 1.13e-16 | -3.57e-01 | 0.1517 |
| 821 | CANX | GSM4909298 | Human | Breast | IDC | 1.48e-02 | 5.65e-02 | 0.1551 |
| 821 | CANX | GSM4909309 | Human | Breast | IDC | 2.83e-03 | -6.20e-02 | 0.0483 |
| 821 | CANX | GSM4909311 | Human | Breast | IDC | 7.73e-36 | -5.13e-01 | 0.1534 |
| 821 | CANX | GSM4909312 | Human | Breast | IDC | 9.83e-11 | -1.06e-01 | 0.1552 |
| 821 | CANX | GSM4909313 | Human | Breast | IDC | 3.23e-05 | -5.39e-03 | 0.0391 |
| 821 | CANX | GSM4909315 | Human | Breast | IDC | 1.41e-04 | -4.02e-01 | 0.21 |
| 821 | CANX | GSM4909316 | Human | Breast | IDC | 5.86e-09 | -5.88e-01 | 0.21 |
| 821 | CANX | GSM4909319 | Human | Breast | IDC | 6.87e-47 | -6.36e-01 | 0.1563 |
| 821 | CANX | GSM4909320 | Human | Breast | IDC | 1.68e-15 | -5.18e-01 | 0.1575 |
| 821 | CANX | GSM4909321 | Human | Breast | IDC | 4.83e-16 | -3.34e-01 | 0.1559 |
| 821 | CANX | brca1 | Human | Breast | Precancer | 2.92e-02 | -2.80e-01 | -0.0338 |
| 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 | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00064578 | Breast | Precancer | protein folding | 43/1080 | 212/18723 | 3.48e-13 | 7.45e-11 | 43 |
| GO:00160329 | Breast | Precancer | viral process | 58/1080 | 415/18723 | 3.42e-10 | 3.16e-08 | 58 |
| GO:00349769 | Breast | Precancer | response to endoplasmic reticulum stress | 38/1080 | 256/18723 | 7.89e-08 | 4.60e-06 | 38 |
| GO:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:00075688 | Breast | Precancer | aging | 41/1080 | 339/18723 | 5.95e-06 | 1.71e-04 | 41 |
| GO:00349758 | Breast | Precancer | protein folding in endoplasmic reticulum | 6/1080 | 11/18723 | 1.31e-05 | 3.30e-04 | 6 |
| GO:00431619 | Breast | Precancer | proteasome-mediated ubiquitin-dependent protein catabolic process | 42/1080 | 412/18723 | 2.49e-04 | 3.72e-03 | 42 |
| GO:00068986 | Breast | Precancer | receptor-mediated endocytosis | 27/1080 | 244/18723 | 9.01e-04 | 1.03e-02 | 27 |
| GO:00716926 | Breast | Precancer | protein localization to extracellular region | 34/1080 | 368/18723 | 4.65e-03 | 3.58e-02 | 34 |
| GO:00093067 | Breast | Precancer | protein secretion | 33/1080 | 359/18723 | 5.65e-03 | 4.08e-02 | 33 |
| GO:00355927 | Breast | Precancer | establishment of protein localization to extracellular region | 33/1080 | 360/18723 | 5.89e-03 | 4.21e-02 | 33 |
| GO:001603214 | Breast | IDC | viral process | 75/1434 | 415/18723 | 1.98e-12 | 4.02e-10 | 75 |
| GO:000645713 | Breast | IDC | protein folding | 47/1434 | 212/18723 | 2.31e-11 | 3.86e-09 | 47 |
| GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:003497614 | Breast | IDC | response to endoplasmic reticulum stress | 43/1434 | 256/18723 | 8.42e-07 | 3.82e-05 | 43 |
| GO:000756813 | Breast | IDC | aging | 52/1434 | 339/18723 | 1.14e-06 | 5.10e-05 | 52 |
| GO:004316114 | Breast | IDC | proteasome-mediated ubiquitin-dependent protein catabolic process | 57/1434 | 412/18723 | 9.55e-06 | 2.68e-04 | 57 |
| GO:003497513 | Breast | IDC | protein folding in endoplasmic reticulum | 6/1434 | 11/18723 | 6.59e-05 | 1.35e-03 | 6 |
| GO:000689813 | Breast | IDC | receptor-mediated endocytosis | 35/1434 | 244/18723 | 2.38e-04 | 3.75e-03 | 35 |
| GO:007169212 | Breast | IDC | protein localization to extracellular region | 42/1434 | 368/18723 | 6.13e-03 | 4.38e-02 | 42 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414118 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
| hsa0461218 | Breast | Precancer | Antigen processing and presentation | 19/684 | 78/8465 | 9.61e-06 | 1.12e-04 | 8.62e-05 | 19 |
| hsa0516618 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
| hsa0414119 | Breast | Precancer | Protein processing in endoplasmic reticulum | 33/684 | 174/8465 | 2.78e-06 | 3.83e-05 | 2.94e-05 | 33 |
| hsa0461219 | Breast | Precancer | Antigen processing and presentation | 19/684 | 78/8465 | 9.61e-06 | 1.12e-04 | 8.62e-05 | 19 |
| hsa0516619 | Breast | Precancer | Human T-cell leukemia virus 1 infection | 33/684 | 222/8465 | 4.29e-04 | 3.31e-03 | 2.53e-03 | 33 |
| hsa0461223 | Breast | IDC | Antigen processing and presentation | 24/867 | 78/8465 | 4.61e-07 | 8.33e-06 | 6.23e-06 | 24 |
| hsa0414522 | Breast | IDC | Phagosome | 34/867 | 152/8465 | 8.00e-06 | 9.99e-05 | 7.48e-05 | 34 |
| hsa0414124 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
| hsa0516624 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
| hsa0461233 | Breast | IDC | Antigen processing and presentation | 24/867 | 78/8465 | 4.61e-07 | 8.33e-06 | 6.23e-06 | 24 |
| hsa0414532 | Breast | IDC | Phagosome | 34/867 | 152/8465 | 8.00e-06 | 9.99e-05 | 7.48e-05 | 34 |
| hsa0414134 | Breast | IDC | Protein processing in endoplasmic reticulum | 36/867 | 174/8465 | 2.73e-05 | 2.86e-04 | 2.14e-04 | 36 |
| hsa0516634 | Breast | IDC | Human T-cell leukemia virus 1 infection | 40/867 | 222/8465 | 2.52e-04 | 2.21e-03 | 1.66e-03 | 40 |
| hsa0461242 | Breast | DCIS | Antigen processing and presentation | 25/846 | 78/8465 | 6.75e-08 | 1.28e-06 | 9.45e-07 | 25 |
| hsa0414541 | Breast | DCIS | Phagosome | 35/846 | 152/8465 | 1.67e-06 | 2.45e-05 | 1.81e-05 | 35 |
| hsa0414143 | Breast | DCIS | Protein processing in endoplasmic reticulum | 36/846 | 174/8465 | 1.60e-05 | 1.91e-04 | 1.41e-04 | 36 |
| hsa0516642 | Breast | DCIS | Human T-cell leukemia virus 1 infection | 41/846 | 222/8465 | 7.03e-05 | 6.88e-04 | 5.07e-04 | 41 |
| hsa0461252 | Breast | DCIS | Antigen processing and presentation | 25/846 | 78/8465 | 6.75e-08 | 1.28e-06 | 9.45e-07 | 25 |
| hsa0414551 | Breast | DCIS | Phagosome | 35/846 | 152/8465 | 1.67e-06 | 2.45e-05 | 1.81e-05 | 35 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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 |
| CANX | MVA | Stomach | CAG | INHBB,HSP90B1,ST3GAL4, etc. | 9.29e-02 |  |
| CANX | LYMEND | Stomach | CSG | INHBB,HSP90B1,ST3GAL4, etc. | 0.00e+00 |  |
| CANX | MYOFIB | Stomach | WIM | INHBB,HSP90B1,ST3GAL4, etc. | 1.23e-01 |  |
| CANX | MSC | Stomach | WIM | INHBB,HSP90B1,ST3GAL4, etc. | 8.59e-02 | |
| ∗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 |
| CANX | SNV | Missense_Mutation | novel | c.883N>C | p.Asp295His | p.D295H | P27824 | protein_coding | deleterious(0.02) | probably_damaging(0.992) | TCGA-56-7731-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CANX | SNV | Missense_Mutation | c.1640N>T | p.Lys547Ile | p.K547I | P27824 | protein_coding | tolerated(0.07) | benign(0.017) | TCGA-70-6722-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | PD | |
| CANX | SNV | Missense_Mutation | novel | c.1556C>A | p.Ala519Glu | p.A519E | P27824 | protein_coding | tolerated(0.61) | benign(0.001) | TCGA-94-A5I4-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| CANX | SNV | Missense_Mutation | novel | c.319G>A | p.Glu107Lys | p.E107K | P27824 | protein_coding | deleterious(0) | benign(0.206) | TCGA-O2-A52S-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| CANX | SNV | Missense_Mutation | novel | c.1038N>T | p.Met346Ile | p.M346I | P27824 | protein_coding | tolerated(0.12) | benign(0.033) | TCGA-CN-6010-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | PD |
| CANX | SNV | Missense_Mutation | novel | c.879C>G | p.Ile293Met | p.I293M | P27824 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-CV-A45W-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| CANX | SNV | Missense_Mutation | novel | c.100N>A | p.Asp34Asn | p.D34N | P27824 | protein_coding | tolerated(0.13) | benign(0.307) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| CANX | insertion | Frame_Shift_Ins | novel | c.1011_1012insTATTCTA | p.Lys338TyrfsTer5 | p.K338Yfs*5 | P27824 | protein_coding | TCGA-H7-8502-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | unknown | SD | ||
| CANX | SNV | Missense_Mutation | c.59N>T | p.Ala20Val | p.A20V | P27824 | protein_coding | tolerated(0.33) | benign(0.007) | TCGA-HU-A4GT-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Chemotherapy | copolang | SD | |
| CANX | SNV | Missense_Mutation | c.158C>A | p.Pro53His | p.P53H | P27824 | protein_coding | tolerated(0.07) | possibly_damaging(0.864) | TCGA-HU-A4H8-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | didox | PD |
| Page: 1 2 3 4 5 6 7 |
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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 |
| 821 | CANX | NA | MPO | MYELOPEROXIDASE | 11818449 |
| Page: 1 |
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