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Gene: MICALL2 |
Gene summary for MICALL2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MICALL2 | Gene ID | 79778 |
| Gene name | MICAL like 2 | |
| Gene Alias | JRAB | |
| Cytomap | 7p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q6UWK3 |
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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 |
| 79778 | MICALL2 | C08 | Human | Oral cavity | OSCC | 5.65e-11 | 2.70e-01 | 0.1919 |
| 79778 | MICALL2 | C09 | Human | Oral cavity | OSCC | 1.63e-07 | 3.22e-01 | 0.1431 |
| 79778 | MICALL2 | LN46 | Human | Oral cavity | OSCC | 2.59e-17 | 6.06e-01 | 0.1666 |
| 79778 | MICALL2 | NEOLP-3 | Human | Oral cavity | NEOLP | 7.48e-06 | 1.91e-01 | -0.0191 |
| 79778 | MICALL2 | SYSMH1 | Human | Oral cavity | OSCC | 5.82e-10 | 1.43e-01 | 0.1127 |
| 79778 | MICALL2 | SYSMH2 | Human | Oral cavity | OSCC | 1.07e-06 | 2.12e-01 | 0.2326 |
| 79778 | MICALL2 | SYSMH3 | Human | Oral cavity | OSCC | 1.11e-13 | 1.86e-01 | 0.2442 |
| 79778 | MICALL2 | SYSMH4 | Human | Oral cavity | OSCC | 6.14e-04 | 4.39e-02 | 0.1226 |
| 79778 | MICALL2 | SYSMH5 | Human | Oral cavity | OSCC | 3.22e-10 | 1.11e-01 | 0.0647 |
| 79778 | MICALL2 | SYSMH6 | Human | Oral cavity | OSCC | 2.00e-04 | 1.27e-01 | 0.1275 |
| 79778 | MICALL2 | Pat01-B | Human | Stomach | GC | 9.06e-16 | 3.46e-01 | 0.5754 |
| 79778 | MICALL2 | Pat02-B | Human | Stomach | GC | 9.31e-10 | 8.79e-02 | 0.0368 |
| 79778 | MICALL2 | Pat03-B | Human | Stomach | GC | 8.67e-09 | 2.08e-01 | 0.3693 |
| 79778 | MICALL2 | Pat04-B | Human | Stomach | GC | 1.65e-05 | 1.37e-01 | -0.1483 |
| 79778 | MICALL2 | Pat06-B | Human | Stomach | GC | 3.07e-16 | 2.00e-01 | -0.1961 |
| 79778 | MICALL2 | Pat11-B | Human | Stomach | GC | 5.91e-07 | 2.11e-01 | -0.182 |
| 79778 | MICALL2 | Pat12-B | Human | Stomach | GC | 2.64e-05 | 1.61e-01 | 0.0325 |
| 79778 | MICALL2 | Pat15-B | Human | Stomach | GC | 7.68e-03 | 1.93e-01 | -0.0778 |
| 79778 | MICALL2 | Pat16-B | Human | Stomach | GC | 3.07e-03 | 2.51e-01 | 0.1918 |
| 79778 | MICALL2 | Pat17-B | Human | Stomach | GC | 1.67e-03 | 2.43e-01 | 0.3109 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| 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:0007015 | Colorectum | AD | actin filament organization | 167/3918 | 442/18723 | 1.65e-16 | 7.94e-14 | 167 |
| GO:1903829 | Colorectum | AD | positive regulation of cellular protein localization | 110/3918 | 276/18723 | 4.58e-13 | 8.44e-11 | 110 |
| GO:0006839 | Colorectum | AD | mitochondrial transport | 102/3918 | 254/18723 | 1.87e-12 | 3.08e-10 | 102 |
| GO:0008154 | Colorectum | AD | actin polymerization or depolymerization | 90/3918 | 218/18723 | 6.14e-12 | 8.23e-10 | 90 |
| GO:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0030041 | Colorectum | AD | actin filament polymerization | 81/3918 | 191/18723 | 1.35e-11 | 1.69e-09 | 81 |
| GO:0051258 | Colorectum | AD | protein polymerization | 112/3918 | 297/18723 | 1.85e-11 | 2.27e-09 | 112 |
| GO:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0045216 | Colorectum | AD | cell-cell junction organization | 80/3918 | 200/18723 | 5.57e-10 | 4.58e-08 | 80 |
| GO:1904951 | Colorectum | AD | positive regulation of establishment of protein localization | 112/3918 | 319/18723 | 2.55e-09 | 1.80e-07 | 112 |
| GO:0051222 | Colorectum | AD | positive regulation of protein transport | 106/3918 | 303/18723 | 8.45e-09 | 5.08e-07 | 106 |
| GO:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
| GO:0098876 | Colorectum | AD | vesicle-mediated transport to the plasma membrane | 57/3918 | 136/18723 | 2.30e-08 | 1.27e-06 | 57 |
| GO:0006605 | Colorectum | AD | protein targeting | 105/3918 | 314/18723 | 1.39e-07 | 6.44e-06 | 105 |
| GO:0090316 | Colorectum | AD | positive regulation of intracellular protein transport | 62/3918 | 160/18723 | 1.82e-07 | 7.79e-06 | 62 |
| GO:0032388 | Colorectum | AD | positive regulation of intracellular transport | 74/3918 | 202/18723 | 1.83e-07 | 7.80e-06 | 74 |
| GO:0070585 | Colorectum | AD | protein localization to mitochondrion | 51/3918 | 125/18723 | 3.40e-07 | 1.33e-05 | 51 |
| GO:0007043 | Colorectum | AD | cell-cell junction assembly | 57/3918 | 146/18723 | 4.18e-07 | 1.61e-05 | 57 |
| GO:0031589 | Colorectum | AD | cell-substrate adhesion | 116/3918 | 363/18723 | 4.68e-07 | 1.76e-05 | 116 |
| GO:0032386 | Colorectum | AD | regulation of intracellular transport | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04530 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa045301 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa045302 | Colorectum | SER | Tight junction | 59/1580 | 169/8465 | 3.24e-07 | 5.98e-06 | 4.34e-06 | 59 |
| hsa045303 | Colorectum | SER | Tight junction | 59/1580 | 169/8465 | 3.24e-07 | 5.98e-06 | 4.34e-06 | 59 |
| hsa0453039 | Esophagus | HGIN | Tight junction | 40/1383 | 169/8465 | 8.18e-03 | 4.71e-02 | 3.74e-02 | 40 |
| hsa04530115 | Esophagus | HGIN | Tight junction | 40/1383 | 169/8465 | 8.18e-03 | 4.71e-02 | 3.74e-02 | 40 |
| hsa04530211 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| hsa04530310 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| hsa0453042 | Liver | HCC | Tight junction | 110/4020 | 169/8465 | 2.45e-06 | 2.28e-05 | 1.27e-05 | 110 |
| hsa0453052 | Liver | HCC | Tight junction | 110/4020 | 169/8465 | 2.45e-06 | 2.28e-05 | 1.27e-05 | 110 |
| hsa0453030 | Oral cavity | OSCC | Tight junction | 102/3704 | 169/8465 | 8.68e-06 | 3.93e-05 | 2.00e-05 | 102 |
| hsa04530114 | Oral cavity | OSCC | Tight junction | 102/3704 | 169/8465 | 8.68e-06 | 3.93e-05 | 2.00e-05 | 102 |
| hsa0453045 | Oral cavity | NEOLP | Tight junction | 39/1112 | 169/8465 | 2.50e-04 | 1.62e-03 | 1.02e-03 | 39 |
| hsa0453055 | Oral cavity | NEOLP | Tight junction | 39/1112 | 169/8465 | 2.50e-04 | 1.62e-03 | 1.02e-03 | 39 |
| hsa0453012 | Stomach | GC | Tight junction | 33/708 | 169/8465 | 3.03e-06 | 4.65e-05 | 3.28e-05 | 33 |
| hsa0453013 | Stomach | GC | Tight junction | 33/708 | 169/8465 | 3.03e-06 | 4.65e-05 | 3.28e-05 | 33 |
| hsa0453021 | Stomach | CAG with IM | Tight junction | 32/640 | 169/8465 | 9.69e-07 | 1.62e-05 | 1.14e-05 | 32 |
| hsa0453031 | Stomach | CAG with IM | Tight junction | 32/640 | 169/8465 | 9.69e-07 | 1.62e-05 | 1.14e-05 | 32 |
| hsa0453041 | Stomach | CSG | Tight junction | 31/633 | 169/8465 | 2.29e-06 | 3.45e-05 | 2.48e-05 | 31 |
| hsa0453051 | Stomach | CSG | Tight junction | 31/633 | 169/8465 | 2.29e-06 | 3.45e-05 | 2.48e-05 | 31 |
| Page: 1 |
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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 |
| MICALL2 | SNV | Missense_Mutation | c.288G>C | p.Leu96Phe | p.L96F | Q8IY33 | protein_coding | deleterious(0.01) | possibly_damaging(0.906) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response | |
| MICALL2 | SNV | Missense_Mutation | novel | c.1862N>A | p.Pro621His | p.P621H | Q8IY33 | protein_coding | deleterious(0) | possibly_damaging(0.737) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| MICALL2 | SNV | Missense_Mutation | rs747674926 | c.1451N>G | p.Ser484Cys | p.S484C | Q8IY33 | protein_coding | tolerated(0.05) | benign(0.009) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| MICALL2 | insertion | Frame_Shift_Ins | rs751396826 | c.1284_1285insC | p.Gly429ArgfsTer61 | p.G429Rfs*61 | Q8IY33 | protein_coding | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| MICALL2 | SNV | Missense_Mutation | novel | c.1291A>G | p.Ser431Gly | p.S431G | Q8IY33 | protein_coding | tolerated(1) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| MICALL2 | SNV | Missense_Mutation | rs374682289 | c.1910N>A | p.Thr637Asn | p.T637N | Q8IY33 | protein_coding | tolerated(0.07) | benign(0.307) | TCGA-C5-A2M1-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| MICALL2 | SNV | Missense_Mutation | rs760862909 | c.1138G>A | p.Gly380Arg | p.G380R | Q8IY33 | protein_coding | tolerated(0.53) | benign(0.086) | TCGA-C5-A2M2-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| MICALL2 | SNV | Missense_Mutation | novel | c.362N>T | p.Ala121Val | p.A121V | Q8IY33 | protein_coding | deleterious(0) | benign(0.042) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| MICALL2 | SNV | Missense_Mutation | c.2625N>A | p.Met875Ile | p.M875I | Q8IY33 | protein_coding | deleterious(0.01) | benign(0.231) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| MICALL2 | SNV | Missense_Mutation | c.1010N>A | p.Arg337His | p.R337H | Q8IY33 | protein_coding | tolerated(0.17) | benign(0) | TCGA-LP-A7HU-01 | Cervix | cervical & endocervical cancer | 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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