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Gene: SYNJ2 |
Gene summary for SYNJ2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SYNJ2 | Gene ID | 8871 |
| Gene name | synaptojanin 2 | |
| Gene Alias | INPP5H | |
| Cytomap | 6q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | A0A1W2PR85 |
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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 |
| 8871 | SYNJ2 | A015-C-002 | Human | Colorectum | FAP | 2.41e-12 | -6.00e-01 | -0.0763 |
| 8871 | SYNJ2 | A001-C-203 | Human | Colorectum | FAP | 1.61e-07 | -2.22e-01 | -0.0481 |
| 8871 | SYNJ2 | A002-C-116 | Human | Colorectum | FAP | 2.61e-28 | -5.20e-01 | -0.0452 |
| 8871 | SYNJ2 | A014-C-008 | Human | Colorectum | FAP | 1.54e-09 | -3.97e-01 | -0.191 |
| 8871 | SYNJ2 | A018-E-020 | Human | Colorectum | FAP | 8.53e-16 | -4.55e-01 | -0.2034 |
| 8871 | SYNJ2 | F034 | Human | Colorectum | FAP | 2.31e-16 | -3.71e-01 | -0.0665 |
| 8871 | SYNJ2 | F072B | Human | Colorectum | FAP | 1.06e-03 | -8.82e-02 | 0.257 |
| 8871 | SYNJ2 | CRC-1-8810 | Human | Colorectum | CRC | 1.34e-02 | -1.66e-01 | 0.6257 |
| 8871 | SYNJ2 | CRC-3-11773 | Human | Colorectum | CRC | 2.04e-06 | -2.81e-01 | 0.2564 |
| 8871 | SYNJ2 | HCC1_Meng | Human | Liver | HCC | 2.43e-19 | -5.98e-02 | 0.0246 |
| 8871 | SYNJ2 | HCC2_Meng | Human | Liver | HCC | 1.63e-06 | -2.67e-02 | 0.0107 |
| 8871 | SYNJ2 | HCC2 | Human | Liver | HCC | 5.24e-08 | 3.76e+00 | 0.5341 |
| 8871 | SYNJ2 | S027 | Human | Liver | HCC | 2.17e-05 | 9.11e-01 | 0.2446 |
| 8871 | SYNJ2 | S028 | Human | Liver | HCC | 1.08e-15 | 8.95e-01 | 0.2503 |
| 8871 | SYNJ2 | S029 | Human | Liver | HCC | 1.19e-09 | 7.53e-01 | 0.2581 |
| 8871 | SYNJ2 | GSM5252126_BPH283PrGF_Via | Human | Prostate | BPH | 1.77e-02 | 3.71e-01 | -0.1771 |
| 8871 | SYNJ2 | GSM5252130_BPH340PrGF_Via | Human | Prostate | BPH | 9.43e-08 | 5.33e-01 | -0.1972 |
| 8871 | SYNJ2 | GSM5252132_BPH389PrGF | Human | Prostate | BPH | 4.72e-05 | 8.04e-01 | -0.2247 |
| 8871 | SYNJ2 | GSM5252133_BPH389PrSF | Human | Prostate | BPH | 2.91e-03 | 7.15e-01 | -0.2027 |
| 8871 | SYNJ2 | GSM5252134_BPH511PrG_Fcol_3GEX | Human | Prostate | BPH | 9.07e-03 | 4.06e-01 | -0.1433 |
| Page: 1 2 3 4 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0007163 | Colorectum | AD | establishment or maintenance of cell polarity | 77/3918 | 218/18723 | 5.72e-07 | 2.08e-05 | 77 |
| GO:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
| GO:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0001667 | Colorectum | AD | ameboidal-type cell migration | 137/3918 | 475/18723 | 2.17e-05 | 4.33e-04 | 137 |
| GO:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
| GO:0044262 | Colorectum | AD | cellular carbohydrate metabolic process | 87/3918 | 283/18723 | 6.00e-05 | 1.01e-03 | 87 |
| GO:0090132 | Colorectum | AD | epithelium migration | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
| GO:0010632 | Colorectum | AD | regulation of epithelial cell migration | 88/3918 | 292/18723 | 1.19e-04 | 1.75e-03 | 88 |
| GO:0010631 | Colorectum | AD | epithelial cell migration | 104/3918 | 357/18723 | 1.33e-04 | 1.90e-03 | 104 |
| GO:0030258 | Colorectum | AD | lipid modification | 67/3918 | 212/18723 | 1.66e-04 | 2.27e-03 | 67 |
| GO:0090130 | Colorectum | AD | tissue migration | 105/3918 | 365/18723 | 2.10e-04 | 2.77e-03 | 105 |
| GO:0045197 | Colorectum | AD | establishment or maintenance of epithelial cell apical/basal polarity | 20/3918 | 44/18723 | 2.26e-04 | 2.94e-03 | 20 |
| GO:0035088 | Colorectum | AD | establishment or maintenance of apical/basal cell polarity | 21/3918 | 49/18723 | 4.31e-04 | 4.82e-03 | 21 |
| GO:0061245 | Colorectum | AD | establishment or maintenance of bipolar cell polarity | 21/3918 | 49/18723 | 4.31e-04 | 4.82e-03 | 21 |
| GO:0043409 | Colorectum | AD | negative regulation of MAPK cascade | 57/3918 | 180/18723 | 4.61e-04 | 5.14e-03 | 57 |
| GO:0050673 | Colorectum | AD | epithelial cell proliferation | 119/3918 | 437/18723 | 8.75e-04 | 8.51e-03 | 119 |
| GO:0043542 | Colorectum | AD | endothelial cell migration | 78/3918 | 279/18723 | 2.97e-03 | 2.22e-02 | 78 |
| GO:0006650 | Colorectum | AD | glycerophospholipid metabolic process | 83/3918 | 306/18723 | 5.40e-03 | 3.55e-02 | 83 |
| GO:0006644 | Colorectum | AD | phospholipid metabolic process | 101/3918 | 383/18723 | 5.80e-03 | 3.67e-02 | 101 |
| GO:0046164 | Colorectum | AD | alcohol catabolic process | 20/3918 | 55/18723 | 6.03e-03 | 3.78e-02 | 20 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04070 | Colorectum | CRC | Phosphatidylinositol signaling system | 25/1091 | 97/8465 | 4.27e-04 | 4.60e-03 | 3.12e-03 | 25 |
| hsa00562 | Colorectum | CRC | Inositol phosphate metabolism | 18/1091 | 73/8465 | 4.38e-03 | 2.52e-02 | 1.71e-02 | 18 |
| hsa040701 | Colorectum | CRC | Phosphatidylinositol signaling system | 25/1091 | 97/8465 | 4.27e-04 | 4.60e-03 | 3.12e-03 | 25 |
| hsa005621 | Colorectum | CRC | Inositol phosphate metabolism | 18/1091 | 73/8465 | 4.38e-03 | 2.52e-02 | 1.71e-02 | 18 |
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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 |
| SYNJ2 | SNV | Missense_Mutation | c.2150C>T | p.Ser717Phe | p.S717F | O15056 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SYNJ2 | SNV | Missense_Mutation | c.4275G>C | p.Leu1425Phe | p.L1425F | O15056 | protein_coding | tolerated_low_confidence(0.06) | benign(0.296) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SYNJ2 | SNV | Missense_Mutation | c.1877C>T | p.Ser626Leu | p.S626L | O15056 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SYNJ2 | SNV | Missense_Mutation | novel | c.599N>T | p.Gln200Leu | p.Q200L | O15056 | protein_coding | deleterious(0) | possibly_damaging(0.801) | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD |
| SYNJ2 | insertion | In_Frame_Ins | novel | c.2162_2163insCTTCCTAGGAGTAGACACTCC | p.Phe722_Trp723insLeuGlyValAspThrProPhe | p.F722_W723insLGVDTPF | O15056 | protein_coding | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| SYNJ2 | insertion | Nonsense_Mutation | novel | c.600_601insTTCCCATATTTAATATGATTTTTAATCACTTATTGATCATGATT | p.Ala201PhefsTer6 | p.A201Ffs*6 | O15056 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| SYNJ2 | insertion | Frame_Shift_Ins | novel | c.2115_2116insCCATGTTTCTATGGACTCGTATGCGTCATAAGTGGGC | p.Lys706ProfsTer26 | p.K706Pfs*26 | O15056 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| SYNJ2 | insertion | Frame_Shift_Ins | novel | c.3204_3205insTTCCTAACGCAGACCTGTGCTGGCGATCGTGGAGGTGG | p.Lys1069PhefsTer62 | p.K1069Ffs*62 | O15056 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| SYNJ2 | deletion | Frame_Shift_Del | novel | c.2143_2147delGTTTT | p.Val715PhefsTer3 | p.V715Ffs*3 | O15056 | protein_coding | TCGA-BH-A0AV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | ||
| SYNJ2 | deletion | Frame_Shift_Del | c.3821delN | p.Pro1275LeufsTer4 | p.P1275Lfs*4 | O15056 | protein_coding | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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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