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Gene: SPINK4 |
Gene summary for SPINK4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SPINK4 | Gene ID | 27290 |
| Gene name | serine peptidase inhibitor Kazal type 4 | |
| Gene Alias | HEL136 | |
| Cytomap | 9p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | O60575 |
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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 |
| 27290 | SPINK4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.90e-06 | 6.64e-01 | -0.1808 |
| 27290 | SPINK4 | HTA11_78_2000001011 | Human | Colorectum | AD | 8.72e-07 | 6.69e-01 | -0.1088 |
| 27290 | SPINK4 | HTA11_2112_2000001011 | Human | Colorectum | SER | 5.62e-06 | 2.18e+00 | -0.2196 |
| 27290 | SPINK4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.03e-07 | 9.91e-01 | -0.1207 |
| 27290 | SPINK4 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.87e-40 | 2.29e+00 | -0.1464 |
| 27290 | SPINK4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 5.20e-03 | 6.16e-01 | -0.059 |
| 27290 | SPINK4 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.28e-02 | 1.21e-01 | 0.096 |
| 27290 | SPINK4 | Pat01-B | Human | Stomach | GC | 1.73e-11 | 5.72e-01 | 0.5754 |
| 27290 | SPINK4 | Pat02-B | Human | Stomach | GC | 1.90e-08 | 2.89e-01 | 0.0368 |
| 27290 | SPINK4 | Pat07-B | Human | Stomach | GC | 1.06e-04 | 4.63e-01 | 0.0935 |
| 27290 | SPINK4 | Pat13-B | Human | Stomach | GC | 1.38e-23 | 1.16e+00 | 0.0555 |
| 27290 | SPINK4 | Pat16-B | Human | Stomach | GC | 4.99e-07 | 4.51e-01 | 0.1918 |
| 27290 | SPINK4 | Pat17-B | Human | Stomach | GC | 1.69e-09 | 5.37e-01 | 0.3109 |
| 27290 | SPINK4 | Pat19-B | Human | Stomach | GC | 2.29e-05 | 3.56e-01 | 0.0826 |
| 27290 | SPINK4 | SIM_1 | Human | Stomach | SIM | 3.03e-10 | 6.22e-01 | 0.3573 |
| 27290 | SPINK4 | SIM_2 | Human | Stomach | SIM | 3.57e-07 | 5.44e-01 | 0.3139 |
| 27290 | SPINK4 | SIM_4 | Human | Stomach | SIM | 1.39e-06 | 5.87e-01 | 0.2664 |
| Page: 1 |
| 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 | ||
| 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 |
| ∗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:0052547 | Colorectum | AD | regulation of peptidase activity | 137/3918 | 461/18723 | 4.12e-06 | 1.12e-04 | 137 |
| GO:0045861 | Colorectum | AD | negative regulation of proteolysis | 106/3918 | 351/18723 | 2.33e-05 | 4.57e-04 | 106 |
| GO:0052548 | Colorectum | AD | regulation of endopeptidase activity | 124/3918 | 432/18723 | 6.58e-05 | 1.07e-03 | 124 |
| GO:0009410 | Colorectum | AD | response to xenobiotic stimulus | 128/3918 | 462/18723 | 2.69e-04 | 3.31e-03 | 128 |
| GO:00525471 | Colorectum | SER | regulation of peptidase activity | 114/2897 | 461/18723 | 1.18e-07 | 7.17e-06 | 114 |
| GO:00458611 | Colorectum | SER | negative regulation of proteolysis | 88/2897 | 351/18723 | 1.74e-06 | 7.50e-05 | 88 |
| GO:00525481 | Colorectum | SER | regulation of endopeptidase activity | 103/2897 | 432/18723 | 2.86e-06 | 1.16e-04 | 103 |
| GO:0051346 | Colorectum | SER | negative regulation of hydrolase activity | 82/2897 | 379/18723 | 8.19e-04 | 1.01e-02 | 82 |
| GO:0010466 | Colorectum | SER | negative regulation of peptidase activity | 57/2897 | 262/18723 | 4.15e-03 | 3.38e-02 | 57 |
| GO:00525476 | Stomach | GC | regulation of peptidase activity | 67/1159 | 461/18723 | 5.35e-11 | 1.10e-08 | 67 |
| GO:00525486 | Stomach | GC | regulation of endopeptidase activity | 63/1159 | 432/18723 | 1.76e-10 | 2.82e-08 | 63 |
| GO:00094106 | Stomach | GC | response to xenobiotic stimulus | 61/1159 | 462/18723 | 1.68e-08 | 1.43e-06 | 61 |
| GO:00458616 | Stomach | GC | negative regulation of proteolysis | 50/1159 | 351/18723 | 2.96e-08 | 2.33e-06 | 50 |
| GO:00513466 | Stomach | GC | negative regulation of hydrolase activity | 51/1159 | 379/18723 | 1.38e-07 | 8.14e-06 | 51 |
| GO:00104666 | Stomach | GC | negative regulation of peptidase activity | 38/1159 | 262/18723 | 8.47e-07 | 4.18e-05 | 38 |
| GO:00109516 | Stomach | GC | negative regulation of endopeptidase activity | 37/1159 | 252/18723 | 8.69e-07 | 4.26e-05 | 37 |
| GO:00525475 | Stomach | SIM | regulation of peptidase activity | 54/708 | 461/18723 | 1.46e-13 | 6.25e-11 | 54 |
| GO:00525485 | Stomach | SIM | regulation of endopeptidase activity | 51/708 | 432/18723 | 5.26e-13 | 2.07e-10 | 51 |
| GO:00513465 | Stomach | SIM | negative regulation of hydrolase activity | 42/708 | 379/18723 | 4.58e-10 | 8.00e-08 | 42 |
| GO:00104665 | Stomach | SIM | negative regulation of peptidase activity | 33/708 | 262/18723 | 1.39e-09 | 2.26e-07 | 33 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| SPINK4 | insertion | Frame_Shift_Ins | novel | c.199_200insCTTATGATGTCCCCCACCTGGTGTCCAAGGCCCCT | p.Leu67ProfsTer18 | p.L67Pfs*18 | O60575 | protein_coding | TCGA-AN-A0AL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
| SPINK4 | SNV | Missense_Mutation | c.76N>A | p.Asp26Asn | p.D26N | protein_coding | tolerated_low_confidence(0.43) | benign(0) | TCGA-EK-A3GJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SPINK4 | SNV | Missense_Mutation | novel | c.206N>C | p.Leu69Ser | p.L69S | O60575 | protein_coding | deleterious(0.03) | benign(0.2) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| SPINK4 | SNV | Missense_Mutation | c.251G>A | p.Gly84Asp | p.G84D | O60575 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
| SPINK4 | SNV | Missense_Mutation | novel | c.41N>T | p.Ala14Val | p.A14V | O60575 | protein_coding | tolerated(0.17) | benign(0.005) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| SPINK4 | SNV | Missense_Mutation | novel | c.164N>A | p.Gly55Asp | p.G55D | O60575 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SPINK4 | SNV | Missense_Mutation | c.82N>C | p.Lys28Gln | p.K28Q | O60575 | protein_coding | tolerated(0.06) | possibly_damaging(0.559) | TCGA-D1-A16Y-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SPINK4 | SNV | Missense_Mutation | novel | c.247N>T | p.Asp83Tyr | p.D83Y | O60575 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-EY-A1G8-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SPINK4 | SNV | Missense_Mutation | novel | c.155N>C | p.Leu52Pro | p.L52P | O60575 | protein_coding | tolerated(0.51) | benign(0.001) | TCGA-2Y-A9HA-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| SPINK4 | SNV | Missense_Mutation | novel | c.142N>A | p.Gln48Lys | p.Q48K | O60575 | protein_coding | tolerated(1) | benign(0.011) | TCGA-46-3766-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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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