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Gene: SIK3 |
Gene summary for SIK3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SIK3 | Gene ID | 23387 |
Gene name | SIK family kinase 3 | |
Gene Alias | L19 | |
Cytomap | 11q23.3 | |
Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | A1A5A9 |
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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 |
23387 | SIK3 | CCI_1 | Human | Cervix | CC | 9.92e-12 | 1.04e+00 | 0.528 |
23387 | SIK3 | CCI_2 | Human | Cervix | CC | 2.41e-13 | 1.49e+00 | 0.5249 |
23387 | SIK3 | CCI_3 | Human | Cervix | CC | 2.88e-17 | 9.73e-01 | 0.516 |
23387 | SIK3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.06e-34 | -8.63e-01 | 0.0155 |
23387 | SIK3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.36e-04 | -5.38e-01 | -0.1808 |
23387 | SIK3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.14e-02 | -4.51e-01 | -0.0811 |
23387 | SIK3 | HTA11_78_2000001011 | Human | Colorectum | AD | 4.65e-04 | -5.20e-01 | -0.1088 |
23387 | SIK3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.80e-08 | -6.43e-01 | -0.1207 |
23387 | SIK3 | HTA11_696_2000001011 | Human | Colorectum | AD | 5.16e-06 | -3.72e-01 | -0.1464 |
23387 | SIK3 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.85e-09 | -4.58e-01 | -0.1001 |
23387 | SIK3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.13e-02 | -5.42e-01 | -0.1706 |
23387 | SIK3 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.40e-10 | -7.23e-01 | -0.2061 |
23387 | SIK3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 4.94e-08 | -5.58e-01 | -0.0179 |
23387 | SIK3 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.18e-19 | -8.00e-01 | 0.096 |
23387 | SIK3 | HTA11_9408_2000001011 | Human | Colorectum | AD | 1.98e-02 | -8.23e-01 | 0.0451 |
23387 | SIK3 | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.75e-05 | -6.50e-01 | 0.0528 |
23387 | SIK3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.49e-20 | -6.49e-01 | 0.0674 |
23387 | SIK3 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.16e-04 | -4.50e-01 | 0.0112 |
23387 | SIK3 | HTA11_11156_2000001011 | Human | Colorectum | AD | 2.15e-05 | -6.57e-01 | 0.0397 |
23387 | SIK3 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.42e-08 | -7.24e-01 | 0.0588 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0031929 | Colorectum | MSS | TOR signaling | 35/3467 | 126/18723 | 6.91e-03 | 4.44e-02 | 35 |
GO:00319292 | Liver | Cirrhotic | TOR signaling | 44/4634 | 126/18723 | 6.69e-03 | 3.30e-02 | 44 |
GO:00319291 | Liver | HCC | TOR signaling | 78/7958 | 126/18723 | 8.49e-06 | 9.97e-05 | 78 |
GO:0032006 | Liver | HCC | regulation of TOR signaling | 63/7958 | 104/18723 | 1.50e-04 | 1.20e-03 | 63 |
GO:0032008 | Liver | HCC | positive regulation of TOR signaling | 31/7958 | 47/18723 | 9.90e-04 | 5.71e-03 | 31 |
GO:1904263 | Liver | HCC | positive regulation of TORC1 signaling | 14/7958 | 20/18723 | 1.21e-02 | 4.41e-02 | 14 |
GO:00319293 | Oral cavity | OSCC | TOR signaling | 67/7305 | 126/18723 | 8.52e-04 | 4.50e-03 | 67 |
GO:0038203 | Oral cavity | OSCC | TORC2 signaling | 10/7305 | 12/18723 | 2.25e-03 | 1.00e-02 | 10 |
GO:00320081 | Oral cavity | OSCC | positive regulation of TOR signaling | 28/7305 | 47/18723 | 3.41e-03 | 1.45e-02 | 28 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
SIK3 | SNV | Missense_Mutation | rs267602706 | c.334N>T | p.Arg112Trp | p.R112W | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A7-A4SB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | CR | |
SIK3 | SNV | Missense_Mutation | novel | c.2480N>T | p.Gly827Val | p.G827V | protein_coding | deleterious_low_confidence(0.01) | benign(0.419) | TCGA-A8-A09W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
SIK3 | SNV | Missense_Mutation | c.292G>C | p.Asp98His | p.D98H | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
SIK3 | SNV | Missense_Mutation | novel | c.1567C>A | p.Gln523Lys | p.Q523K | protein_coding | deleterious_low_confidence(0.04) | benign(0.258) | TCGA-D8-A1XF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
SIK3 | SNV | Missense_Mutation | c.1886N>T | p.Ala629Val | p.A629V | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.999) | TCGA-EW-A1IZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | ||
SIK3 | insertion | Nonsense_Mutation | novel | c.3048_3049insTGCTGAAAACTCAGCCCCAGGGGGAATTC | p.Glu1017CysfsTer2 | p.E1017Cfs*2 | protein_coding | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD | |||
SIK3 | insertion | Nonsense_Mutation | novel | c.731_732insACAACCTTTTTTAACTCCAGCTTGCTGA | p.Asp245GlnfsTer9 | p.D245Qfs*9 | protein_coding | TCGA-BH-A0BV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD | |||
SIK3 | deletion | Frame_Shift_Del | c.2253delC | p.Met752Ter | p.M752* | protein_coding | TCGA-BH-A0W3-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||||
SIK3 | SNV | Missense_Mutation | rs769986194 | c.3931N>A | p.Glu1311Lys | p.E1311K | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.829) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
SIK3 | SNV | Missense_Mutation | novel | c.278C>A | p.Ala93Asp | p.A93D | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EA-A410-01 | 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 |
23387 | SIK3 | DRUGGABLE GENOME, KINASE, SERINE THREONINE KINASE, ENZYME | inhibitor | 178102336 | BOSUTINIB | |
23387 | SIK3 | DRUGGABLE GENOME, KINASE, SERINE THREONINE KINASE, ENZYME | inhibitor | 340590212 | ||
23387 | SIK3 | DRUGGABLE GENOME, KINASE, SERINE THREONINE KINASE, ENZYME | inhibitor | 178102305 | DASATINIB | |
23387 | SIK3 | DRUGGABLE GENOME, KINASE, SERINE THREONINE KINASE, ENZYME | inhibitor | 249565729 |
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