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Gene: SYCP2 |
Gene summary for SYCP2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SYCP2 | Gene ID | 10388 |
Gene name | synaptonemal complex protein 2 | |
Gene Alias | SCP-2 | |
Cytomap | 20q13.33 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9BX26 |
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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 |
10388 | SYCP2 | CA_HPV_2 | Human | Cervix | CC | 2.14e-13 | 3.55e-01 | 0.0391 |
10388 | SYCP2 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 6.49e-16 | 4.22e-01 | 0.0208 |
10388 | SYCP2 | CCI_1 | Human | Cervix | CC | 5.05e-10 | 7.66e-01 | 0.528 |
10388 | SYCP2 | CCI_2 | Human | Cervix | CC | 1.77e-07 | 6.24e-01 | 0.5249 |
10388 | SYCP2 | CCI_3 | Human | Cervix | CC | 1.00e-20 | 8.81e-01 | 0.516 |
10388 | SYCP2 | CCII_1 | Human | Cervix | CC | 4.87e-04 | 2.20e-01 | 0.3249 |
10388 | SYCP2 | Tumor | Human | Cervix | CC | 2.62e-11 | 2.67e-01 | 0.1241 |
10388 | SYCP2 | sample1 | Human | Cervix | CC | 2.31e-03 | 2.92e-01 | 0.0959 |
10388 | SYCP2 | sample3 | Human | Cervix | CC | 9.38e-20 | 3.74e-01 | 0.1387 |
10388 | SYCP2 | T1 | Human | Cervix | CC | 8.52e-04 | 2.33e-01 | 0.0918 |
10388 | SYCP2 | T3 | Human | Cervix | CC | 4.40e-21 | 3.82e-01 | 0.1389 |
10388 | SYCP2 | LZE7T | Human | Esophagus | ESCC | 1.95e-03 | 3.13e-01 | 0.0667 |
10388 | SYCP2 | LZE24T | Human | Esophagus | ESCC | 1.93e-05 | 1.50e-01 | 0.0596 |
10388 | SYCP2 | P2T-E | Human | Esophagus | ESCC | 8.97e-05 | 1.11e-01 | 0.1177 |
10388 | SYCP2 | P10T-E | Human | Esophagus | ESCC | 1.73e-03 | 5.90e-02 | 0.116 |
10388 | SYCP2 | P12T-E | Human | Esophagus | ESCC | 4.14e-54 | 1.07e+00 | 0.1122 |
10388 | SYCP2 | P16T-E | Human | Esophagus | ESCC | 7.04e-12 | 1.32e-01 | 0.1153 |
10388 | SYCP2 | P26T-E | Human | Esophagus | ESCC | 2.19e-02 | 1.00e-01 | 0.1276 |
10388 | SYCP2 | P36T-E | Human | Esophagus | ESCC | 1.75e-19 | 8.50e-01 | 0.1187 |
10388 | SYCP2 | P37T-E | Human | Esophagus | ESCC | 1.31e-03 | 8.68e-02 | 0.1371 |
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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:00614588 | Cervix | CC | reproductive system development | 87/2311 | 427/18723 | 1.37e-06 | 4.55e-05 | 87 |
GO:00486088 | Cervix | CC | reproductive structure development | 86/2311 | 424/18723 | 1.90e-06 | 5.97e-05 | 86 |
GO:00482851 | Cervix | CC | organelle fission | 78/2311 | 488/18723 | 9.70e-03 | 4.79e-02 | 78 |
GO:004860813 | Cervix | HSIL_HPV | reproductive structure development | 32/737 | 424/18723 | 3.52e-04 | 5.54e-03 | 32 |
GO:006145814 | Cervix | HSIL_HPV | reproductive system development | 32/737 | 427/18723 | 3.98e-04 | 6.14e-03 | 32 |
GO:000705911 | Esophagus | ESCC | chromosome segregation | 238/8552 | 346/18723 | 1.72e-18 | 1.82e-16 | 238 |
GO:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
GO:00988133 | Esophagus | ESCC | nuclear chromosome segregation | 187/8552 | 281/18723 | 1.00e-12 | 4.36e-11 | 187 |
GO:00002802 | Esophagus | ESCC | nuclear division | 270/8552 | 439/18723 | 1.17e-11 | 4.24e-10 | 270 |
GO:0061458110 | Esophagus | ESCC | reproductive system development | 247/8552 | 427/18723 | 2.24e-07 | 3.42e-06 | 247 |
GO:004860818 | Esophagus | ESCC | reproductive structure development | 245/8552 | 424/18723 | 2.82e-07 | 4.14e-06 | 245 |
GO:00070592 | Oral cavity | OSCC | chromosome segregation | 206/7305 | 346/18723 | 5.82e-15 | 3.76e-13 | 206 |
GO:00482852 | Oral cavity | OSCC | organelle fission | 265/7305 | 488/18723 | 3.22e-12 | 1.27e-10 | 265 |
GO:00002801 | Oral cavity | OSCC | nuclear division | 237/7305 | 439/18723 | 9.62e-11 | 2.90e-09 | 237 |
GO:00988132 | Oral cavity | OSCC | nuclear chromosome segregation | 162/7305 | 281/18723 | 1.56e-10 | 4.56e-09 | 162 |
GO:006145817 | Oral cavity | OSCC | reproductive system development | 217/7305 | 427/18723 | 3.75e-07 | 5.63e-06 | 217 |
GO:004860816 | Oral cavity | OSCC | reproductive structure development | 214/7305 | 424/18723 | 8.58e-07 | 1.18e-05 | 214 |
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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 |
SYCP2 | SNV | Missense_Mutation | c.1089N>A | p.Ser363Arg | p.S363R | Q9BX26 | protein_coding | deleterious(0.01) | possibly_damaging(0.667) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
SYCP2 | SNV | Missense_Mutation | c.892N>A | p.Asp298Asn | p.D298N | Q9BX26 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
SYCP2 | SNV | Missense_Mutation | c.335N>C | p.Gln112Pro | p.Q112P | Q9BX26 | protein_coding | deleterious(0) | benign(0.001) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
SYCP2 | SNV | Missense_Mutation | c.319N>C | p.Ser107Pro | p.S107P | Q9BX26 | protein_coding | tolerated(0.09) | probably_damaging(0.935) | TCGA-AX-A063-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SYCP2 | SNV | Missense_Mutation | novel | c.2555N>T | p.Arg852Ile | p.R852I | Q9BX26 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
SYCP2 | SNV | Missense_Mutation | rs770812931 | c.535N>G | p.Met179Val | p.M179V | Q9BX26 | protein_coding | deleterious(0) | benign(0.322) | TCGA-AX-A0IW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unspecific | Carboplatin & Paclitaxel | SD |
SYCP2 | SNV | Missense_Mutation | rs781085520 | c.3170N>T | p.Arg1057Ile | p.R1057I | Q9BX26 | protein_coding | deleterious(0.01) | possibly_damaging(0.778) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SYCP2 | SNV | Missense_Mutation | c.2232N>G | p.Ile744Met | p.I744M | Q9BX26 | protein_coding | deleterious(0.03) | benign(0.021) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SYCP2 | SNV | Missense_Mutation | c.1204N>C | p.Ile402Leu | p.I402L | Q9BX26 | protein_coding | deleterious(0.05) | benign(0.178) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SYCP2 | SNV | Missense_Mutation | rs768114400 | c.461N>A | p.Arg154His | p.R154H | Q9BX26 | protein_coding | tolerated(0.05) | benign(0.158) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | 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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