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Gene: SPATA13 |
Gene summary for SPATA13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SPATA13 | Gene ID | 221178 |
| Gene name | spermatogenesis associated 13 | |
| Gene Alias | ARHGEF29 | |
| Cytomap | 13q12.12 | |
| Gene Type | protein-coding | GO ID | GO:0006928 | UniProtAcc | Q96N96 |
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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 |
| 221178 | SPATA13 | AEH-subject1 | Human | Endometrium | AEH | 2.23e-12 | 4.25e-01 | -0.3059 |
| 221178 | SPATA13 | AEH-subject3 | Human | Endometrium | AEH | 7.82e-14 | 4.84e-01 | -0.2576 |
| 221178 | SPATA13 | AEH-subject4 | Human | Endometrium | AEH | 5.21e-11 | 5.98e-01 | -0.2657 |
| 221178 | SPATA13 | AEH-subject5 | Human | Endometrium | AEH | 6.28e-20 | 6.92e-01 | -0.2953 |
| 221178 | SPATA13 | EEC-subject1 | Human | Endometrium | EEC | 1.54e-04 | 3.61e-01 | -0.2682 |
| 221178 | SPATA13 | EEC-subject2 | Human | Endometrium | EEC | 9.91e-06 | 3.22e-01 | -0.2607 |
| 221178 | SPATA13 | EEC-subject3 | Human | Endometrium | EEC | 4.17e-04 | 2.51e-01 | -0.2525 |
| 221178 | SPATA13 | EEC-subject4 | Human | Endometrium | EEC | 3.25e-13 | 5.21e-01 | -0.2571 |
| 221178 | SPATA13 | EEC-subject5 | Human | Endometrium | EEC | 1.33e-08 | 4.11e-01 | -0.249 |
| 221178 | SPATA13 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 9.54e-06 | -2.09e-02 | -0.1883 |
| 221178 | SPATA13 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 3.12e-06 | -3.53e-02 | -0.1917 |
| 221178 | SPATA13 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 5.52e-05 | -8.86e-02 | -0.1916 |
| 221178 | SPATA13 | S41 | Human | Liver | Cirrhotic | 1.21e-06 | 6.49e-01 | -0.0343 |
| 221178 | SPATA13 | HCC1_Meng | Human | Liver | HCC | 4.65e-28 | -2.86e-02 | 0.0246 |
| 221178 | SPATA13 | HCC2_Meng | Human | Liver | HCC | 1.07e-20 | 1.52e-01 | 0.0107 |
| 221178 | SPATA13 | cirrhotic2 | Human | Liver | Cirrhotic | 2.25e-03 | 1.37e-01 | 0.0201 |
| 221178 | SPATA13 | HCC1 | Human | Liver | HCC | 3.91e-13 | 4.22e+00 | 0.5336 |
| 221178 | SPATA13 | HCC2 | Human | Liver | HCC | 1.30e-27 | 3.89e+00 | 0.5341 |
| 221178 | SPATA13 | HCC5 | Human | Liver | HCC | 1.93e-06 | 1.40e+00 | 0.4932 |
| 221178 | SPATA13 | Pt13.b | Human | Liver | HCC | 8.12e-05 | 1.82e-02 | 0.0251 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00510567 | Endometrium | AEH | regulation of small GTPase mediated signal transduction | 59/2100 | 302/18723 | 1.43e-05 | 3.03e-04 | 59 |
| GO:00975818 | Endometrium | AEH | lamellipodium organization | 20/2100 | 90/18723 | 2.01e-03 | 1.56e-02 | 20 |
| GO:00300326 | Endometrium | AEH | lamellipodium assembly | 17/2100 | 72/18723 | 2.14e-03 | 1.65e-02 | 17 |
| GO:005105612 | Endometrium | EEC | regulation of small GTPase mediated signal transduction | 61/2168 | 302/18723 | 9.42e-06 | 2.08e-04 | 61 |
| GO:009758113 | Endometrium | EEC | lamellipodium organization | 20/2168 | 90/18723 | 2.92e-03 | 2.06e-02 | 20 |
| GO:003003212 | Endometrium | EEC | lamellipodium assembly | 17/2168 | 72/18723 | 3.01e-03 | 2.10e-02 | 17 |
| GO:009758111 | Liver | Cirrhotic | lamellipodium organization | 40/4634 | 90/18723 | 3.48e-05 | 4.26e-04 | 40 |
| GO:003003211 | Liver | Cirrhotic | lamellipodium assembly | 30/4634 | 72/18723 | 1.18e-03 | 7.98e-03 | 30 |
| GO:009758121 | Liver | HCC | lamellipodium organization | 58/7958 | 90/18723 | 2.16e-05 | 2.30e-04 | 58 |
| GO:003003221 | Liver | HCC | lamellipodium assembly | 44/7958 | 72/18723 | 1.10e-03 | 6.32e-03 | 44 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0481018 | Endometrium | AEH | Regulation of actin cytoskeleton | 50/1197 | 229/8465 | 9.08e-04 | 5.78e-03 | 4.23e-03 | 50 |
| hsa0481019 | Endometrium | AEH | Regulation of actin cytoskeleton | 50/1197 | 229/8465 | 9.08e-04 | 5.78e-03 | 4.23e-03 | 50 |
| hsa0481024 | Endometrium | EEC | Regulation of actin cytoskeleton | 49/1237 | 229/8465 | 3.20e-03 | 1.78e-02 | 1.33e-02 | 49 |
| hsa0481034 | Endometrium | EEC | Regulation of actin cytoskeleton | 49/1237 | 229/8465 | 3.20e-03 | 1.78e-02 | 1.33e-02 | 49 |
| hsa0481021 | Liver | Cirrhotic | Regulation of actin cytoskeleton | 100/2530 | 229/8465 | 5.28e-06 | 5.50e-05 | 3.39e-05 | 100 |
| hsa0481031 | Liver | Cirrhotic | Regulation of actin cytoskeleton | 100/2530 | 229/8465 | 5.28e-06 | 5.50e-05 | 3.39e-05 | 100 |
| hsa0481041 | Liver | HCC | Regulation of actin cytoskeleton | 134/4020 | 229/8465 | 4.48e-04 | 1.94e-03 | 1.08e-03 | 134 |
| hsa0481051 | Liver | HCC | Regulation of actin cytoskeleton | 134/4020 | 229/8465 | 4.48e-04 | 1.94e-03 | 1.08e-03 | 134 |
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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 |
| SPATA13 | SNV | Missense_Mutation | novel | c.359N>T | p.Ser120Leu | p.S120L | Q96N96 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.536) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| SPATA13 | SNV | Missense_Mutation | c.1331N>G | p.Ser444Cys | p.S444C | Q96N96 | protein_coding | tolerated_low_confidence(0.07) | benign(0.003) | TCGA-AR-A1AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| SPATA13 | SNV | Missense_Mutation | novel | c.3120N>T | p.Lys1040Asn | p.K1040N | Q96N96 | protein_coding | deleterious(0) | possibly_damaging(0.481) | TCGA-AR-A1AM-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| SPATA13 | SNV | Missense_Mutation | c.2320N>T | p.Val774Leu | p.V774L | Q96N96 | protein_coding | tolerated(0.07) | probably_damaging(0.998) | TCGA-D8-A1JI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD | |
| SPATA13 | insertion | Frame_Shift_Ins | novel | c.2404_2405insAAGATCATGCTATGTTCTCTTCAAT | p.Leu802GlnfsTer22 | p.L802Qfs*22 | Q96N96 | protein_coding | TCGA-BH-A0H7-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | ||
| SPATA13 | SNV | Missense_Mutation | novel | c.1225G>A | p.Val409Ile | p.V409I | Q96N96 | protein_coding | tolerated_low_confidence(0.05) | benign(0.011) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SPATA13 | SNV | Missense_Mutation | rs752240893 | c.3169G>A | p.Asp1057Asn | p.D1057N | Q96N96 | protein_coding | tolerated(0.07) | benign(0.074) | TCGA-C5-A7CK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| SPATA13 | SNV | Missense_Mutation | novel | c.1181G>A | p.Gly394Asp | p.G394D | Q96N96 | protein_coding | tolerated_low_confidence(0.39) | benign(0.01) | TCGA-DG-A2KM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| SPATA13 | SNV | Missense_Mutation | novel | c.1621N>A | p.Ala541Thr | p.A541T | Q96N96 | protein_coding | tolerated_low_confidence(0.18) | benign(0.022) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SPATA13 | SNV | Missense_Mutation | c.529N>C | p.Glu177Gln | p.E177Q | Q96N96 | protein_coding | tolerated_low_confidence(0.17) | benign(0.382) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
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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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