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Gene: SSB |
Gene summary for SSB |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SSB | Gene ID | 6741 |
| Gene name | small RNA binding exonuclease protection factor La | |
| Gene Alias | LARP3 | |
| Cytomap | 2q31.1 | |
| Gene Type | protein-coding | GO ID | GO:0000956 | UniProtAcc | P05455 |
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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 |
| 6741 | SSB | CA_HPV_1 | Human | Cervix | CC | 1.95e-06 | -7.50e-02 | 0.0264 |
| 6741 | SSB | CCI_1 | Human | Cervix | CC | 2.89e-07 | -5.70e-01 | 0.528 |
| 6741 | SSB | CCI_2 | Human | Cervix | CC | 1.35e-03 | -4.83e-01 | 0.5249 |
| 6741 | SSB | CCI_3 | Human | Cervix | CC | 2.35e-07 | -5.14e-01 | 0.516 |
| 6741 | SSB | CCII_1 | Human | Cervix | CC | 3.96e-16 | -5.94e-01 | 0.3249 |
| 6741 | SSB | sample3 | Human | Cervix | CC | 2.70e-03 | -2.60e-01 | 0.1387 |
| 6741 | SSB | L1 | Human | Cervix | CC | 1.82e-09 | -3.65e-01 | 0.0802 |
| 6741 | SSB | T1 | Human | Cervix | CC | 4.04e-05 | -3.02e-01 | 0.0918 |
| 6741 | SSB | T3 | Human | Cervix | CC | 1.46e-02 | -2.63e-01 | 0.1389 |
| 6741 | SSB | AEH-subject1 | Human | Endometrium | AEH | 2.29e-18 | -5.09e-01 | -0.3059 |
| 6741 | SSB | AEH-subject2 | Human | Endometrium | AEH | 1.32e-21 | -5.38e-01 | -0.2525 |
| 6741 | SSB | AEH-subject3 | Human | Endometrium | AEH | 6.38e-16 | -3.80e-01 | -0.2576 |
| 6741 | SSB | AEH-subject4 | Human | Endometrium | AEH | 8.29e-06 | -3.56e-01 | -0.2657 |
| 6741 | SSB | AEH-subject5 | Human | Endometrium | AEH | 3.25e-12 | -4.34e-01 | -0.2953 |
| 6741 | SSB | EEC-subject1 | Human | Endometrium | EEC | 4.96e-16 | -4.13e-01 | -0.2682 |
| 6741 | SSB | EEC-subject2 | Human | Endometrium | EEC | 3.66e-24 | -5.05e-01 | -0.2607 |
| 6741 | SSB | EEC-subject3 | Human | Endometrium | EEC | 4.89e-53 | -5.03e-01 | -0.2525 |
| 6741 | SSB | EEC-subject4 | Human | Endometrium | EEC | 7.89e-10 | -2.88e-01 | -0.2571 |
| 6741 | SSB | EEC-subject5 | Human | Endometrium | EEC | 2.53e-08 | -2.98e-01 | -0.249 |
| 6741 | SSB | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 1.93e-33 | -2.89e-01 | -0.1869 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:003304417 | Skin | cSCC | regulation of chromosome organization | 100/4864 | 187/18723 | 8.97e-16 | 7.70e-14 | 100 |
| GO:0006401111 | Skin | cSCC | RNA catabolic process | 133/4864 | 278/18723 | 2.71e-15 | 2.23e-13 | 133 |
| GO:0006402111 | Skin | cSCC | mRNA catabolic process | 115/4864 | 232/18723 | 9.01e-15 | 6.57e-13 | 115 |
| GO:0034655111 | Skin | cSCC | nucleobase-containing compound catabolic process | 172/4864 | 407/18723 | 4.11e-13 | 2.43e-11 | 172 |
| GO:007116613 | Skin | cSCC | ribonucleoprotein complex localization | 49/4864 | 77/18723 | 3.94e-12 | 2.13e-10 | 49 |
| GO:001593119 | Skin | cSCC | nucleobase-containing compound transport | 105/4864 | 222/18723 | 5.49e-12 | 2.89e-10 | 105 |
| GO:007142613 | Skin | cSCC | ribonucleoprotein complex export from nucleus | 48/4864 | 76/18723 | 9.76e-12 | 4.97e-10 | 48 |
| GO:0046700110 | Skin | cSCC | heterocycle catabolic process | 178/4864 | 445/18723 | 4.45e-11 | 2.13e-09 | 178 |
| GO:0044270110 | Skin | cSCC | cellular nitrogen compound catabolic process | 179/4864 | 451/18723 | 8.34e-11 | 3.79e-09 | 179 |
| GO:0019439110 | Skin | cSCC | aromatic compound catabolic process | 183/4864 | 467/18723 | 1.76e-10 | 7.68e-09 | 183 |
| GO:0000956110 | Skin | cSCC | nuclear-transcribed mRNA catabolic process | 59/4864 | 112/18723 | 1.46e-09 | 5.60e-08 | 59 |
| GO:1901361110 | Skin | cSCC | organic cyclic compound catabolic process | 188/4864 | 495/18723 | 1.92e-09 | 7.01e-08 | 188 |
| GO:001908019 | Skin | cSCC | viral gene expression | 50/4864 | 94/18723 | 1.68e-08 | 5.04e-07 | 50 |
| GO:000640513 | Skin | cSCC | RNA export from nucleus | 46/4864 | 84/18723 | 1.89e-08 | 5.56e-07 | 46 |
| GO:001908118 | Skin | cSCC | viral translation | 15/4864 | 16/18723 | 1.97e-08 | 5.79e-07 | 15 |
| GO:003150315 | Skin | cSCC | protein-containing complex localization | 95/4864 | 220/18723 | 2.00e-08 | 5.82e-07 | 95 |
| GO:00311234 | Skin | cSCC | RNA 3'-end processing | 58/4864 | 116/18723 | 2.47e-08 | 6.89e-07 | 58 |
| GO:2001252110 | Skin | cSCC | positive regulation of chromosome organization | 45/4864 | 82/18723 | 2.47e-08 | 6.89e-07 | 45 |
| GO:000626012 | Skin | cSCC | DNA replication | 106/4864 | 260/18723 | 1.18e-07 | 2.77e-06 | 106 |
| GO:007552215 | Skin | cSCC | IRES-dependent viral translational initiation | 11/4864 | 11/18723 | 3.61e-07 | 7.18e-06 | 11 |
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| 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 |
| SSB | SNV | Missense_Mutation | c.925N>A | p.Glu309Lys | p.E309K | P05455 | protein_coding | tolerated(0.07) | benign(0.106) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SSB | SNV | Missense_Mutation | c.638N>A | p.Ala213Glu | p.A213E | P05455 | protein_coding | tolerated(1) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SSB | deletion | Frame_Shift_Del | novel | c.54delN | p.His19IlefsTer18 | p.H19Ifs*18 | P05455 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| SSB | SNV | Missense_Mutation | rs201142063 | c.676C>G | p.Leu226Val | p.L226V | P05455 | protein_coding | tolerated(0.09) | benign(0.017) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| SSB | SNV | Missense_Mutation | c.1048N>C | p.Ser350Pro | p.S350P | P05455 | protein_coding | tolerated(0.29) | benign(0.003) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| SSB | SNV | Missense_Mutation | novel | c.787N>T | p.Asp263Tyr | p.D263Y | P05455 | protein_coding | deleterious(0) | probably_damaging(0.916) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| SSB | SNV | Missense_Mutation | c.290N>C | p.Leu97Pro | p.L97P | P05455 | protein_coding | deleterious(0) | possibly_damaging(0.896) | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | |
| SSB | SNV | Missense_Mutation | c.1039N>A | p.Gln347Lys | p.Q347K | P05455 | protein_coding | tolerated(0.37) | benign(0.007) | TCGA-AG-3882-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SSB | SNV | Missense_Mutation | novel | c.452N>C | p.Lys151Thr | p.K151T | P05455 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| SSB | SNV | Missense_Mutation | c.587N>T | p.Arg196Ile | p.R196I | P05455 | protein_coding | deleterious(0) | possibly_damaging(0.572) | TCGA-AJ-A3EL-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 |
| Page: 1 |
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