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Gene: SPEF2 |
Gene summary for SPEF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SPEF2 | Gene ID | 79925 |
| Gene name | sperm flagellar 2 | |
| Gene Alias | CT122 | |
| Cytomap | 5p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A140VKD0 |
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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 |
| 79925 | SPEF2 | male-WTA | Human | Thyroid | PTC | 7.78e-04 | 2.10e-02 | 0.1037 |
| 79925 | SPEF2 | PTC01 | Human | Thyroid | PTC | 6.41e-08 | 4.08e-02 | 0.1899 |
| 79925 | SPEF2 | PTC03 | Human | Thyroid | PTC | 6.47e-03 | 1.06e-01 | 0.1784 |
| 79925 | SPEF2 | PTC04 | Human | Thyroid | PTC | 6.85e-06 | 1.65e-02 | 0.1927 |
| 79925 | SPEF2 | PTC05 | Human | Thyroid | PTC | 4.83e-05 | 1.94e-01 | 0.2065 |
| 79925 | SPEF2 | PTC06 | Human | Thyroid | PTC | 3.38e-07 | 1.96e-01 | 0.2057 |
| 79925 | SPEF2 | PTC07 | Human | Thyroid | PTC | 5.82e-15 | 1.69e-01 | 0.2044 |
| 79925 | SPEF2 | ATC12 | Human | Thyroid | ATC | 1.01e-08 | 1.02e-01 | 0.34 |
| 79925 | SPEF2 | ATC13 | Human | Thyroid | ATC | 8.85e-32 | 5.89e-01 | 0.34 |
| 79925 | SPEF2 | ATC4 | Human | Thyroid | ATC | 2.16e-07 | 1.26e-01 | 0.34 |
| 79925 | SPEF2 | ATC5 | Human | Thyroid | ATC | 2.44e-37 | 6.29e-01 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:00991115 | Thyroid | PTC | microtubule-based transport | 88/5968 | 190/18723 | 2.08e-05 | 2.08e-04 | 88 |
| GO:006054115 | Thyroid | PTC | respiratory system development | 86/5968 | 203/18723 | 1.02e-03 | 6.08e-03 | 86 |
| GO:006054121 | Thyroid | ATC | respiratory system development | 100/6293 | 203/18723 | 2.66e-06 | 3.08e-05 | 100 |
| GO:009911112 | Thyroid | ATC | microtubule-based transport | 91/6293 | 190/18723 | 2.97e-05 | 2.48e-04 | 91 |
| GO:00487053 | Thyroid | ATC | skeletal system morphogenesis | 101/6293 | 220/18723 | 9.48e-05 | 6.93e-04 | 101 |
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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 |
| SPEF2 | SNV | Missense_Mutation | novel | c.4683N>G | p.Phe1561Leu | p.F1561L | Q9C093 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| SPEF2 | SNV | Missense_Mutation | novel | c.385N>G | p.Gln129Glu | p.Q129E | Q9C093 | protein_coding | deleterious(0.01) | probably_damaging(0.93) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| SPEF2 | SNV | Missense_Mutation | c.1590N>G | p.Cys530Trp | p.C530W | Q9C093 | protein_coding | tolerated(0.1) | benign(0.145) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SPEF2 | SNV | Missense_Mutation | novel | c.4765N>T | p.Asp1589Tyr | p.D1589Y | Q9C093 | protein_coding | deleterious(0.01) | benign(0.006) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SPEF2 | SNV | Missense_Mutation | c.3061N>C | p.Glu1021Gln | p.E1021Q | Q9C093 | protein_coding | tolerated(0.26) | probably_damaging(0.979) | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | |
| SPEF2 | SNV | Missense_Mutation | novel | c.1945N>G | p.Leu649Val | p.L649V | Q9C093 | protein_coding | tolerated(0.28) | benign(0.01) | TCGA-AR-A5QQ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
| SPEF2 | SNV | Missense_Mutation | rs768830338 | c.4958T>G | p.Val1653Gly | p.V1653G | Q9C093 | protein_coding | deleterious(0.01) | benign(0.157) | TCGA-BH-A0HQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| SPEF2 | deletion | In_Frame_Del | c.2707_2718delNNNNNNNNNNNN | p.Ala904_Ala907del | p.A904_A907del | Q9C093 | protein_coding | TCGA-A8-A09E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD | |||
| SPEF2 | insertion | Frame_Shift_Ins | novel | c.317_318insGT | p.Lys107Ter | p.K107* | Q9C093 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| SPEF2 | insertion | Frame_Shift_Ins | novel | c.319_320insATAC | p.Lys107AsnfsTer29 | p.K107Nfs*29 | Q9C093 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive 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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