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Gene: KHDC4 |
Gene summary for KHDC4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | KHDC4 | Gene ID | 22889 |
| Gene name | KH domain containing 4, pre-mRNA splicing factor | |
| Gene Alias | BLOM7 | |
| Cytomap | 1q22 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | Q7Z7F0 |
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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 |
| 22889 | KHDC4 | CCI_1 | Human | Cervix | CC | 9.09e-12 | 1.04e+00 | 0.528 |
| 22889 | KHDC4 | CCI_2 | Human | Cervix | CC | 7.47e-06 | 7.68e-01 | 0.5249 |
| 22889 | KHDC4 | CCI_3 | Human | Cervix | CC | 6.68e-04 | 6.48e-01 | 0.516 |
| 22889 | KHDC4 | Tumor | Human | Cervix | CC | 4.13e-06 | -1.75e-01 | 0.1241 |
| 22889 | KHDC4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.45e-03 | -3.23e-01 | 0.0155 |
| 22889 | KHDC4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.44e-33 | -5.26e-01 | 0.294 |
| 22889 | KHDC4 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.69e-10 | -5.26e-01 | 0.281 |
| 22889 | KHDC4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.38e-30 | -5.26e-01 | 0.3859 |
| 22889 | KHDC4 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.13e-07 | -5.26e-01 | 0.2585 |
| 22889 | KHDC4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 8.80e-32 | -5.26e-01 | 0.3005 |
| 22889 | KHDC4 | A002-C-010 | Human | Colorectum | FAP | 1.31e-03 | -1.99e-01 | 0.242 |
| 22889 | KHDC4 | A001-C-207 | Human | Colorectum | FAP | 1.03e-02 | -2.14e-01 | 0.1278 |
| 22889 | KHDC4 | A015-C-203 | Human | Colorectum | FAP | 1.52e-21 | -4.26e-01 | -0.1294 |
| 22889 | KHDC4 | A015-C-204 | Human | Colorectum | FAP | 4.22e-04 | -2.82e-01 | -0.0228 |
| 22889 | KHDC4 | A014-C-040 | Human | Colorectum | FAP | 3.56e-02 | -3.38e-01 | -0.1184 |
| 22889 | KHDC4 | A002-C-201 | Human | Colorectum | FAP | 4.09e-13 | -3.83e-01 | 0.0324 |
| 22889 | KHDC4 | A002-C-203 | Human | Colorectum | FAP | 2.78e-04 | -2.16e-01 | 0.2786 |
| 22889 | KHDC4 | A001-C-119 | Human | Colorectum | FAP | 3.19e-06 | -3.59e-01 | -0.1557 |
| 22889 | KHDC4 | A001-C-108 | Human | Colorectum | FAP | 1.32e-11 | -2.32e-01 | -0.0272 |
| 22889 | KHDC4 | A002-C-205 | Human | Colorectum | FAP | 9.57e-16 | -3.53e-01 | -0.1236 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:002261310 | Cervix | CC | ribonucleoprotein complex biogenesis | 88/2311 | 463/18723 | 2.11e-05 | 3.82e-04 | 88 |
| GO:002261810 | Cervix | CC | ribonucleoprotein complex assembly | 49/2311 | 220/18723 | 2.52e-05 | 4.29e-04 | 49 |
| GO:007182610 | Cervix | CC | ribonucleoprotein complex subunit organization | 49/2311 | 227/18723 | 5.91e-05 | 8.54e-04 | 49 |
| GO:000838010 | Cervix | CC | RNA splicing | 76/2311 | 434/18723 | 9.79e-04 | 8.19e-03 | 76 |
| GO:000037710 | Cervix | CC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000039810 | Cervix | CC | mRNA splicing, via spliceosome | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000037510 | Cervix | CC | RNA splicing, via transesterification reactions | 55/2311 | 324/18723 | 8.61e-03 | 4.44e-02 | 55 |
| GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
| GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
| GO:0022618 | Colorectum | AD | ribonucleoprotein complex assembly | 92/3918 | 220/18723 | 1.49e-12 | 2.60e-10 | 92 |
| GO:0071826 | Colorectum | AD | ribonucleoprotein complex subunit organization | 94/3918 | 227/18723 | 1.70e-12 | 2.87e-10 | 94 |
| GO:0022613 | Colorectum | AD | ribonucleoprotein complex biogenesis | 151/3918 | 463/18723 | 1.96e-09 | 1.39e-07 | 151 |
| GO:0000245 | Colorectum | AD | spliceosomal complex assembly | 33/3918 | 79/18723 | 2.15e-05 | 4.33e-04 | 33 |
| GO:0006376 | Colorectum | AD | mRNA splice site selection | 18/3918 | 49/18723 | 7.93e-03 | 4.73e-02 | 18 |
| GO:00083802 | Colorectum | MSS | RNA splicing | 159/3467 | 434/18723 | 1.75e-19 | 1.22e-16 | 159 |
| GO:00003772 | Colorectum | MSS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
| GO:00003982 | Colorectum | MSS | mRNA splicing, via spliceosome | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
| GO:00003752 | Colorectum | MSS | RNA splicing, via transesterification reactions | 122/3467 | 324/18723 | 2.75e-16 | 8.58e-14 | 122 |
| Page: 1 2 3 4 5 6 |
| 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 |
| Page: 1 |
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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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