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Gene: DENND4C |
Gene summary for DENND4C |
Gene summary. |
Gene information | Species | Human | Gene symbol | DENND4C | Gene ID | 55667 |
Gene name | DENN domain containing 4C | |
Gene Alias | C9orf55 | |
Cytomap | 9p22.1 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q5VZ89 |
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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 |
55667 | DENND4C | CCI_1 | Human | Cervix | CC | 9.71e-04 | 5.81e-01 | 0.528 |
55667 | DENND4C | CCI_2 | Human | Cervix | CC | 1.50e-08 | 1.13e+00 | 0.5249 |
55667 | DENND4C | CCI_3 | Human | Cervix | CC | 1.44e-08 | 7.96e-01 | 0.516 |
55667 | DENND4C | HTA11_347_2000001011 | Human | Colorectum | AD | 8.10e-11 | 5.74e-01 | -0.1954 |
55667 | DENND4C | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.14e-02 | 5.73e-01 | 0.281 |
55667 | DENND4C | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.47e-03 | -3.49e-01 | 0.3005 |
55667 | DENND4C | A002-C-010 | Human | Colorectum | FAP | 3.23e-02 | 4.66e-02 | 0.242 |
55667 | DENND4C | A001-C-207 | Human | Colorectum | FAP | 4.08e-03 | -1.46e-01 | 0.1278 |
55667 | DENND4C | A015-C-203 | Human | Colorectum | FAP | 1.33e-34 | -3.50e-01 | -0.1294 |
55667 | DENND4C | A015-C-204 | Human | Colorectum | FAP | 5.88e-07 | -3.27e-01 | -0.0228 |
55667 | DENND4C | A014-C-040 | Human | Colorectum | FAP | 3.24e-03 | -2.28e-01 | -0.1184 |
55667 | DENND4C | A002-C-201 | Human | Colorectum | FAP | 1.70e-13 | -2.98e-01 | 0.0324 |
55667 | DENND4C | A002-C-203 | Human | Colorectum | FAP | 1.29e-03 | -9.22e-02 | 0.2786 |
55667 | DENND4C | A001-C-119 | Human | Colorectum | FAP | 6.02e-06 | -2.52e-01 | -0.1557 |
55667 | DENND4C | A001-C-108 | Human | Colorectum | FAP | 4.40e-18 | -1.63e-01 | -0.0272 |
55667 | DENND4C | A002-C-205 | Human | Colorectum | FAP | 1.43e-23 | -4.11e-01 | -0.1236 |
55667 | DENND4C | A001-C-104 | Human | Colorectum | FAP | 3.70e-02 | -1.14e-01 | 0.0184 |
55667 | DENND4C | A015-C-005 | Human | Colorectum | FAP | 5.02e-03 | -2.85e-01 | -0.0336 |
55667 | DENND4C | A015-C-006 | Human | Colorectum | FAP | 3.11e-19 | -5.17e-01 | -0.0994 |
55667 | DENND4C | A015-C-106 | Human | Colorectum | FAP | 4.96e-12 | -1.61e-01 | -0.0511 |
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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:007265910 | Cervix | CC | protein localization to plasma membrane | 73/2311 | 284/18723 | 4.95e-10 | 6.73e-08 | 73 |
GO:00510566 | Cervix | CC | regulation of small GTPase mediated signal transduction | 75/2311 | 302/18723 | 1.54e-09 | 1.74e-07 | 75 |
GO:00072656 | Cervix | CC | Ras protein signal transduction | 79/2311 | 337/18723 | 9.49e-09 | 7.77e-07 | 79 |
GO:19907788 | Cervix | CC | protein localization to cell periphery | 78/2311 | 333/18723 | 1.22e-08 | 9.73e-07 | 78 |
GO:19016538 | Cervix | CC | cellular response to peptide | 72/2311 | 359/18723 | 1.89e-05 | 3.48e-04 | 72 |
GO:00465785 | Cervix | CC | regulation of Ras protein signal transduction | 44/2311 | 189/18723 | 2.05e-05 | 3.73e-04 | 44 |
GO:00434349 | Cervix | CC | response to peptide hormone | 77/2311 | 414/18723 | 1.40e-04 | 1.70e-03 | 77 |
GO:00713757 | Cervix | CC | cellular response to peptide hormone stimulus | 57/2311 | 290/18723 | 2.32e-04 | 2.59e-03 | 57 |
GO:00328698 | Cervix | CC | cellular response to insulin stimulus | 42/2311 | 203/18723 | 4.95e-04 | 4.83e-03 | 42 |
GO:00328688 | Cervix | CC | response to insulin | 50/2311 | 264/18723 | 1.28e-03 | 1.02e-02 | 50 |
GO:0072659 | Colorectum | AD | protein localization to plasma membrane | 122/3918 | 284/18723 | 2.86e-17 | 1.49e-14 | 122 |
GO:1990778 | Colorectum | AD | protein localization to cell periphery | 129/3918 | 333/18723 | 5.51e-14 | 1.15e-11 | 129 |
GO:0032868 | Colorectum | AD | response to insulin | 91/3918 | 264/18723 | 2.02e-07 | 8.48e-06 | 91 |
GO:1901653 | Colorectum | AD | cellular response to peptide | 114/3918 | 359/18723 | 8.32e-07 | 2.88e-05 | 114 |
GO:0032869 | Colorectum | AD | cellular response to insulin stimulus | 72/3918 | 203/18723 | 1.10e-06 | 3.68e-05 | 72 |
GO:0071375 | Colorectum | AD | cellular response to peptide hormone stimulus | 95/3918 | 290/18723 | 1.50e-06 | 4.66e-05 | 95 |
GO:0043434 | Colorectum | AD | response to peptide hormone | 126/3918 | 414/18723 | 2.70e-06 | 7.86e-05 | 126 |
GO:0007265 | Colorectum | AD | Ras protein signal transduction | 104/3918 | 337/18723 | 1.01e-05 | 2.35e-04 | 104 |
GO:0051056 | Colorectum | AD | regulation of small GTPase mediated signal transduction | 94/3918 | 302/18723 | 1.81e-05 | 3.76e-04 | 94 |
GO:0046578 | Colorectum | AD | regulation of Ras protein signal transduction | 56/3918 | 189/18723 | 2.85e-03 | 2.14e-02 | 56 |
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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 |
DENND4C | SNV | Missense_Mutation | rs542086159 | c.5629N>G | p.Ile1877Val | p.I1877V | protein_coding | tolerated(0.26) | benign(0.072) | TCGA-C5-A7X3-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | SD | |
DENND4C | SNV | Missense_Mutation | rs756614591 | c.1243N>C | p.Glu415Gln | p.E415Q | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-DG-A2KK-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
DENND4C | SNV | Missense_Mutation | c.5762N>A | p.Gly1921Glu | p.G1921E | protein_coding | tolerated(0.05) | benign(0.007) | TCGA-EK-A2RK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | ||
DENND4C | SNV | Missense_Mutation | rs764163681 | c.4127N>T | p.Ser1376Leu | p.S1376L | protein_coding | deleterious(0.05) | benign(0.127) | TCGA-EK-A3GJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
DENND4C | SNV | Missense_Mutation | c.1598A>C | p.Lys533Thr | p.K533T | protein_coding | tolerated(0.31) | possibly_damaging(0.471) | TCGA-FU-A3HZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
DENND4C | SNV | Missense_Mutation | c.1265N>T | p.Ser422Phe | p.S422F | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | ||
DENND4C | SNV | Missense_Mutation | novel | c.3124N>C | p.Asp1042His | p.D1042H | protein_coding | deleterious(0.02) | possibly_damaging(0.897) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
DENND4C | SNV | Missense_Mutation | novel | c.4778C>T | p.Ala1593Val | p.A1593V | protein_coding | deleterious(0.05) | possibly_damaging(0.571) | TCGA-VS-A9UT-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
DENND4C | SNV | Missense_Mutation | c.5844N>T | p.Trp1948Cys | p.W1948C | protein_coding | deleterious(0.05) | benign(0.026) | TCGA-A6-4105-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
DENND4C | SNV | Missense_Mutation | rs753295343 | c.3067N>T | p.Pro1023Ser | p.P1023S | protein_coding | tolerated(0.15) | benign(0.019) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | 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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