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Gene: RAPGEF6 |
Gene summary for RAPGEF6 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RAPGEF6 | Gene ID | 51735 |
Gene name | Rap guanine nucleotide exchange factor 6 | |
Gene Alias | KIA001LB | |
Cytomap | 5q31.1 | |
Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | B2RTU6 |
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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 |
51735 | RAPGEF6 | AEH-subject1 | Human | Endometrium | AEH | 7.90e-19 | 4.11e-01 | -0.3059 |
51735 | RAPGEF6 | AEH-subject2 | Human | Endometrium | AEH | 8.80e-04 | 2.51e-01 | -0.2525 |
51735 | RAPGEF6 | AEH-subject3 | Human | Endometrium | AEH | 8.88e-06 | 2.88e-01 | -0.2576 |
51735 | RAPGEF6 | AEH-subject4 | Human | Endometrium | AEH | 1.24e-09 | 3.81e-01 | -0.2657 |
51735 | RAPGEF6 | AEH-subject5 | Human | Endometrium | AEH | 1.06e-19 | 5.40e-01 | -0.2953 |
51735 | RAPGEF6 | EEC-subject1 | Human | Endometrium | EEC | 1.44e-24 | 5.73e-01 | -0.2682 |
51735 | RAPGEF6 | EEC-subject2 | Human | Endometrium | EEC | 2.71e-14 | 3.88e-01 | -0.2607 |
51735 | RAPGEF6 | EEC-subject3 | Human | Endometrium | EEC | 1.71e-04 | 2.45e-01 | -0.2525 |
51735 | RAPGEF6 | EEC-subject4 | Human | Endometrium | EEC | 6.85e-10 | 3.30e-01 | -0.2571 |
51735 | RAPGEF6 | EEC-subject5 | Human | Endometrium | EEC | 3.23e-17 | 4.64e-01 | -0.249 |
51735 | RAPGEF6 | LZE2T | Human | Esophagus | ESCC | 2.26e-02 | 3.98e-01 | 0.082 |
51735 | RAPGEF6 | LZE4T | Human | Esophagus | ESCC | 1.36e-05 | 3.09e-01 | 0.0811 |
51735 | RAPGEF6 | LZE7T | Human | Esophagus | ESCC | 8.89e-03 | 3.00e-01 | 0.0667 |
51735 | RAPGEF6 | LZE8T | Human | Esophagus | ESCC | 6.75e-04 | 2.16e-01 | 0.067 |
51735 | RAPGEF6 | LZE22D1 | Human | Esophagus | HGIN | 1.09e-02 | 1.64e-01 | 0.0595 |
51735 | RAPGEF6 | LZE22T | Human | Esophagus | ESCC | 1.28e-02 | 2.05e-01 | 0.068 |
51735 | RAPGEF6 | LZE24T | Human | Esophagus | ESCC | 9.31e-15 | 3.56e-01 | 0.0596 |
51735 | RAPGEF6 | LZE6T | Human | Esophagus | ESCC | 2.23e-03 | 1.87e-01 | 0.0845 |
51735 | RAPGEF6 | P2T-E | Human | Esophagus | ESCC | 1.04e-15 | 2.87e-01 | 0.1177 |
51735 | RAPGEF6 | P4T-E | Human | Esophagus | ESCC | 3.34e-09 | 1.12e-01 | 0.1323 |
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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:007265914 | Endometrium | AEH | protein localization to plasma membrane | 63/2100 | 284/18723 | 7.58e-08 | 3.92e-06 | 63 |
GO:19907789 | Endometrium | AEH | protein localization to cell periphery | 68/2100 | 333/18723 | 6.38e-07 | 2.38e-05 | 68 |
GO:00430878 | Endometrium | AEH | regulation of GTPase activity | 66/2100 | 348/18723 | 1.26e-05 | 2.77e-04 | 66 |
GO:00072657 | Endometrium | AEH | Ras protein signal transduction | 63/2100 | 337/18723 | 3.09e-05 | 5.66e-04 | 63 |
GO:00435477 | Endometrium | AEH | positive regulation of GTPase activity | 48/2100 | 255/18723 | 2.18e-04 | 2.67e-03 | 48 |
GO:007265915 | Endometrium | EEC | protein localization to plasma membrane | 64/2168 | 284/18723 | 1.05e-07 | 5.05e-06 | 64 |
GO:199077814 | Endometrium | EEC | protein localization to cell periphery | 69/2168 | 333/18723 | 9.71e-07 | 3.31e-05 | 69 |
GO:004308712 | Endometrium | EEC | regulation of GTPase activity | 67/2168 | 348/18723 | 1.84e-05 | 3.43e-04 | 67 |
GO:000726513 | Endometrium | EEC | Ras protein signal transduction | 64/2168 | 337/18723 | 4.31e-05 | 7.10e-04 | 64 |
GO:004354712 | Endometrium | EEC | positive regulation of GTPase activity | 50/2168 | 255/18723 | 1.26e-04 | 1.66e-03 | 50 |
GO:007265920 | Esophagus | HGIN | protein localization to plasma membrane | 66/2587 | 284/18723 | 1.11e-05 | 3.18e-04 | 66 |
GO:199077818 | Esophagus | HGIN | protein localization to cell periphery | 71/2587 | 333/18723 | 1.05e-04 | 2.24e-03 | 71 |
GO:0072659110 | Esophagus | ESCC | protein localization to plasma membrane | 193/8552 | 284/18723 | 1.95e-14 | 1.03e-12 | 193 |
GO:199077819 | Esophagus | ESCC | protein localization to cell periphery | 217/8552 | 333/18723 | 4.08e-13 | 1.88e-11 | 217 |
GO:000726510 | Esophagus | ESCC | Ras protein signal transduction | 201/8552 | 337/18723 | 1.44e-07 | 2.30e-06 | 201 |
GO:00300339 | Esophagus | ESCC | microvillus assembly | 13/8552 | 16/18723 | 4.05e-03 | 1.62e-02 | 13 |
GO:004308715 | Esophagus | ESCC | regulation of GTPase activity | 183/8552 | 348/18723 | 5.34e-03 | 2.00e-02 | 183 |
GO:00726598 | Lung | IAC | protein localization to plasma membrane | 60/2061 | 284/18723 | 4.74e-07 | 3.10e-05 | 60 |
GO:19907787 | Lung | IAC | protein localization to cell periphery | 66/2061 | 333/18723 | 1.44e-06 | 7.22e-05 | 66 |
GO:00430876 | Lung | IAC | regulation of GTPase activity | 67/2061 | 348/18723 | 3.43e-06 | 1.44e-04 | 67 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0453026 | Endometrium | AEH | Tight junction | 54/1197 | 169/8465 | 1.99e-09 | 3.80e-08 | 2.78e-08 | 54 |
hsa0401514 | Endometrium | AEH | Rap1 signaling pathway | 49/1197 | 210/8465 | 2.03e-04 | 1.78e-03 | 1.30e-03 | 49 |
hsa04530112 | Endometrium | AEH | Tight junction | 54/1197 | 169/8465 | 1.99e-09 | 3.80e-08 | 2.78e-08 | 54 |
hsa0401515 | Endometrium | AEH | Rap1 signaling pathway | 49/1197 | 210/8465 | 2.03e-04 | 1.78e-03 | 1.30e-03 | 49 |
hsa0453027 | Endometrium | EEC | Tight junction | 54/1237 | 169/8465 | 6.56e-09 | 1.27e-07 | 9.46e-08 | 54 |
hsa0401522 | Endometrium | EEC | Rap1 signaling pathway | 49/1237 | 210/8465 | 4.45e-04 | 3.47e-03 | 2.59e-03 | 49 |
hsa0453036 | Endometrium | EEC | Tight junction | 54/1237 | 169/8465 | 6.56e-09 | 1.27e-07 | 9.46e-08 | 54 |
hsa0401532 | Endometrium | EEC | Rap1 signaling pathway | 49/1237 | 210/8465 | 4.45e-04 | 3.47e-03 | 2.59e-03 | 49 |
hsa0453039 | Esophagus | HGIN | Tight junction | 40/1383 | 169/8465 | 8.18e-03 | 4.71e-02 | 3.74e-02 | 40 |
hsa04530115 | Esophagus | HGIN | Tight junction | 40/1383 | 169/8465 | 8.18e-03 | 4.71e-02 | 3.74e-02 | 40 |
hsa04530211 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
hsa04530310 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
hsa0453016 | Lung | IAC | Tight junction | 43/1053 | 169/8465 | 2.44e-06 | 8.81e-05 | 5.85e-05 | 43 |
hsa0401510 | Lung | IAC | Rap1 signaling pathway | 41/1053 | 210/8465 | 2.01e-03 | 1.07e-02 | 7.10e-03 | 41 |
hsa0453017 | Lung | IAC | Tight junction | 43/1053 | 169/8465 | 2.44e-06 | 8.81e-05 | 5.85e-05 | 43 |
hsa0401511 | Lung | IAC | Rap1 signaling pathway | 41/1053 | 210/8465 | 2.01e-03 | 1.07e-02 | 7.10e-03 | 41 |
hsa0453023 | Lung | AIS | Tight junction | 46/961 | 169/8465 | 7.79e-09 | 4.33e-07 | 2.77e-07 | 46 |
hsa0401521 | Lung | AIS | Rap1 signaling pathway | 41/961 | 210/8465 | 3.23e-04 | 3.38e-03 | 2.16e-03 | 41 |
hsa0453033 | Lung | AIS | Tight junction | 46/961 | 169/8465 | 7.79e-09 | 4.33e-07 | 2.77e-07 | 46 |
hsa0401531 | Lung | AIS | Rap1 signaling pathway | 41/961 | 210/8465 | 3.23e-04 | 3.38e-03 | 2.16e-03 | 41 |
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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 |
RAPGEF6 | SNV | Missense_Mutation | c.422G>C | p.Arg141Thr | p.R141T | Q8TEU7 | protein_coding | deleterious(0.04) | possibly_damaging(0.795) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
RAPGEF6 | SNV | Missense_Mutation | c.625N>G | p.Gln209Glu | p.Q209E | Q8TEU7 | protein_coding | deleterious(0.04) | probably_damaging(0.989) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
RAPGEF6 | SNV | Missense_Mutation | c.3955N>C | p.Glu1319Gln | p.E1319Q | Q8TEU7 | protein_coding | tolerated_low_confidence(0.31) | benign(0.013) | TCGA-EW-A1IW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | aromasin | SD | |
RAPGEF6 | SNV | Missense_Mutation | c.715N>A | p.Glu239Lys | p.E239K | Q8TEU7 | protein_coding | tolerated(0.35) | benign(0.04) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
RAPGEF6 | SNV | Missense_Mutation | rs761250497 | c.2629N>T | p.Arg877Cys | p.R877C | Q8TEU7 | protein_coding | tolerated(0.09) | benign(0.055) | TCGA-WT-AB44-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
RAPGEF6 | insertion | Frame_Shift_Ins | novel | c.4709_4710insATGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAG | p.Pro1571TrpfsTer21 | p.P1571Wfs*21 | Q8TEU7 | protein_coding | TCGA-A8-A07F-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
RAPGEF6 | insertion | Nonsense_Mutation | novel | c.2008_2009insAACAGTCTAA | p.Ser670Ter | p.S670* | Q8TEU7 | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RAPGEF6 | insertion | Nonsense_Mutation | novel | c.2006_2007insCTGACTATTAACAGTCCTTTAGCAGTTTAT | p.Val669_Ser670insTer | p.V669_S670ins* | Q8TEU7 | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RAPGEF6 | insertion | Nonsense_Mutation | novel | c.2089_2090insTTTGATTAATGTTTATTGGTCTTGAGCTTACCTATATTTATCCTTCA | p.Gly697ValfsTer2 | p.G697Vfs*2 | Q8TEU7 | protein_coding | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RAPGEF6 | insertion | Frame_Shift_Ins | novel | c.389_390insGAACTCCCACTGGT | p.Arg131AsnfsTer5 | p.R131Nfs*5 | Q8TEU7 | 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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