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Gene: PLEKHF1 |
Gene summary for PLEKHF1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PLEKHF1 | Gene ID | 79156 |
Gene name | pleckstrin homology and FYVE domain containing 1 | |
Gene Alias | APPD | |
Cytomap | 19q12 | |
Gene Type | protein-coding | GO ID | GO:0006914 | UniProtAcc | Q96S99 |
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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 |
79156 | PLEKHF1 | P36T-E | Human | Esophagus | ESCC | 1.14e-09 | 3.66e-01 | 0.1187 |
79156 | PLEKHF1 | P37T-E | Human | Esophagus | ESCC | 2.76e-17 | 3.33e-01 | 0.1371 |
79156 | PLEKHF1 | P38T-E | Human | Esophagus | ESCC | 2.33e-10 | 5.92e-01 | 0.127 |
79156 | PLEKHF1 | P40T-E | Human | Esophagus | ESCC | 3.82e-03 | 2.85e-01 | 0.109 |
79156 | PLEKHF1 | P42T-E | Human | Esophagus | ESCC | 3.59e-03 | 1.03e-01 | 0.1175 |
79156 | PLEKHF1 | P44T-E | Human | Esophagus | ESCC | 2.26e-07 | 1.92e-01 | 0.1096 |
79156 | PLEKHF1 | P47T-E | Human | Esophagus | ESCC | 6.84e-13 | 3.21e-01 | 0.1067 |
79156 | PLEKHF1 | P49T-E | Human | Esophagus | ESCC | 4.82e-09 | 4.86e-01 | 0.1768 |
79156 | PLEKHF1 | P52T-E | Human | Esophagus | ESCC | 1.57e-14 | 4.01e-01 | 0.1555 |
79156 | PLEKHF1 | P57T-E | Human | Esophagus | ESCC | 1.25e-08 | 1.25e-01 | 0.0926 |
79156 | PLEKHF1 | P62T-E | Human | Esophagus | ESCC | 6.03e-19 | 2.96e-01 | 0.1302 |
79156 | PLEKHF1 | P65T-E | Human | Esophagus | ESCC | 9.47e-12 | 2.86e-01 | 0.0978 |
79156 | PLEKHF1 | P74T-E | Human | Esophagus | ESCC | 5.87e-22 | 6.89e-01 | 0.1479 |
79156 | PLEKHF1 | P75T-E | Human | Esophagus | ESCC | 1.67e-30 | 7.43e-01 | 0.1125 |
79156 | PLEKHF1 | P76T-E | Human | Esophagus | ESCC | 1.04e-23 | 5.57e-01 | 0.1207 |
79156 | PLEKHF1 | P79T-E | Human | Esophagus | ESCC | 6.48e-15 | 2.47e-01 | 0.1154 |
79156 | PLEKHF1 | P80T-E | Human | Esophagus | ESCC | 3.70e-08 | 3.48e-01 | 0.155 |
79156 | PLEKHF1 | P82T-E | Human | Esophagus | ESCC | 1.29e-06 | 7.14e-01 | 0.1072 |
79156 | PLEKHF1 | P83T-E | Human | Esophagus | ESCC | 8.89e-17 | 5.42e-01 | 0.1738 |
79156 | PLEKHF1 | P126T-E | Human | Esophagus | ESCC | 2.93e-02 | 3.64e-01 | 0.1125 |
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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:0097193111 | Esophagus | ESCC | intrinsic apoptotic signaling pathway | 222/8552 | 288/18723 | 5.87e-28 | 2.02e-25 | 222 |
GO:2001233111 | Esophagus | ESCC | regulation of apoptotic signaling pathway | 256/8552 | 356/18723 | 4.11e-24 | 1.04e-21 | 256 |
GO:0009896111 | Esophagus | ESCC | positive regulation of catabolic process | 332/8552 | 492/18723 | 4.36e-23 | 9.22e-21 | 332 |
GO:0031331111 | Esophagus | ESCC | positive regulation of cellular catabolic process | 292/8552 | 427/18723 | 8.67e-22 | 1.53e-19 | 292 |
GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
GO:001050617 | Esophagus | ESCC | regulation of autophagy | 220/8552 | 317/18723 | 6.72e-18 | 6.36e-16 | 220 |
GO:2001242111 | Esophagus | ESCC | regulation of intrinsic apoptotic signaling pathway | 128/8552 | 164/18723 | 1.75e-17 | 1.50e-15 | 128 |
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:2001235110 | Esophagus | ESCC | positive regulation of apoptotic signaling pathway | 92/8552 | 126/18723 | 3.91e-10 | 1.05e-08 | 92 |
GO:000703214 | Esophagus | ESCC | endosome organization | 61/8552 | 82/18723 | 1.13e-07 | 1.85e-06 | 61 |
GO:001050816 | Esophagus | ESCC | positive regulation of autophagy | 81/8552 | 124/18723 | 7.74e-06 | 7.65e-05 | 81 |
GO:200124417 | Esophagus | ESCC | positive regulation of intrinsic apoptotic signaling pathway | 43/8552 | 58/18723 | 9.86e-06 | 9.37e-05 | 43 |
GO:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
GO:001050621 | Liver | HCC | regulation of autophagy | 210/7958 | 317/18723 | 7.59e-18 | 8.45e-16 | 210 |
GO:200123322 | Liver | HCC | regulation of apoptotic signaling pathway | 226/7958 | 356/18723 | 7.26e-16 | 5.68e-14 | 226 |
GO:001605021 | Liver | HCC | vesicle organization | 194/7958 | 300/18723 | 5.58e-15 | 3.97e-13 | 194 |
GO:009719322 | Liver | HCC | intrinsic apoptotic signaling pathway | 184/7958 | 288/18723 | 1.50e-13 | 8.32e-12 | 184 |
GO:007265921 | Liver | HCC | protein localization to plasma membrane | 177/7958 | 284/18723 | 1.02e-11 | 4.18e-10 | 177 |
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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 |
PLEKHF1 | SNV | Missense_Mutation | rs780377669 | c.355N>T | p.Arg119Cys | p.R119C | Q96S99 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-AC-A62X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PLEKHF1 | deletion | Frame_Shift_Del | novel | c.6delN | p.Asp3ThrfsTer40 | p.D3Tfs*40 | Q96S99 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
PLEKHF1 | SNV | Missense_Mutation | rs867833514 | c.296N>A | p.Arg99His | p.R99H | Q96S99 | protein_coding | deleterious(0.04) | probably_damaging(0.953) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PLEKHF1 | SNV | Missense_Mutation | novel | c.239N>C | p.Ile80Thr | p.I80T | Q96S99 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-MA-AA3X-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
PLEKHF1 | SNV | Missense_Mutation | c.583N>T | p.Arg195Cys | p.R195C | Q96S99 | protein_coding | tolerated(0.11) | benign(0.111) | TCGA-5M-AAT5-01 | Colorectum | colon adenocarcinoma | Unknown | Unknown | I/II | Unknown | Unknown | Unknown | |
PLEKHF1 | SNV | Missense_Mutation | c.370N>T | p.Ser124Cys | p.S124C | Q96S99 | protein_coding | tolerated(0.06) | benign(0.033) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
PLEKHF1 | deletion | Frame_Shift_Del | c.240delN | p.Leu82TrpfsTer20 | p.L82Wfs*20 | Q96S99 | protein_coding | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
PLEKHF1 | SNV | Missense_Mutation | rs531732264 | c.751G>A | p.Glu251Lys | p.E251K | Q96S99 | protein_coding | tolerated(0.1) | benign(0.225) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
PLEKHF1 | SNV | Missense_Mutation | rs867833514 | c.296N>A | p.Arg99His | p.R99H | Q96S99 | protein_coding | deleterious(0.04) | probably_damaging(0.953) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
PLEKHF1 | SNV | Missense_Mutation | novel | c.466G>A | p.Asp156Asn | p.D156N | Q96S99 | protein_coding | tolerated(0.52) | benign(0.115) | TCGA-B5-A3FC-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 |
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