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Gene: PHLDA2 |
Gene summary for PHLDA2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PHLDA2 | Gene ID | 7262 |
Gene name | pleckstrin homology like domain family A member 2 | |
Gene Alias | BRW1C | |
Cytomap | 11p15.4 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q53GA4 |
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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 |
7262 | PHLDA2 | GSM4909280 | Human | Breast | Precancer | 2.97e-09 | 7.28e-01 | 0.0305 |
7262 | PHLDA2 | GSM4909281 | Human | Breast | IDC | 3.84e-12 | -4.58e-01 | 0.21 |
7262 | PHLDA2 | GSM4909282 | Human | Breast | IDC | 5.50e-05 | 4.01e-01 | -0.0288 |
7262 | PHLDA2 | GSM4909286 | Human | Breast | IDC | 1.43e-31 | -6.14e-01 | 0.1081 |
7262 | PHLDA2 | GSM4909288 | Human | Breast | IDC | 2.16e-06 | -5.32e-01 | 0.0988 |
7262 | PHLDA2 | GSM4909293 | Human | Breast | IDC | 3.40e-14 | -4.66e-01 | 0.1581 |
7262 | PHLDA2 | GSM4909294 | Human | Breast | IDC | 1.76e-05 | -3.09e-01 | 0.2022 |
7262 | PHLDA2 | GSM4909296 | Human | Breast | IDC | 1.81e-06 | -1.99e-01 | 0.1524 |
7262 | PHLDA2 | GSM4909297 | Human | Breast | IDC | 4.79e-07 | 1.46e-01 | 0.1517 |
7262 | PHLDA2 | GSM4909298 | Human | Breast | IDC | 3.72e-08 | -4.17e-01 | 0.1551 |
7262 | PHLDA2 | GSM4909301 | Human | Breast | IDC | 9.81e-10 | -3.92e-01 | 0.1577 |
7262 | PHLDA2 | GSM4909302 | Human | Breast | IDC | 7.17e-03 | -3.31e-01 | 0.1545 |
7262 | PHLDA2 | GSM4909306 | Human | Breast | IDC | 2.62e-05 | -3.36e-01 | 0.1564 |
7262 | PHLDA2 | GSM4909308 | Human | Breast | IDC | 3.64e-03 | 1.94e-01 | 0.158 |
7262 | PHLDA2 | GSM4909311 | Human | Breast | IDC | 8.70e-23 | -4.84e-01 | 0.1534 |
7262 | PHLDA2 | GSM4909312 | Human | Breast | IDC | 1.82e-25 | -5.29e-01 | 0.1552 |
7262 | PHLDA2 | GSM4909315 | Human | Breast | IDC | 7.24e-04 | -2.91e-01 | 0.21 |
7262 | PHLDA2 | GSM4909317 | Human | Breast | IDC | 1.17e-02 | 3.50e-01 | 0.1355 |
7262 | PHLDA2 | GSM4909319 | Human | Breast | IDC | 7.15e-30 | -3.94e-01 | 0.1563 |
7262 | PHLDA2 | GSM4909320 | Human | Breast | IDC | 7.05e-03 | -2.24e-01 | 0.1575 |
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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:00485685 | Prostate | Tumor | embryonic organ development | 93/3246 | 427/18723 | 9.84e-03 | 4.18e-02 | 93 |
GO:0006091111 | Skin | cSCC | generation of precursor metabolites and energy | 224/4864 | 490/18723 | 1.13e-21 | 2.21e-19 | 224 |
GO:001598026 | Skin | cSCC | energy derivation by oxidation of organic compounds | 154/4864 | 318/18723 | 4.19e-18 | 5.15e-16 | 154 |
GO:005109827 | Skin | cSCC | regulation of binding | 152/4864 | 363/18723 | 2.21e-11 | 1.10e-09 | 152 |
GO:000170124 | Skin | cSCC | in utero embryonic development | 150/4864 | 367/18723 | 2.47e-10 | 1.04e-08 | 150 |
GO:004339325 | Skin | cSCC | regulation of protein binding | 79/4864 | 196/18723 | 7.59e-06 | 1.04e-04 | 79 |
GO:000189223 | Skin | cSCC | embryonic placenta development | 39/4864 | 82/18723 | 2.08e-05 | 2.43e-04 | 39 |
GO:006145825 | Skin | cSCC | reproductive system development | 149/4864 | 427/18723 | 2.30e-05 | 2.65e-04 | 149 |
GO:004860824 | Skin | cSCC | reproductive structure development | 148/4864 | 424/18723 | 2.40e-05 | 2.74e-04 | 148 |
GO:000189024 | Skin | cSCC | placenta development | 60/4864 | 144/18723 | 2.84e-05 | 3.17e-04 | 60 |
GO:004346720 | Skin | cSCC | regulation of generation of precursor metabolites and energy | 51/4864 | 130/18723 | 6.18e-04 | 4.46e-03 | 51 |
GO:000599610 | Skin | cSCC | monosaccharide metabolic process | 85/4864 | 257/18723 | 6.43e-03 | 3.14e-02 | 85 |
GO:004599521 | Skin | cSCC | regulation of embryonic development | 26/4864 | 64/18723 | 7.34e-03 | 3.47e-02 | 26 |
GO:000600610 | Skin | cSCC | glucose metabolic process | 66/4864 | 196/18723 | 9.75e-03 | 4.32e-02 | 66 |
GO:00060916 | Stomach | GC | generation of precursor metabolites and energy | 88/1159 | 490/18723 | 6.82e-20 | 9.27e-17 | 88 |
GO:00159806 | Stomach | GC | energy derivation by oxidation of organic compounds | 64/1159 | 318/18723 | 2.79e-17 | 2.16e-14 | 64 |
GO:00510986 | Stomach | GC | regulation of binding | 46/1159 | 363/18723 | 3.02e-06 | 1.25e-04 | 46 |
GO:00620124 | Stomach | GC | regulation of small molecule metabolic process | 40/1159 | 334/18723 | 4.84e-05 | 1.15e-03 | 40 |
GO:00434675 | Stomach | GC | regulation of generation of precursor metabolites and energy | 20/1159 | 130/18723 | 1.43e-04 | 2.64e-03 | 20 |
GO:00059964 | Stomach | GC | monosaccharide metabolic process | 31/1159 | 257/18723 | 2.90e-04 | 4.67e-03 | 31 |
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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 |
PHLDA2 | MYOFIB | Cervix | HSIL_HPV | SERPINI1,NDUFA4L2,CRIP1, etc. | 1.00e-01 | |
PHLDA2 | M1MAC | Pancreas | PDAC | UTP6,BCL2L13,CCL20, etc. | 7.45e-02 |
∗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 |
PHLDA2 | SNV | Missense_Mutation | c.28N>C | p.Glu10Gln | p.E10Q | Q53GA4 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
PHLDA2 | SNV | Missense_Mutation | c.137N>C | p.Arg46Pro | p.R46P | Q53GA4 | protein_coding | deleterious(0) | benign(0.013) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PHLDA2 | SNV | Missense_Mutation | novel | c.80A>T | p.Lys27Met | p.K27M | Q53GA4 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PHLDA2 | SNV | Missense_Mutation | novel | c.278N>T | p.Ala93Val | p.A93V | Q53GA4 | protein_coding | tolerated(0.11) | benign(0.019) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
PHLDA2 | SNV | Missense_Mutation | novel | c.250N>G | p.Cys84Gly | p.C84G | Q53GA4 | protein_coding | deleterious(0.02) | probably_damaging(0.961) | TCGA-D1-A167-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PHLDA2 | SNV | Missense_Mutation | c.259N>A | p.Glu87Lys | p.E87K | Q53GA4 | protein_coding | deleterious(0.02) | benign(0.204) | TCGA-95-7948-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
PHLDA2 | SNV | Missense_Mutation | novel | c.161N>G | p.Ser54Cys | p.S54C | Q53GA4 | protein_coding | tolerated(0.05) | probably_damaging(0.971) | TCGA-BA-5152-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
PHLDA2 | SNV | Missense_Mutation | rs755568865 | c.16N>A | p.Glu6Lys | p.E6K | Q53GA4 | protein_coding | tolerated(1) | benign(0.148) | TCGA-CV-7423-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
PHLDA2 | SNV | Missense_Mutation | rs878960560 | c.98C>T | p.Ser33Phe | p.S33F | Q53GA4 | protein_coding | deleterious(0) | benign(0.321) | TCGA-P3-A6T5-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PHLDA2 | SNV | Missense_Mutation | c.228N>A | p.Asp76Glu | p.D76E | Q53GA4 | protein_coding | tolerated(0.5) | possibly_damaging(0.754) | TCGA-BR-4294-01 | Stomach | stomach adenocarcinoma | Male | >=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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