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Gene: INPP4A |
Gene summary for INPP4A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | INPP4A | Gene ID | 3631 |
| Gene name | inositol polyphosphate-4-phosphatase type I A | |
| Gene Alias | INPP4 | |
| Cytomap | 2q11.2 | |
| Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | Q96PE3 |
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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 |
| 3631 | INPP4A | HTA11_696_2000001011 | Human | Colorectum | AD | 6.70e-05 | 5.37e-01 | -0.1464 |
| 3631 | INPP4A | HTA11_2992_2000001011 | Human | Colorectum | SER | 5.49e-03 | 6.26e-01 | -0.1706 |
| 3631 | INPP4A | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.99e-05 | 6.10e-01 | -0.2061 |
| 3631 | INPP4A | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.23e-03 | -2.10e-01 | 0.294 |
| 3631 | INPP4A | A002-C-010 | Human | Colorectum | FAP | 6.50e-04 | -1.65e-01 | 0.242 |
| 3631 | INPP4A | A015-C-203 | Human | Colorectum | FAP | 5.15e-20 | -3.47e-01 | -0.1294 |
| 3631 | INPP4A | A002-C-201 | Human | Colorectum | FAP | 1.06e-05 | -2.21e-01 | 0.0324 |
| 3631 | INPP4A | A002-C-203 | Human | Colorectum | FAP | 1.24e-02 | -1.25e-01 | 0.2786 |
| 3631 | INPP4A | A001-C-119 | Human | Colorectum | FAP | 3.98e-03 | -2.15e-01 | -0.1557 |
| 3631 | INPP4A | A001-C-108 | Human | Colorectum | FAP | 1.47e-09 | -2.21e-01 | -0.0272 |
| 3631 | INPP4A | A002-C-205 | Human | Colorectum | FAP | 4.62e-10 | -3.26e-01 | -0.1236 |
| 3631 | INPP4A | A001-C-104 | Human | Colorectum | FAP | 3.84e-03 | -1.50e-01 | 0.0184 |
| 3631 | INPP4A | A015-C-006 | Human | Colorectum | FAP | 3.59e-05 | -2.88e-01 | -0.0994 |
| 3631 | INPP4A | A015-C-106 | Human | Colorectum | FAP | 6.30e-10 | -2.17e-01 | -0.0511 |
| 3631 | INPP4A | A002-C-114 | Human | Colorectum | FAP | 4.18e-07 | -2.55e-01 | -0.1561 |
| 3631 | INPP4A | A015-C-104 | Human | Colorectum | FAP | 1.21e-18 | -3.09e-01 | -0.1899 |
| 3631 | INPP4A | A001-C-014 | Human | Colorectum | FAP | 1.33e-09 | -2.41e-01 | 0.0135 |
| 3631 | INPP4A | A002-C-016 | Human | Colorectum | FAP | 1.58e-11 | -1.98e-01 | 0.0521 |
| 3631 | INPP4A | A015-C-002 | Human | Colorectum | FAP | 7.88e-04 | -2.00e-01 | -0.0763 |
| 3631 | INPP4A | A001-C-203 | Human | Colorectum | FAP | 1.12e-07 | -1.76e-01 | -0.0481 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
| GO:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
| GO:0006650 | Colorectum | AD | glycerophospholipid metabolic process | 83/3918 | 306/18723 | 5.40e-03 | 3.55e-02 | 83 |
| GO:0006644 | Colorectum | AD | phospholipid metabolic process | 101/3918 | 383/18723 | 5.80e-03 | 3.67e-02 | 101 |
| GO:0045017 | Colorectum | AD | glycerolipid biosynthetic process | 69/3918 | 252/18723 | 8.33e-03 | 4.88e-02 | 69 |
| GO:00060661 | Colorectum | SER | alcohol metabolic process | 79/2897 | 353/18723 | 3.50e-04 | 5.50e-03 | 79 |
| GO:0046486 | Colorectum | SER | glycerolipid metabolic process | 82/2897 | 392/18723 | 2.26e-03 | 2.17e-02 | 82 |
| GO:00163111 | Colorectum | SER | dephosphorylation | 86/2897 | 417/18723 | 2.73e-03 | 2.46e-02 | 86 |
| GO:00066441 | Colorectum | SER | phospholipid metabolic process | 79/2897 | 383/18723 | 3.94e-03 | 3.24e-02 | 79 |
| GO:00450171 | Colorectum | SER | glycerolipid biosynthetic process | 55/2897 | 252/18723 | 4.47e-03 | 3.56e-02 | 55 |
| GO:00066501 | Colorectum | SER | glycerophospholipid metabolic process | 64/2897 | 306/18723 | 6.41e-03 | 4.60e-02 | 64 |
| GO:00060662 | Colorectum | MSS | alcohol metabolic process | 92/3467 | 353/18723 | 2.57e-04 | 3.46e-03 | 92 |
| GO:00163112 | Colorectum | MSS | dephosphorylation | 101/3467 | 417/18723 | 1.98e-03 | 1.70e-02 | 101 |
| GO:00163113 | Colorectum | FAP | dephosphorylation | 95/2622 | 417/18723 | 7.07e-07 | 3.32e-05 | 95 |
| GO:0008654 | Colorectum | FAP | phospholipid biosynthetic process | 54/2622 | 253/18723 | 8.88e-04 | 9.08e-03 | 54 |
| GO:00066502 | Colorectum | FAP | glycerophospholipid metabolic process | 62/2622 | 306/18723 | 1.54e-03 | 1.38e-02 | 62 |
| GO:00066442 | Colorectum | FAP | phospholipid metabolic process | 74/2622 | 383/18723 | 2.24e-03 | 1.83e-02 | 74 |
| GO:00060663 | Colorectum | FAP | alcohol metabolic process | 69/2622 | 353/18723 | 2.29e-03 | 1.85e-02 | 69 |
| GO:0046474 | Colorectum | FAP | glycerophospholipid biosynthetic process | 44/2622 | 211/18723 | 3.98e-03 | 2.76e-02 | 44 |
| GO:00450172 | Colorectum | FAP | glycerolipid biosynthetic process | 50/2622 | 252/18723 | 6.32e-03 | 3.95e-02 | 50 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04070 | Colorectum | CRC | Phosphatidylinositol signaling system | 25/1091 | 97/8465 | 4.27e-04 | 4.60e-03 | 3.12e-03 | 25 |
| hsa00562 | Colorectum | CRC | Inositol phosphate metabolism | 18/1091 | 73/8465 | 4.38e-03 | 2.52e-02 | 1.71e-02 | 18 |
| hsa040701 | Colorectum | CRC | Phosphatidylinositol signaling system | 25/1091 | 97/8465 | 4.27e-04 | 4.60e-03 | 3.12e-03 | 25 |
| hsa005621 | Colorectum | CRC | Inositol phosphate metabolism | 18/1091 | 73/8465 | 4.38e-03 | 2.52e-02 | 1.71e-02 | 18 |
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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 |
| INPP4A | SNV | Missense_Mutation | rs768206909 | c.2548C>T | p.Arg850Cys | p.R850C | Q96PE3 | protein_coding | deleterious(0.04) | probably_damaging(0.949) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| INPP4A | SNV | Missense_Mutation | c.998T>G | p.Phe333Cys | p.F333C | Q96PE3 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A07G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| INPP4A | SNV | Missense_Mutation | rs750178020 | c.1426N>A | p.Ala476Thr | p.A476T | Q96PE3 | protein_coding | tolerated(0.53) | possibly_damaging(0.81) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| INPP4A | SNV | Missense_Mutation | rs371798563 | c.2263G>A | p.Ala755Thr | p.A755T | Q96PE3 | protein_coding | tolerated(0.41) | benign(0) | TCGA-AN-A0FW-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| INPP4A | SNV | Missense_Mutation | c.2832N>C | p.Lys944Asn | p.K944N | Q96PE3 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| INPP4A | SNV | Missense_Mutation | c.2592N>C | p.Gln864His | p.Q864H | Q96PE3 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-E2-A1LG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| INPP4A | SNV | Missense_Mutation | novel | c.1895N>A | p.Pro632Gln | p.P632Q | Q96PE3 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-OL-A6VR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| INPP4A | insertion | Frame_Shift_Ins | novel | c.1855_1856insCTTTTTTCTGTGGCATTTATCACATTGT | p.Glu619AlafsTer16 | p.E619Afs*16 | Q96PE3 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| INPP4A | SNV | Missense_Mutation | novel | c.39G>T | p.Arg13Ser | p.R13S | Q96PE3 | protein_coding | deleterious_low_confidence(0) | benign(0.131) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| INPP4A | SNV | Missense_Mutation | novel | c.2272N>A | p.Leu758Met | p.L758M | Q96PE3 | protein_coding | deleterious(0.05) | probably_damaging(0.961) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | 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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