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Gene: CLIP2 |
Gene summary for CLIP2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | CLIP2 | Gene ID | 7461 |
Gene name | CAP-Gly domain containing linker protein 2 | |
Gene Alias | CLIP | |
Cytomap | 7q11.23 | |
Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | A0A140VJG6 |
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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 |
7461 | CLIP2 | A002-C-114 | Human | Colorectum | FAP | 4.17e-10 | -1.01e-01 | -0.1561 |
7461 | CLIP2 | A015-C-104 | Human | Colorectum | FAP | 1.98e-27 | -3.89e-02 | -0.1899 |
7461 | CLIP2 | A001-C-014 | Human | Colorectum | FAP | 4.18e-12 | -2.39e-01 | 0.0135 |
7461 | CLIP2 | A002-C-016 | Human | Colorectum | FAP | 1.31e-19 | -1.94e-01 | 0.0521 |
7461 | CLIP2 | A015-C-002 | Human | Colorectum | FAP | 1.99e-05 | -9.92e-02 | -0.0763 |
7461 | CLIP2 | A001-C-203 | Human | Colorectum | FAP | 2.26e-07 | 7.57e-03 | -0.0481 |
7461 | CLIP2 | A002-C-116 | Human | Colorectum | FAP | 1.23e-30 | -1.80e-01 | -0.0452 |
7461 | CLIP2 | A014-C-008 | Human | Colorectum | FAP | 3.47e-08 | -2.31e-01 | -0.191 |
7461 | CLIP2 | A018-E-020 | Human | Colorectum | FAP | 6.29e-12 | -8.48e-02 | -0.2034 |
7461 | CLIP2 | F034 | Human | Colorectum | FAP | 2.69e-20 | 1.24e-02 | -0.0665 |
7461 | CLIP2 | F072B | Human | Colorectum | FAP | 1.32e-13 | -2.17e-01 | 0.257 |
7461 | CLIP2 | CRC-1-8810 | Human | Colorectum | CRC | 2.34e-04 | -1.81e-01 | 0.6257 |
7461 | CLIP2 | CRC-3-11773 | Human | Colorectum | CRC | 1.24e-07 | 2.80e-01 | 0.2564 |
7461 | CLIP2 | AEH-subject4 | Human | Endometrium | AEH | 3.40e-04 | 2.60e-01 | -0.2657 |
7461 | CLIP2 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 7.20e-04 | -2.71e-02 | -0.1917 |
7461 | CLIP2 | P2T-E | Human | Esophagus | ESCC | 1.80e-10 | 5.52e-02 | 0.1177 |
7461 | CLIP2 | P5T-E | Human | Esophagus | ESCC | 1.42e-05 | 5.04e-02 | 0.1327 |
7461 | CLIP2 | P8T-E | Human | Esophagus | ESCC | 6.50e-03 | 1.11e-02 | 0.0889 |
7461 | CLIP2 | P9T-E | Human | Esophagus | ESCC | 8.83e-03 | 6.84e-02 | 0.1131 |
7461 | CLIP2 | P10T-E | Human | Esophagus | ESCC | 1.29e-18 | 1.41e-01 | 0.116 |
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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:0031122 | Colorectum | FAP | cytoplasmic microtubule organization | 17/2622 | 56/18723 | 1.24e-03 | 1.16e-02 | 17 |
GO:00311221 | Colorectum | CRC | cytoplasmic microtubule organization | 16/2078 | 56/18723 | 2.72e-04 | 4.37e-03 | 16 |
GO:00311227 | Esophagus | ESCC | cytoplasmic microtubule organization | 38/8552 | 56/18723 | 6.60e-04 | 3.50e-03 | 38 |
GO:00311222 | Liver | HCC | cytoplasmic microtubule organization | 35/7958 | 56/18723 | 2.00e-03 | 1.01e-02 | 35 |
GO:00311225 | Prostate | BPH | cytoplasmic microtubule organization | 22/3107 | 56/18723 | 4.21e-05 | 4.48e-04 | 22 |
GO:00311229 | Thyroid | PTC | cytoplasmic microtubule organization | 34/5968 | 56/18723 | 8.20e-06 | 9.42e-05 | 34 |
GO:003112215 | Thyroid | ATC | cytoplasmic microtubule organization | 34/6293 | 56/18723 | 2.92e-05 | 2.45e-04 | 34 |
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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 |
CLIP2 | SNV | Missense_Mutation | rs150588666 | c.1727N>T | p.Ala576Val | p.A576V | Q9UDT6 | protein_coding | deleterious(0.03) | benign(0.014) | TCGA-3C-AAAU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | zoladex | SD |
CLIP2 | SNV | Missense_Mutation | rs782223327 | c.2299N>A | p.Glu767Lys | p.E767K | Q9UDT6 | protein_coding | tolerated(0.12) | benign(0) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD |
CLIP2 | SNV | Missense_Mutation | c.1925N>G | p.Gln642Arg | p.Q642R | Q9UDT6 | protein_coding | deleterious(0) | possibly_damaging(0.574) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
CLIP2 | SNV | Missense_Mutation | rs782280647 | c.2539N>A | p.Glu847Lys | p.E847K | Q9UDT6 | protein_coding | deleterious(0.03) | benign(0.086) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CLIP2 | SNV | Missense_Mutation | c.2221G>C | p.Glu741Gln | p.E741Q | Q9UDT6 | protein_coding | tolerated(0.09) | benign(0.399) | TCGA-BH-A18F-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
CLIP2 | SNV | Missense_Mutation | c.1124G>A | p.Arg375Gln | p.R375Q | Q9UDT6 | protein_coding | deleterious(0.02) | probably_damaging(0.992) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
CLIP2 | SNV | Missense_Mutation | rs553860682 | c.77G>T | p.Gly26Val | p.G26V | Q9UDT6 | protein_coding | deleterious(0.03) | probably_damaging(0.999) | TCGA-EW-A3U0-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
CLIP2 | insertion | In_Frame_Ins | novel | c.913_914insTAGGAAAAAAAAATTTCTGGAAAGGAAAAGTAACTA | p.Ala305delinsValGlyLysLysAsnPheTrpLysGlyLysValThrThr | p.A305delinsVGKKNFWKGKVTT | Q9UDT6 | protein_coding | TCGA-AN-A0FS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
CLIP2 | SNV | Missense_Mutation | rs199904386 | c.419C>T | p.Thr140Met | p.T140M | Q9UDT6 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
CLIP2 | SNV | Missense_Mutation | rs368779286 | c.2762G>A | p.Arg921His | p.R921H | Q9UDT6 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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