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Gene: CLMN |
Gene summary for CLMN |
Gene summary. |
Gene information | Species | Human | Gene symbol | CLMN | Gene ID | 79789 |
Gene name | calmin | |
Gene Alias | CLMN | |
Cytomap | 14q32.13 | |
Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q6NUQ2 |
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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 |
79789 | CLMN | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.69e-24 | -6.60e-01 | 0.0155 |
79789 | CLMN | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.36e-04 | -7.07e-01 | 0.0216 |
79789 | CLMN | HTA11_347_2000001011 | Human | Colorectum | AD | 7.90e-27 | 1.01e+00 | -0.1954 |
79789 | CLMN | HTA11_411_2000001011 | Human | Colorectum | SER | 2.39e-02 | 7.03e-01 | -0.2602 |
79789 | CLMN | HTA11_866_3004761011 | Human | Colorectum | AD | 2.04e-13 | -5.81e-01 | 0.096 |
79789 | CLMN | HTA11_8622_2000001021 | Human | Colorectum | SER | 2.09e-03 | -5.06e-01 | 0.0528 |
79789 | CLMN | HTA11_10711_2000001011 | Human | Colorectum | AD | 8.48e-08 | -4.93e-01 | 0.0338 |
79789 | CLMN | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.50e-04 | -3.72e-01 | 0.0674 |
79789 | CLMN | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.07e-13 | -5.43e-01 | 0.294 |
79789 | CLMN | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.54e-26 | -6.98e-01 | 0.3859 |
79789 | CLMN | HTA11_99999974143_84620 | Human | Colorectum | MSS | 9.98e-30 | -7.49e-01 | 0.3005 |
79789 | CLMN | F007 | Human | Colorectum | FAP | 2.31e-14 | -7.09e-01 | 0.1176 |
79789 | CLMN | A001-C-207 | Human | Colorectum | FAP | 8.12e-14 | -5.29e-01 | 0.1278 |
79789 | CLMN | A015-C-203 | Human | Colorectum | FAP | 5.10e-39 | -6.22e-01 | -0.1294 |
79789 | CLMN | A015-C-204 | Human | Colorectum | FAP | 1.71e-08 | -3.61e-01 | -0.0228 |
79789 | CLMN | A014-C-040 | Human | Colorectum | FAP | 1.44e-08 | -6.13e-01 | -0.1184 |
79789 | CLMN | A002-C-201 | Human | Colorectum | FAP | 5.19e-20 | -4.98e-01 | 0.0324 |
79789 | CLMN | A002-C-203 | Human | Colorectum | FAP | 6.96e-05 | -3.08e-01 | 0.2786 |
79789 | CLMN | A001-C-119 | Human | Colorectum | FAP | 1.70e-08 | -4.94e-01 | -0.1557 |
79789 | CLMN | A001-C-108 | Human | Colorectum | FAP | 6.82e-22 | -3.97e-01 | -0.0272 |
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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:0051656 | Colorectum | AD | establishment of organelle localization | 131/3918 | 390/18723 | 3.00e-09 | 2.06e-07 | 131 |
GO:0007097 | Colorectum | AD | nuclear migration | 10/3918 | 20/18723 | 3.67e-03 | 2.60e-02 | 10 |
GO:0051647 | Colorectum | AD | nucleus localization | 11/3918 | 24/18723 | 5.43e-03 | 3.55e-02 | 11 |
GO:00516561 | Colorectum | SER | establishment of organelle localization | 100/2897 | 390/18723 | 1.11e-07 | 6.79e-06 | 100 |
GO:00070971 | Colorectum | SER | nuclear migration | 8/2897 | 20/18723 | 7.14e-03 | 4.99e-02 | 8 |
GO:00516471 | Colorectum | SER | nucleus localization | 9/2897 | 24/18723 | 7.19e-03 | 4.99e-02 | 9 |
GO:00516562 | Colorectum | MSS | establishment of organelle localization | 115/3467 | 390/18723 | 7.30e-08 | 3.67e-06 | 115 |
GO:00070972 | Colorectum | MSS | nuclear migration | 9/3467 | 20/18723 | 5.90e-03 | 3.98e-02 | 9 |
GO:00516472 | Colorectum | MSS | nucleus localization | 10/3467 | 24/18723 | 7.25e-03 | 4.63e-02 | 10 |
GO:00516563 | Colorectum | FAP | establishment of organelle localization | 97/2622 | 390/18723 | 5.91e-09 | 9.48e-07 | 97 |
GO:00070973 | Colorectum | FAP | nuclear migration | 9/2622 | 20/18723 | 7.94e-04 | 8.35e-03 | 9 |
GO:00516473 | Colorectum | FAP | nucleus localization | 9/2622 | 24/18723 | 3.66e-03 | 2.60e-02 | 9 |
GO:00516564 | Colorectum | CRC | establishment of organelle localization | 76/2078 | 390/18723 | 6.53e-07 | 4.50e-05 | 76 |
GO:00070974 | Colorectum | CRC | nuclear migration | 8/2078 | 20/18723 | 8.36e-04 | 1.04e-02 | 8 |
GO:00516474 | Colorectum | CRC | nucleus localization | 8/2078 | 24/18723 | 3.25e-03 | 2.81e-02 | 8 |
GO:005165616 | Esophagus | HGIN | establishment of organelle localization | 90/2587 | 390/18723 | 4.27e-07 | 1.94e-05 | 90 |
GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
GO:00070979 | Esophagus | ESCC | nuclear migration | 15/8552 | 20/18723 | 7.60e-03 | 2.71e-02 | 15 |
GO:00516478 | Esophagus | ESCC | nucleus localization | 17/8552 | 24/18723 | 1.13e-02 | 3.81e-02 | 17 |
GO:00070975 | Liver | NAFLD | nuclear migration | 7/1882 | 20/18723 | 2.44e-03 | 2.27e-02 | 7 |
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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 |
CLMN | insertion | Nonsense_Mutation | novel | c.623_624insTGACTGAACCCTTGCCCCTGGC | p.Gln209AspfsTer2 | p.Q209Dfs*2 | Q96JQ2 | protein_coding | TCGA-BH-A0H7-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | ||
CLMN | deletion | Frame_Shift_Del | novel | c.114delN | p.Phe38LeufsTer5 | p.F38Lfs*5 | Q96JQ2 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
CLMN | SNV | Missense_Mutation | c.316G>C | p.Asp106His | p.D106H | Q96JQ2 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-C5-A1BL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
CLMN | SNV | Missense_Mutation | rs749650604 | c.1705N>A | p.Asp569Asn | p.D569N | Q96JQ2 | protein_coding | deleterious_low_confidence(0.05) | benign(0.022) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
CLMN | SNV | Missense_Mutation | c.1232N>C | p.Arg411Thr | p.R411T | Q96JQ2 | protein_coding | deleterious(0.01) | possibly_damaging(0.747) | TCGA-DS-A0VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
CLMN | SNV | Missense_Mutation | c.2177T>C | p.Leu726Pro | p.L726P | Q96JQ2 | protein_coding | deleterious(0.03) | probably_damaging(0.936) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | |
CLMN | SNV | Missense_Mutation | novel | c.2945N>A | p.Leu982His | p.L982H | Q96JQ2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
CLMN | SNV | Missense_Mutation | c.2570A>G | p.Lys857Arg | p.K857R | Q96JQ2 | protein_coding | tolerated(0.12) | benign(0.024) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD | |
CLMN | SNV | Missense_Mutation | rs182308272 | c.1777G>A | p.Glu593Lys | p.E593K | Q96JQ2 | protein_coding | tolerated_low_confidence(0.17) | possibly_damaging(0.456) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
CLMN | SNV | Missense_Mutation | c.2491N>T | p.Asp831Tyr | p.D831Y | Q96JQ2 | protein_coding | deleterious(0.02) | possibly_damaging(0.459) | TCGA-AA-3510-01 | Colorectum | colon 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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