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Gene: PICALM |
Gene summary for PICALM |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PICALM | Gene ID | 8301 |
| Gene name | phosphatidylinositol binding clathrin assembly protein | |
| Gene Alias | CALM | |
| Cytomap | 11q14.2 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | A0A024R5L7 |
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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 |
| 8301 | PICALM | CCI_2 | Human | Cervix | CC | 3.23e-10 | 1.19e+00 | 0.5249 |
| 8301 | PICALM | CCI_3 | Human | Cervix | CC | 2.00e-12 | 1.10e+00 | 0.516 |
| 8301 | PICALM | sample3 | Human | Cervix | CC | 3.87e-04 | 1.97e-01 | 0.1387 |
| 8301 | PICALM | T3 | Human | Cervix | CC | 3.49e-05 | 2.00e-01 | 0.1389 |
| 8301 | PICALM | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.07e-11 | -4.90e-01 | 0.0155 |
| 8301 | PICALM | HTA11_696_2000001011 | Human | Colorectum | AD | 1.54e-05 | -3.44e-01 | -0.1464 |
| 8301 | PICALM | HTA11_866_3004761011 | Human | Colorectum | AD | 5.22e-13 | -5.51e-01 | 0.096 |
| 8301 | PICALM | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.15e-03 | -5.38e-01 | 0.0528 |
| 8301 | PICALM | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.90e-20 | -4.77e-01 | 0.0674 |
| 8301 | PICALM | HTA11_6818_2000001021 | Human | Colorectum | AD | 4.15e-03 | -4.42e-01 | 0.0588 |
| 8301 | PICALM | HTA11_99999973899_84307 | Human | Colorectum | MSS | 3.97e-02 | -4.39e-01 | 0.2585 |
| 8301 | PICALM | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.28e-28 | -6.22e-01 | 0.3005 |
| 8301 | PICALM | A002-C-010 | Human | Colorectum | FAP | 6.48e-03 | -1.80e-01 | 0.242 |
| 8301 | PICALM | A001-C-207 | Human | Colorectum | FAP | 2.67e-04 | -2.93e-01 | 0.1278 |
| 8301 | PICALM | A015-C-203 | Human | Colorectum | FAP | 7.74e-43 | -6.39e-01 | -0.1294 |
| 8301 | PICALM | A015-C-204 | Human | Colorectum | FAP | 2.19e-11 | -4.34e-01 | -0.0228 |
| 8301 | PICALM | A014-C-040 | Human | Colorectum | FAP | 1.46e-07 | -6.11e-01 | -0.1184 |
| 8301 | PICALM | A002-C-201 | Human | Colorectum | FAP | 3.19e-20 | -4.90e-01 | 0.0324 |
| 8301 | PICALM | A002-C-203 | Human | Colorectum | FAP | 9.37e-08 | -2.93e-01 | 0.2786 |
| 8301 | PICALM | A001-C-119 | Human | Colorectum | FAP | 5.15e-12 | -5.34e-01 | -0.1557 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid 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:00109502 | Colorectum | MSS | positive regulation of endopeptidase activity | 54/3467 | 179/18723 | 1.03e-04 | 1.61e-03 | 54 |
| GO:00068981 | Colorectum | MSS | receptor-mediated endocytosis | 69/3467 | 244/18723 | 1.18e-04 | 1.82e-03 | 69 |
| GO:00516482 | Colorectum | MSS | vesicle localization | 53/3467 | 177/18723 | 1.47e-04 | 2.16e-03 | 53 |
| GO:00075681 | Colorectum | MSS | aging | 90/3467 | 339/18723 | 1.51e-04 | 2.19e-03 | 90 |
| GO:19043761 | Colorectum | MSS | negative regulation of protein localization to cell periphery | 13/3467 | 26/18723 | 2.71e-04 | 3.63e-03 | 13 |
| GO:19052452 | Colorectum | MSS | regulation of aspartic-type peptidase activity | 8/3467 | 12/18723 | 3.33e-04 | 4.24e-03 | 8 |
| GO:00074092 | Colorectum | MSS | axonogenesis | 105/3467 | 418/18723 | 4.32e-04 | 5.23e-03 | 105 |
| GO:00550722 | Colorectum | MSS | iron ion homeostasis | 29/3467 | 85/18723 | 4.44e-04 | 5.32e-03 | 29 |
| GO:00482681 | Colorectum | MSS | clathrin coat assembly | 10/3467 | 18/18723 | 4.76e-04 | 5.58e-03 | 10 |
| GO:19029592 | Colorectum | MSS | regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process | 7/3467 | 10/18723 | 5.26e-04 | 5.99e-03 | 7 |
| GO:19012142 | Colorectum | MSS | regulation of neuron death | 83/3467 | 319/18723 | 5.28e-04 | 5.99e-03 | 83 |
| GO:00615642 | Colorectum | MSS | axon development | 115/3467 | 467/18723 | 5.33e-04 | 6.00e-03 | 115 |
| GO:00435471 | Colorectum | MSS | positive regulation of GTPase activity | 68/3467 | 255/18723 | 7.97e-04 | 8.38e-03 | 68 |
| GO:19038282 | Colorectum | MSS | negative regulation of cellular protein localization | 36/3467 | 117/18723 | 9.19e-04 | 9.34e-03 | 36 |
| GO:00163582 | Colorectum | MSS | dendrite development | 65/3467 | 243/18723 | 9.41e-04 | 9.50e-03 | 65 |
| GO:00717092 | Colorectum | MSS | membrane assembly | 19/3467 | 50/18723 | 9.61e-04 | 9.67e-03 | 19 |
| GO:00990031 | Colorectum | MSS | vesicle-mediated transport in synapse | 54/3467 | 200/18723 | 1.94e-03 | 1.67e-02 | 54 |
| GO:19012161 | Colorectum | MSS | positive regulation of neuron death | 30/3467 | 97/18723 | 2.15e-03 | 1.80e-02 | 30 |
| GO:00450562 | Colorectum | MSS | transcytosis | 10/3467 | 21/18723 | 2.23e-03 | 1.84e-02 | 10 |
| GO:00482591 | Colorectum | MSS | regulation of receptor-mediated endocytosis | 33/3467 | 110/18723 | 2.33e-03 | 1.90e-02 | 33 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 |
| 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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| PICALM | SNV | Missense_Mutation | c.1625C>T | p.Ser542Leu | p.S542L | Q13492 | protein_coding | deleterious(0.02) | possibly_damaging(0.471) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PICALM | SNV | Missense_Mutation | novel | c.1612N>A | p.Asp538Asn | p.D538N | Q13492 | protein_coding | tolerated(1) | benign(0.015) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PICALM | SNV | Missense_Mutation | c.886N>A | p.Ala296Thr | p.A296T | Q13492 | protein_coding | tolerated(0.05) | benign(0.063) | TCGA-C8-A8HP-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| PICALM | insertion | Nonsense_Mutation | novel | c.1866_1867insTAAGAAAGAT | p.Met623Ter | p.M623* | Q13492 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PICALM | SNV | Missense_Mutation | novel | c.887N>T | p.Ala296Val | p.A296V | Q13492 | protein_coding | deleterious(0.02) | possibly_damaging(0.719) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PICALM | SNV | Missense_Mutation | c.59C>T | p.Ser20Phe | p.S20F | Q13492 | protein_coding | deleterious(0) | possibly_damaging(0.686) | TCGA-EA-A3HT-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PICALM | SNV | Missense_Mutation | c.632A>G | p.Tyr211Cys | p.Y211C | Q13492 | protein_coding | deleterious(0) | probably_damaging(0.92) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PICALM | SNV | Missense_Mutation | rs377101068 | c.1777N>G | p.Met593Val | p.M593V | Q13492 | protein_coding | tolerated(0.34) | benign(0.019) | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| PICALM | SNV | Missense_Mutation | rs760482423 | c.1228N>G | p.Thr410Ala | p.T410A | Q13492 | protein_coding | tolerated(0.76) | benign(0.003) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PICALM | SNV | Missense_Mutation | novel | c.523A>G | p.Met175Val | p.M175V | Q13492 | protein_coding | tolerated(0.08) | benign(0.106) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 |
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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 |
| 8301 | PICALM | CLINICALLY ACTIONABLE, CELL SURFACE | calcium channel blockers | 24192120 |
| Page: 1 |
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