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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 |
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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:00508901 | Prostate | Tumor | cognition | 69/3246 | 296/18723 | 5.03e-03 | 2.45e-02 | 69 |
GO:190504811 | Prostate | Tumor | regulation of metallopeptidase activity | 10/3246 | 25/18723 | 6.30e-03 | 2.89e-02 | 10 |
GO:004354713 | Prostate | Tumor | positive regulation of GTPase activity | 60/3246 | 255/18723 | 6.87e-03 | 3.11e-02 | 60 |
GO:190524512 | Prostate | Tumor | regulation of aspartic-type peptidase activity | 6/3246 | 12/18723 | 9.63e-03 | 4.10e-02 | 6 |
GO:1902991 | Prostate | Tumor | regulation of amyloid precursor protein catabolic process | 17/3246 | 55/18723 | 9.71e-03 | 4.13e-02 | 17 |
GO:006156416 | Skin | AK | axon development | 91/1910 | 467/18723 | 8.60e-10 | 8.63e-08 | 91 |
GO:003425025 | Skin | AK | positive regulation of cellular amide metabolic process | 43/1910 | 162/18723 | 2.77e-09 | 2.40e-07 | 43 |
GO:005254727 | Skin | AK | regulation of peptidase activity | 88/1910 | 461/18723 | 4.65e-09 | 3.44e-07 | 88 |
GO:004586127 | Skin | AK | negative regulation of proteolysis | 72/1910 | 351/18723 | 5.40e-09 | 3.90e-07 | 72 |
GO:004586228 | Skin | AK | positive regulation of proteolysis | 74/1910 | 372/18723 | 1.32e-08 | 8.20e-07 | 74 |
GO:005254827 | Skin | AK | regulation of endopeptidase activity | 82/1910 | 432/18723 | 2.03e-08 | 1.18e-06 | 82 |
GO:000740916 | Skin | AK | axonogenesis | 80/1910 | 418/18723 | 2.07e-08 | 1.19e-06 | 80 |
GO:007265925 | Skin | AK | protein localization to plasma membrane | 59/1910 | 284/18723 | 8.01e-08 | 3.80e-06 | 59 |
GO:199077820 | Skin | AK | protein localization to cell periphery | 66/1910 | 333/18723 | 9.18e-08 | 4.21e-06 | 66 |
GO:000756826 | Skin | AK | aging | 63/1910 | 339/18723 | 1.83e-06 | 5.42e-05 | 63 |
GO:001635817 | Skin | AK | dendrite development | 49/1910 | 243/18723 | 2.42e-06 | 6.72e-05 | 49 |
GO:005165618 | Skin | AK | establishment of organelle localization | 69/1910 | 390/18723 | 3.69e-06 | 9.11e-05 | 69 |
GO:001046625 | Skin | AK | negative regulation of peptidase activity | 51/1910 | 262/18723 | 4.43e-06 | 1.07e-04 | 51 |
GO:005134626 | Skin | AK | negative regulation of hydrolase activity | 67/1910 | 379/18723 | 5.22e-06 | 1.21e-04 | 67 |
GO:001095120 | Skin | AK | negative regulation of endopeptidase activity | 49/1910 | 252/18723 | 6.98e-06 | 1.55e-04 | 49 |
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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 |
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 |
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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 |
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