WormMine

WS294

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00012341 Gene Name  catp-6
Sequence Name  ? W08D2.5 Brief Description  catp-6 encodes a predicted lysosomal P-type transmembrane cation transporting ATPase orthologous to human ATP13A2/PARK9 and yeast Ypk9; catp-6 is an essential gene: loss-of-function catp-6 mutations result in embryonic lethality at the one-cell stage and maternal sterility; catp-6 mutation can also result in nicotine hypersensitivity and catp-6 interacts genetically with human alpha-synuclein; when human alpha-synuclein is overexpressed in dopaminergic neurons, coexpression of catp-6 can partially rescue the resulting neuronal deterioration; in addition, loss of capt-6 activity in muscle cells overexpressing alpha-synuclein enhances the resulting protein aggregation defects in an age-dependent manner.
Organism  Caenorhabditis elegans Automated Description  Predicted to enable ATPase-coupled monoatomic cation transmembrane transporter activity and polyamine transmembrane transporter activity. Involved in protein folding. Located in cytoplasmic vesicle and plasma membrane. Expressed in several structures, including coelomocyte; egg-laying apparatus; gonad; pharynx; and somatic gonad precursor. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in primary pulmonary hypertension. Is an ortholog of human ATP13A3 (ATPase 13A3).
Biotype  SO:0001217 Genetic Position  IV :4.42498 ±0.000925
Length (nt)  ? 7169
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00012341

Genomics

3 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:W08D2.5a.1 W08D2.5a.1 4102   IV: 9817412-9824580
Transcript:W08D2.5b.1 W08D2.5b.1 2682   IV: 9817710-9821393
Transcript:W08D2.5c.1 W08D2.5c.1 3624   IV: 9817710-9824278
 

Other

3 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:W08D2.5a W08D2.5a 3804   IV: 9817710-9817842
CDS:W08D2.5b W08D2.5b 2682   IV: 9817710-9817842
CDS:W08D2.5c W08D2.5c 3624   IV: 9817710-9817842

8 RNAi Result

WormBase ID
WBRNAi00001518
WBRNAi00054975
WBRNAi00019715
WBRNAi00076748
WBRNAi00036373
WBRNAi00066537
WBRNAi00078098
WBRNAi00113892

90 Allele

Public Name
otn10037
gk964278
gk964078
gk964500
gk962765
gk963883
gk963884
h11267
gk964226
gk964227
gk914719
gk744810
gk734889
gk922406
gk675346
ttTi33319
gk209659
gk209660
WBVar01710276
gk592744
gk468875
gk209658
gk364966
gk544545
gk209661
h11934
tm3190
WBVar00191588
WBVar00191589
ok3473

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00012341 9817412 9824580 -1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIV_9816311..9817411   1101 IV: 9816311-9817411 Caenorhabditis elegans

112 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. WBPaper00060811:L1_vs_adult_upregulated_neural
  Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. DESeq. False discovry rate (FDR) < 0.1. WBPaper00048988:neuron_expressed
adult vs dauer larva Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. N.A. WBPaper00050488:adult_vs_dauer_regulated_N2_20C
Osmotic stress Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present DESeq(version 1.10.1), FDR < 0.05. WBPaper00050726:OsmoticStress_regulated_Food
Osmotic stress Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present DESeq(version 1.10.1), FDR < 0.05. WBPaper00050726:OsmoticStress_regulated_NoFood
  Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:bodywall-muscle_L1-larva_expressed
  Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:body-muscle_expressed
  Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. Cufflinks FPKM value >=1. WBPaper00050990:GABAergic-neuron_expressed
  Maternal class (M): genes that are called present in at least one of the three PC6 replicates. A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. [cgc5767]:expression_class_M
  Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic. A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. [cgc5767]:expression_class_SM
Bacteria infection: Bacillus thuringiensis mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq. Cuffdiff, ajusted p-value < 0.01. WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq. Cuffdiff, ajusted p-value < 0.01. WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq. Cuffdiff, ajusted p-value < 0.01. WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. Cuffdiff, ajusted p-value < 0.01. WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
  Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation). CuffDiff2 WBPaper00051265:F4_hrde-1(tm1200)_upregulated
  Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2. DESeq2, Fold change > 1.5. WBPaper00051404:alg-1(gk214)_upregulated
  Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. Sleuth WBPaper00051558:aging_regulated
Transgeneration hypoxia treatment. Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage. For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR. WBPaper00064871:hypoxia_upregulated_F1
Temprature shift to 28C for 24 hours. Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours. Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. WBPaper00061341:28C_24h_downregulated
  Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment. The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. WBPaper00065373:sek-1(km4)_downregulated_cisplatin
  Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:dopaminergic-neurons_L3-L4-larva_expressed
  Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:germline-precursors_blastula-embryo_expressed
  Transcripts that showed significantly decreased expression in rbr-2(tm3141) comparing to in N2 animals. Mapped reads were analyzed for transcript assembly and differential expression using Cufflinks 2.1.1 with a filter of twofold difference and FDR correction (P < 0.05). WBPaper00050080:rbr-2(tm3141)_downregulated
  Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:hypodermis_L3-L4-larva_expressed
  Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference). A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. WBPaper00037950:PVD-OLL-neurons_L3-L4-larva_expressed
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
Fungi infection: Haptoglossa zoospora. Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours. Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01. WBPaper00062354:H.zoospora_6h_regulated
  Transcripts that showed significantly increased expression in crh-1(n3315) comparing to in N2 animals. DESeq2 v1.26.0, FDR < 0.01. Fold change > 2. WBPaper00062440:crh-1(n3315)_upregulated
Bacteria: B.thuringiensis Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. Cuffdiff WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
Bacteria: B.thuringiensis Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. Cuffdiff WBPaper00060358:B.thuringiensis_pathogen_regulated_N2

18 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr14613   In the gonadal sheath cells, native GFP::CATP-7 localizes to large, raft-like patches on the plasma membrane, where it colocalizes with native CATP-6::mKate2. Moreover, we observe areas of the sheath cell that are positive for native CATP-6::mKate2, but not for native GFP::CATP-7. In favorable cross-section images, we were able to observe that native GFP::CATP-7 and native CATP-6::mKate2 are present on both the outer (pseudocoelom-facing) inner (germline-facing) plasma membrane surfaces of the sheath cell.
    Expr2009733 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  
    Expr11357 CATP-6::GFP is expressed in multiple tissues throughout development. These include a) many neurons in the head and tail, b) all body muscles, c) most pharyngeal cells, particularly in the posterior bulb, d) vulval muscles, e) coelomocytes, f) spermatheca, g) gonadal sheath cells, and h) lateral hypodermis. In many cases, particularly neurons, the fusion protein localizes to cytoplasmic puncta that probably correspond to membranous vesicles. In other tissues, e.g., pharyngeal cells and gonadal sheath cells, CATP-6::GFP is closely associated with the plasma membrane. Most significantly with regard to the effect of catp-6(0) on gonadogenesis, CATP-6::GFP is associated with the plasma membrane of the somatic gonad precursor cells, Z1 and Z4. Although the authors detect CATP-6::GFP in close association with the plasma membrane in some tissues, they cannot certain that the protein is actually located within the plasma membrane. For example, in the case of Z1 and Z4 the fluorescence pattern of CATP-6::GFP (unlike that of GEM-1::GFP) is often discontinuous along the periphery of the cell. Thus, it remains possible that the protein localizes to vesicles that are just beneath the plasma membrane. Furthermore, it is possible that CATP-6 localizes to both plasma membrane and vesicular compartments and that the relative distribution differs between cell types. Higher resolution microscopy will be necessary to resolve this issue.
    Expr14602 CATP-6::FP is expressed in a punctate pattern in many neurons in the head and tail, all body wall muscles, the posterior gut, the spermatheca, the DTC and the pharyngeal cells. CATP-6::FP is also expressed in the gonadal sheath cells, where it appears to be closely associated with the plasma membrane and is not punctate. Notably, native CATP-6::FP is strongly expressed in the germ line within the mitotic region, the transition zone and the pachytene region, and appears to localize to the plasma membrane. CATP-6::GFP is expressed in a punctate pattern in many neurons in the head and tail, all body wall muscles, the posterior gut, the spermatheca, the DTC and the pharyngeal cells. CATP-6::FP is also expressed in the gonadal sheath cells, where it appears to be closely associated with the plasma membrane and is not punctate. Notably, native CATP-6::FP is strongly expressed in the germ line within the mitotic region, the transition zone and the pachytene region, and appears to localize to the plasma membrane.  
    Expr14603 CATP-6::FP is expressed in a punctate pattern in many neurons in the head and tail, all body wall muscles, the posterior gut, the spermatheca, the DTC and the pharyngeal cells. CATP-6::FP is also expressed in the gonadal sheath cells, where it appears to be closely associated with the plasma membrane and is not punctate. Notably, native CATP-6::FP is strongly expressed in the germ line within the mitotic region, the transition zone and the pachytene region, and appears to localize to the plasma membrane.  
    Expr2027973 Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).  
    Expr1035461 Tiling arrays expression graphs  
    Expr1158510 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr14604   Notably, native CATP-6::FP is strongly expressed in the germ line within the mitotic region, the transition zone and the pachytene region, and appears to localize to the plasma membrane.
    Expr14605   Notably, native CATP-6::FP is strongly expressed in the germ line within the mitotic region, the transition zone and the pachytene region, and appears to localize to the plasma membrane.
    Expr1010635 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr14608   In first stage larvae, native GFP::CATP-7 and native CATP-6::mKate2 localize to the apical brush border of the intestinal cells.
    Expr14609   Native GFP::CATP-7 and transgene CATP-7::GFP localize to small vesicles immediately beneath the apical brush border in the intestine. We also observed that both GFP::CATP-7 and CATP-6::GFP localize to tubular structures in the basolateral domain of the intestinal cells. In first stage larvae, native GFP::CATP-7 and native CATP-6::mKate2 localize to the apical brush border of the intestinal cells.
    Expr14610   In double-tagged animals, it is clear that the localization patterns of the two proteins within the spermathecal cells are distinct: CATP-6::mKate2 localizes to punctae in the basolateral domain, whereas GFP::CATP-7 localizes to the lateral and luminal cell borders, as well as to spermatids.
    Expr14615 Native GFP::CATP-7, as well as CATP-6::mKate2 are expressed in the DTCs of early stage gonads. Native GFP::CATP-7 and native CATP-6::mKate2 are also both expressed in the DTCs of L4 animals, although the CATP-6 expression is comparatively weak. CATP-6::mKate2 is also expressed in larval germ cells, exhibiting a puncate localization pattern, consistent with endosomal localization.
    Expr14617   In addition to somatic gonad cells, native GFP::CATP-7 and CATP-6::mKate2 are both strongly expressed in the developing vulva. Again, GFP::CATP-7 appears continuously associated with the plasma membrane, whereas CATP-6::mKate2 localization is punctate.
    Expr14618   CATP-6::mKate2 is also associated with the plasma membrane of diakinesis-stage oocytes. We also detect a weak cytoplasmic signal for CATP-6::mKate2 in spermatids.
Original chronogram file: chronogram.1448.xml [W08D2.5:gfp] transcriptional fusion. Chronogram439    

25 GO Annotation

Annotation Extension Qualifier
  located_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  enables
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  enables
  enables
  enables
  enables
  enables
  enables
  enables
  enables
  enables

11 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue
least diverged orthologue

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00012341 9817412 9824580 -1

25 Ontology Annotations

Annotation Extension Qualifier
  located_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  enables
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  located_in
  enables
  enables
  enables
  enables
  enables
  enables
  enables
  enables
  enables

0 Regulates Expr Cluster

1 Sequence

Length
7169

1 Sequence Ontology Term