diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml index b84cc750e..0b4049024 100644 --- a/Model/lib/wdk/model/questions/params/geneParams.xml +++ b/Model/lib/wdk/model/questions/params/geneParams.xml @@ -85,7 +85,6 @@ - Select the algorithm for MetaCycle analysis @@ -163,7 +162,7 @@ + includeProjects="VectorBase,UniDB"> Enter the minimum number of total ISRPM (unique intron spaning reads per million intron spanning reads) required to consider an intron. @@ -208,7 +207,7 @@ --> - - Select the lifecycle stage in which you want to look for phenotype changes @@ -369,7 +367,6 @@ - Select gene modification by mutation or disruption @@ -387,7 +384,6 @@ - Select whether the modification was successful or not @@ -405,7 +401,6 @@ - Select the effect on the phenotype from not different to wild-type, changed from wild-type or not tested. Specifics of phenotype changes can be viewed on the gene record pages @@ -432,8 +427,6 @@ multiPick="false" quote="true"> - - Should only protein coding genes be returned? @@ -455,7 +448,6 @@ multiPick="false" visible="false" quote="false"> - For two Channel Microarray experiments, percentiles are computed on raw data. Channel 1 corresponds to the numerator of the ratio and Channel 2 the denominator. Often it is necessary to look at a corresponding bar graph for this study to determine which channel is approprate. If the experiment was a two channel w/ a common reference you are most likely interested in channel 1. @@ -510,7 +502,6 @@ multiPick="false" displayType="checkBox" quote="false"> - -4 means that you would find a match that good every 10,000 basepairs on average on that strand. @@ -540,11 +531,10 @@ - - Choose the minimum number of sites per gene that meet your other criteria. @@ -568,11 +558,10 @@ - - Choose whether the peak should be upstream or downstream of the 5' end of the gene. @@ -638,11 +627,10 @@ - - Choose the number of peaks for this antibody/treatment. Note that the PLK (TypeII) strain was only done with one replicate. Note that this is the total number of peaks per antibody/treatment pair. @@ -662,7 +650,6 @@ prompt="Peak location relative to 5' end of gene" multiPick="false" quote="true"> - Choose whether the peak should be upstream or downstream of the 5' end of the gene. @@ -683,7 +670,7 @@ - Choose a strain from which the samples were prepared. - - - - Choose a ChIP on chip assay/experiment - - - - Choose whether to return genes with new gene product names since the last @PROJECT_ID@ release. @@ -796,7 +782,6 @@ prompt="EC Numbers Changed" multiPick="false" quote="false"> - Choose whether to return genes with altered EC numbers since the last @PROJECT_ID@ release. @@ -820,7 +805,6 @@ prompt="GO Functions Changed" multiPick="false" quote="false"> - Choose whether to return genes with altered Gene Ontology (GO) assignments since the last @PROJECT_ID@ release. @@ -844,7 +828,6 @@ prompt="Coding Sequence Changed" multiPick="false" quote="false"> - Choose whether to return genes with altered coding sequence since the last @PROJECT_ID@ release. @@ -893,7 +876,6 @@ prompt="Status change from old (release 5.5) to new (release 6.0) annotation" multiPick="true" quote="true"> - Choose which genes to return based on their change in status from old to new annotation. @@ -935,7 +917,6 @@ see a list of all possible EC categories that match what you have typed. Then choose an EC category from the list. Use '-' as a wildcard in place of numbers to denote partial EC Numbers. ]]> - @@ -970,7 +951,7 @@ prompt="Transcript Novelty" multiPick="true" quote="true" - includeProjects="PlasmoDB,ToxoDB"> + includeProjects="PlasmoDB,ToxoDB,UniDB"> @@ -984,7 +965,7 @@ multiPick="false" quote="false" visible="true" - includeProjects="PlasmoDB,ToxoDB,EuPathDB"> + includeProjects="PlasmoDB,ToxoDB,UniDB"> @@ -996,7 +977,7 @@ prompt="Incomplete mismatch type" multiPick="true" quote="true" - includeProjects="PlasmoDB,ToxoDB"> + includeProjects="PlasmoDB,ToxoDB,UniDB"> @@ -1011,7 +992,7 @@ multiPick="true" suppressNode="true" quote="true" - includeProjects="PlasmoDB,ToxoDB,EuPathDB" + includeProjects="PlasmoDB,ToxoDB,UniDB" dependedParamRef="geneParams.long_read_datasets"> @@ -1052,7 +1033,7 @@ multiPick="true" suppressNode="true" quote="true" - includeProjects="PlasmoDB,ToxoDB,EuPathDB"> + includeProjects="PlasmoDB,ToxoDB,UniDB"> @@ -1097,7 +1078,6 @@ - Choose whether to search against the total number of exons per gene or the number of exons in each specific transcript. @@ -1205,62 +1185,61 @@ - + includeProjects="PlasmoDB,UniDB"> - + Pf3D7_01_v3 Pf3D7_01_v3 - + Pf3D7_02_v3 Pf3D7_02_v3 - + Pf3D7_03_v3 Pf3D7_03_v3 - + Pf3D7_04_v3 Pf3D7_04_v3 - + Pf3D7_05_v3 Pf3D7_05_v3 - + Pf3D7_06_v3 Pf3D7_06_v3 - + Pf3D7_07_v3 Pf3D7_07_v3 - + Pf3D7_08_v3 Pf3D7_08_v3 - + Pf3D7_09_v3 Pf3D7_09_v3 - + Pf3D7_10_v3 Pf3D7_10_v3 - + Pf3D7_11_v3 Pf3D7_11_v3 - + Pf3D7_12_v3 Pf3D7_12_v3 - + Pf3D7_13_v3 Pf3D7_13_v3 - + Pf3D7_14_v3 Pf3D7_14_v3 @@ -1375,7 +1354,6 @@ queryRef="GeneVQ.hardFloor" dependedParamRef="geneParams.profileset_generic" visible="false"> - @@ -1386,7 +1364,6 @@ queryRef="GeneVQ.antisenseFloor" dependedParamRef="geneParams.samples_comp_antisense" visible="true"> - @@ -1424,7 +1401,6 @@ multiPick="false" visible="true" quote="false"> - Select whether the number of sense transcripts should increase or decrease in the Comparison Sample relative to the Reference Sample. @@ -1435,7 +1411,6 @@ multiPick="false" visible="true" quote="false"> - Select whether the number of antisense transcripts should increase or decrease in the Comparison Sample relative to the Reference Sample. @@ -1474,7 +1449,6 @@ prompt="Direction" multiPick="false" queryRef="GeneVQ.regulatedDirection"> - For ConditionA vs. ConditionB, select 'increase in coverage' for genes where ConditionA > ConditionB and select 'decrease in coverage' for genes where ConditionB > ConditionA. @@ -1486,7 +1460,6 @@ multiPick="false" quote="false" queryRef="GeneVQ.regulatedDirection"> -
  • - Select 'up-regulated' to find genes that have higher expression @@ -1505,7 +1478,7 @@ lower expression in the comparator as compared to the reference.
  • multiPick="false" quote="false" queryRef="GeneVQ.regulatedDirectionImmune"> - +
  • - Select 'increased immunogenicity' to find genes that have higher expression @@ -1523,7 +1496,7 @@ lower expression in the comparator as compared to the reference.
  • - + Comparison. Note that when selecting up-regulated, the minimum value of samples selected in Reference will be used and reported and the maximum value of samples in Comparison. The opposite is true if down-regulated is selected. @@ -1544,7 +1517,7 @@ lower expression in the comparator as compared to the reference. - + - + @@ -1641,7 +1614,7 @@ Choose the operation (min/max/average/med) to be applied to the chosen sample(s) prompt="Apply RNA / nuclei number scaling" multiPick="false" quote="false"> - + - + - + There are two types or directions of correlation (two patterns that correlations can follow). @@ -1714,8 +1687,8 @@ Is the minimum and/or maximum expression value across the entire experiment cont multiPick="true" quote="true" displayType="checkBox" - includeProjects="GiardiaDB,EuPathDB,UniDB"> - + includeProjects="GiardiaDB,UniDB"> + The percentile was calculated on the mean of each sample group over all the spots on the array. @@ -1775,8 +1748,8 @@ Is the minimum and/or maximum expression value across the entire experiment cont multiPick="true" quote="true" displayType="checkBox" - includeProjects="GiardiaDB,EuPathDB,UniDB"> - + includeProjects="GiardiaDB,UniDB"> + The percentile was calculated on the mean of each sample group over all the spots on the array. @@ -1848,7 +1821,7 @@ Is the minimum and/or maximum expression value across the entire experiment cont prompt="Syntenic Orthologs Only?" multiPick="false" quote="true"> - + Only Return Orthologs which also are syntenic @@ -1880,7 +1853,6 @@ Is the minimum and/or maximum expression value across the entire experiment cont - Select whether to reject text matches that start or end in the middle of a word @@ -1898,10 +1870,9 @@ Is the minimum and/or maximum expression value across the entire experiment cont - - Select whether to reject text matches that start or end in the middle of a word @@ -1948,7 +1919,7 @@ polymorphism. ]]> - +
    @@ -1976,7 +1947,7 @@ products of your selected type (or types).

    prompt="Include Pseudogenes" multiPick="false" quote="false"> - +
    Pseudogenes are dysfunctional genes that no longer encode protein or are no longer @@ -2081,7 +2052,7 @@ products of your selected type (or types).

    quote="true" displayType="checkBox" multiPick="true"> - + Choose the evidence of the GO annotation. @@ -2101,7 +2072,7 @@ products of your selected type (or types).

    quote="true" displayType="checkBox" multiPick="false"> - + limit the search to GO Slim generic terms only. @@ -2132,7 +2103,7 @@ products of your selected type (or types).

    - + Indicate whether the protein product of the Gene ID should be the bait (fused to the binding domain) or prey (fused to the activation domain) in the yeast two-hybrid experiment. @@ -2160,7 +2131,7 @@ products of your selected type (or types).

    - + @@ -2248,7 +2219,7 @@ products of your selected type (or types).

    - + Choose whether to allow a 1 amino acid mismatch in the peptide to protein alignment. To restrict the search to exact peptide matches, select "No" @@ -2267,7 +2238,7 @@ products of your selected type (or types).

    - + Choose whether to return genes where the species for the protein containing the IEDB epitope is not the same as for the target protein. To restrict the search to epitopes from the target species or taxa, select "No" @@ -2286,7 +2257,7 @@ products of your selected type (or types).

    - + Choose whether to return genes where the protein containing the IEDB epitope is not an exact match for the target protein. Mismatches may be outside of the epitope regions. To restrict the search to exact protein matches, select "No" @@ -2375,7 +2346,7 @@ products of your selected type (or types).

    - + Click yes to include P. reichenowi snps in this query. P.r snps were generated by alignment of P. reichenowi sequence with the P falciparum 3D7 reference sequence. Note, if you want to only query reichenowi, you must click 'None' in the P. falciparum strains select list. @@ -2395,7 +2366,7 @@ products of your selected type (or types).

    prompt="SNP Class" multiPick="false" quote="false"> - + Choose the class of SNP you want to query on ... choose minumum and maximum numbers below @@ -2432,7 +2403,7 @@ products of your selected type (or types).

    prompt="SNP Class" multiPick="false" quote="false"> - + Choose the class of SNP you want to query on ... choose minumum and maximum numbers below @@ -2468,7 +2439,7 @@ products of your selected type (or types).

    - + Results will be sorted on this column in descending order @@ -2507,7 +2478,7 @@ products of your selected type (or types).

    - + Results will be sorted ascending or descending order @@ -2526,7 +2497,7 @@ products of your selected type (or types).

    + includeProjects="PlasmoDB,ToxoDB,UniDB"> Choose experiment(s) to query. Note that all of the time courses will only return genes that match the search criteria in all experiments. @@ -2563,7 +2534,7 @@ products of your selected type (or types).

    prompt="Require Both Replicates" multiPick="false" quote="false" - includeProjects="TriTrypDB"> + includeProjects="TriTrypDB,UniDB"> Require that both replicates match the search parameters @@ -2583,7 +2554,7 @@ products of your selected type (or types).

    - + Find genes where the expression level is at its highest or lowest point in the time series. @@ -2603,8 +2574,8 @@ products of your selected type (or types).

    prompt="Timing" multiPick="true" quote="false" - includeProjects="EuPathDB,PlasmoDB,UniDB"> - + includeProjects="PlasmoDB,UniDB"> + Time point where expression level was minimal or maximal @@ -2644,8 +2615,8 @@ products of your selected type (or types).

    prompt="Timing" multiPick="true" quote="false" - includeProjects="EuPathDB,ToxoDB,UniDB"> - + includeProjects="ToxoDB,UniDB"> + Time point where expression level was minimal or maximal @@ -2710,8 +2681,8 @@ products of your selected type (or types).

    prompt="Timing" multiPick="true" quote="false" - includeProjects="EuPathDB,PlasmoDB,UniDB"> - + includeProjects="PlasmoDB,UniDB"> + Time point where expression level was minimal or maximal @@ -2757,7 +2728,7 @@ products of your selected type (or types).

    -
    -
    Choose a sample
    -
    - Nonnuclear genomic sequence of various Plasmodium organisms includes the sequence of the mitochondrial and apicoplast genomes. Nonnuclear genomic sequence for T. gondii includes the sequence of the apicoplast genome. - Nonnuclear genomic sequence of various Plasmodium organisms includes the sequence of the mitochondrial and apicoplast genomes. Nonnuclear genomic sequence for T. gondii includes the sequence of the apicoplast genome. + Nonnuclear genomic sequence of various Plasmodium organisms includes the sequence of the mitochondrial and apicoplast genomes. Nonnuclear genomic sequence for T. gondii includes the sequence of the apicoplast genome. @@ -6105,7 +6075,6 @@ products of your selected type (or types).

    - @@ -6138,7 +6107,6 @@ products of your selected type (or types).

    - @@ -6158,7 +6126,6 @@ products of your selected type (or types).

    - @@ -6178,7 +6145,7 @@ products of your selected type (or types).

    - + Choose genes in a previous result based on whether they do or don't have at least one transcript missing from that result @@ -6202,20 +6169,19 @@ products of your selected type (or types).

    queryRef="GeneVQ.missingOrFoundTranscripts" dependedParamRef="geneParams.genesWithTranscripts"> - + Choose transcripts of the genes in a previous result based on whether the transcripts were missing or found in that result
    - - Type of correlation the search should look for @@ -6229,7 +6195,7 @@ products of your selected type (or types).

    - @@ -6240,7 +6206,6 @@ products of your selected type (or types).

    - Type of correlation the search should look for @@ -6265,20 +6230,20 @@ products of your selected type (or types).

    - + Choose which text fields to search. - + Phenotype Phenotype Phenotype - + Rodent Malaria Phenotype RodMalPhenotype RodMalPhenotype @@ -6478,33 +6443,6 @@ products of your selected type (or types).

    - - - - - - - - - - - - - - - - @@ -6520,7 +6458,7 @@ products of your selected type (or types).

    - + @@ -6538,7 +6476,7 @@ products of your selected type (or types).

    - + @@ -6556,7 +6494,7 @@ products of your selected type (or types).

    - + @@ -6571,7 +6509,7 @@ products of your selected type (or types).

    - + @@ -6591,7 +6529,7 @@ products of your selected type (or types).

    - + @@ -7539,7 +7477,7 @@ products of your selected type (or types).

    - + @@ -7556,7 +7494,7 @@ products of your selected type (or types).

    - + @@ -8373,7 +8311,7 @@ products of your selected type (or types).

    - + @@ -8391,7 +8329,7 @@ products of your selected type (or types).

    - + @@ -8413,7 +8351,7 @@ products of your selected type (or types).

    - + @@ -8432,7 +8370,7 @@ products of your selected type (or types).

    - + @@ -8474,7 +8412,7 @@ end as term - + @@ -8565,7 +8503,7 @@ end as term - +