Mercurial > repos > devteam > ctd_batch
changeset 0:4a32700dcaa2 draft default tip
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 10:23:26 -0400 |
| parents | |
| children | |
| files | ctd.pl ctd.xml test-data/ctdBatchInput.txt test-data/ctdBatchOut.txt |
| diffstat | 4 files changed, 604 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctd.pl Wed Sep 25 10:23:26 2013 -0400 @@ -0,0 +1,80 @@ +#!/usr/bin/perl -w +use strict; +use LWP::UserAgent; +require HTTP::Cookies; + +####################################################### +# ctd.pl +# Submit a batch query to CTD and fetch results into galaxy history +# usage: ctd.pl inFile idCol inputType resultType actionType outFile +####################################################### + +if (!@ARGV or scalar @ARGV != 6) { + print "usage: ctd.pl inFile idCol inputType resultType actionType outFile\n"; + exit; +} + +my $in = shift @ARGV; +my $col = shift @ARGV; +if ($col < 1) { + print "The column number is with a 1 start\n"; + exit 1; +} +my $type = shift @ARGV; +my $resType = shift @ARGV; +my $actType = shift @ARGV; +my $out = shift @ARGV; + +my @data; +open(FH, $in) or die "Couldn't open $in, $!\n"; +while (<FH>) { + chomp; + my @f = split(/\t/); + if (scalar @f < $col) { + print "ERROR the requested column is not in the file $col\n"; + exit 1; + } + push(@data, $f[$col-1]); +} +close FH or die "Couldn't close $in, $!\n"; + +my $url = 'http://ctdbase.org/tools/batchQuery.go'; +#my $url = 'http://ctd.mdibl.org/tools/batchQuery.go'; +my $d = join("\n", @data); +#list maintains order, where hash doesn't +#order matters at ctd +#to use input file (gives error can't find file) +#my @form = ('inputType', $type, 'inputTerms', '', 'report', $resType, + #'queryFile', [$in, ''], 'queryFileColumn', $col, 'format', 'tsv', 'action', 'Submit'); +my @form = ('inputType', $type, 'inputTerms', $d, 'report', $resType, + 'queryFile', '', 'format', 'tsv', 'action', 'Submit'); +if ($resType eq 'cgixns') { #only add if this type + push(@form, 'actionTypes', $actType); +} +if ($resType eq 'go' or $resType eq 'go_enriched') { + push(@form, 'ontology', 'go_bp', 'ontology', 'go_mf', 'ontology', 'go_cc'); +} +my $ua = LWP::UserAgent->new; +$ua->cookie_jar(HTTP::Cookies->new( () )); +$ua->agent('Mozilla/5.0'); +my $page = $ua->post($url, \@form, 'Content_Type'=>'form-data'); +if ($page->is_success) { + open(FH, ">", $out) or die "Couldn't open $out, $!\n"; + print FH "#"; + print FH $page->content, "\n"; + close FH or die "Couldn't close $out, $!\n"; +}else { + print "ERROR failed to get page from CTD, ", $page->status_line, "\n"; + print $page->content, "\n"; + my $req = $page->request(); + print "Requested \n"; + foreach my $k(keys %$req) { + if ($k eq '_headers') { + my $t = $req->{$k}; + foreach my $k2 (keys %$t) { print "$k2 => $t->{$k2}\n"; } + }else { print "$k => $req->{$k}\n"; } + } + exit 1; +} +exit; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctd.xml Wed Sep 25 10:23:26 2013 -0400 @@ -0,0 +1,289 @@ +<tool id="ctdBatch_1" name="CTD" version="1.0.0"> + <description>analysis of chemicals, diseases, or genes</description> + <command interpreter="perl">#if $inType.inputType=="disease" #ctd.pl $input $numerical_column $inType.inputType $inType.report ANY $out_file1 +#else if $inType.reportType.report=="cgixns" #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report "$inType.reportType.actType" $out_file1 +#else #ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report ANY $out_file1 +#end if</command> + <inputs> + <param name="input" type="data" format="tabular" label="Dataset" /> + <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" /> + <conditional name="inType"> + <param name="inputType" label="Identifier type" type="select"> + <option value="chem">Chemicals (MeSH names, synonyms or accession IDs, or CAS RNs)</option> + <option value="disease">Diseases (MeSH or OMIM names, synonyms or accession IDs)</option> + <option value="gene" selected="true">Genes (NCBI official symbols or accession IDs)</option> + </param> + <when value="chem"> + <conditional name='reportType'> + <param name="report" label="Data to extract" type="select"> + <option value="cgixns">Curated chemical-gene interactions</option> + <option value="genes">Curated gene associations</option> + <option value="pathways_inferred">Inferred pathway associations</option> + <option value="pathways_enriched">Enriched pathway associations</option> + <option value="diseases" selected="true">All disease relationships</option> + <option value="diseases_curated"> Curated disease relationships only</option> + <option value="diseases_inferred"> Inferred disease relationships only</option> + <option value="go">All GO associations</option> + <option value="go_enriched">Enriched GO associations only</option> + </param> + <when value="genes"> + <!-- do nothing --> + </when> + <when value="pathways_inferred"> + <!-- do nothing --> + </when> + <when value="pathways_enriched"> + <!-- do nothing --> + </when> + <when value="diseases"> + <!-- do nothing --> + </when> + <when value="diseases_curated"> + <!-- do nothing --> + </when> + <when value="diseases_inferred"> + <!-- do nothing --> + </when> + <when value="go"> + <!-- do nothing --> + </when> + <when value="go_enriched"> + <!-- do nothing --> + </when> + <when value="cgixns"> + <param name="actType" label="Interaction type" type="select"> + <option value="ANY">ANY</option> + <option value="abundance">abundance</option> + <option value="activity">activity</option> + <option value="binding">binding</option> + <option value="cotreatment">cotreatment</option> + <option value="expression">expression</option> + <option value="folding">folding</option> + <option value="localization">localization</option> + <option value="metabolic processing">metabolic processing</option> + <option value="acetylation">- acetylation</option> + <option value="acylation">- acylation</option> + <option value="alkylation">- alkylation</option> + <option value="amination">- amination</option> + <option value="carbamoylation">- carbamoylation</option> + <option value="carboxylation">- carboxylation</option> + <option value="chemical synthesis">- chemical synthesis</option> + <option value="degradation">- degradation</option> + <option value="cleavage"> - cleavage</option> + <option value="hydrolysis"> - hydrolysis</option> + <option value="ethylation">- ethylation</option> + <option value="glutathionylation">- glutathionylation</option> + <option value="glycation">- glycation</option> + <option value="glycosylation">- glycosylation</option> + <option value="N-linked glycosylation"> - N-linked glycosylation</option> + <option value="O-linked glycosylation"> - O-linked glycosylation</option> + <option value="glucuronidation"> - glucuronidation</option> + <option value="hydroxylation">- hydroxylation</option> + <option value="lipidation">- lipidation</option> + <option value="farnesylation"> - farnesylation</option> + <option value="geranolyation"> - geranolyation</option> + <option value="myristolylation"> - myristolylation</option> + <option value="palmitoylation"> - palmitoylation</option> + <option value="prenylation"> - prenylation</option> + <option value="methylation">- methylation</option> + <option value="nitrosation">- nitrosation</option> + <option value="nucleotidylation">- nucleotidylation</option> + <option value="oxidation">- oxidation</option> + <option value="phosphorylation">- phosphorylation</option> + <option value="reduction">- reduction</option> + <option value="ribosylation">- ribosylation</option> + <option value="ADP-ribosylation"> - ADP-ribosylation</option> + <option value="sulfation">- sulfation</option> + <option value="sumoylation">- sumoylation</option> + <option value="ubiquitination">- ubiquitination</option> + <option value="mutagenesis">mutagenesis</option> + <option value="reaction">reaction</option> + <option value="response to chemical">response to chemical</option> + <option value="splicing">splicing</option> + <option value="stability">stability</option> + <option value="transport">transport</option> + <option value="secretion">- secretion</option> + <option value="export"> - export</option> + <option value="uptake">- uptake</option> + <option value="import"> - import</option> + </param> + </when> + </conditional> + </when> + <when value="disease"> + <param name="report" label="Data to extract" type="select"> + <option value="chems">Chemical associations</option> + <option value="chems_curated">Curated chemical associations only</option> + <option value="chems_inferred">Inferred chemical associations only</option> + <option value="genes">Gene associations</option> + <option value="genes_curated">Curated gene associations</option> + <option value="genes_inferred">Inferred gene associations</option> + <option value="pathways_inferred">Inferred pathway associations</option> + </param> + </when> + <when value="gene"> + <conditional name='reportType'> + <param name="report" label="Data to extract" type="select"> + <option value="cgixns">Curated chemical-gene interactions</option> + <option value="chems_curated">Curated chemical associations</option> + <option value="pathways_curated">Curated pathway associations</option> + <option value="diseases" selected="true">All disease relationships</option> + <option value="diseases_curated"> Curated disease relationships only</option> + <option value="diseases_inferred"> Inferred disease relationships only</option> + <option value="go">All GO associations</option> + </param> + <when value="chems_curated"> + <!-- do nothing --> + </when> + <when value="pathways_curated"> + <!-- do nothing --> + </when> + <when value="diseases"> + <!-- do nothing --> + </when> + <when value="diseases_curated"> + <!-- do nothing --> + </when> + <when value="diseases_inferred"> + <!-- do nothing --> + </when> + <when value="go"> + <!-- do nothing --> + </when> + <when value="cgixns"> + <param name="actType" label="Interaction type" type="select"> + <option value="ANY">ANY</option> + <option value="abundance">abundance</option> + <option value="activity">activity</option> + <option value="binding">binding</option> + <option value="cotreatment">cotreatment</option> + <option value="expression">expression</option> + <option value="folding">folding</option> + <option value="localization">localization</option> + <option value="metabolic processing">metabolic processing</option> + <option value="acetylation">- acetylation</option> + <option value="acylation">- acylation</option> + <option value="alkylation">- alkylation</option> + <option value="amination">- amination</option> + <option value="carbamoylation">- carbamoylation</option> + <option value="carboxylation">- carboxylation</option> + <option value="chemical synthesis">- chemical synthesis</option> + <option value="degradation">- degradation</option> + <option value="cleavage"> - cleavage</option> + <option value="hydrolysis"> - hydrolysis</option> + <option value="ethylation">- ethylation</option> + <option value="glutathionylation">- glutathionylation</option> + <option value="glycation">- glycation</option> + <option value="glycosylation">- glycosylation</option> + <option value="N-linked glycosylation"> - N-linked glycosylation</option> + <option value="O-linked glycosylation"> - O-linked glycosylation</option> + <option value="glucuronidation"> - glucuronidation</option> + <option value="hydroxylation">- hydroxylation</option> + <option value="lipidation">- lipidation</option> + <option value="farnesylation"> - farnesylation</option> + <option value="geranolyation"> - geranolyation</option> + <option value="myristolylation"> - myristolylation</option> + <option value="palmitoylation"> - palmitoylation</option> + <option value="prenylation"> - prenylation</option> + <option value="methylation">- methylation</option> + <option value="nitrosation">- nitrosation</option> + <option value="nucleotidylation">- nucleotidylation</option> + <option value="oxidation">- oxidation</option> + <option value="phosphorylation">- phosphorylation</option> + <option value="reduction">- reduction</option> + <option value="ribosylation">- ribosylation</option> + <option value="ADP-ribosylation"> - ADP-ribosylation</option> + <option value="sulfation">- sulfation</option> + <option value="sumoylation">- sumoylation</option> + <option value="ubiquitination">- ubiquitination</option> + <option value="mutagenesis">mutagenesis</option> + <option value="reaction">reaction</option> + <option value="response to chemical">response to chemical</option> + <option value="splicing">splicing</option> + <option value="stability">stability</option> + <option value="transport">transport</option> + <option value="secretion">- secretion</option> + <option value="export"> - export</option> + <option value="uptake">- uptake</option> + <option value="import"> - import</option> + </param> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input" ftype="tabular" value="ctdBatchInput.txt" /> + <param name="numerical_column" value="1" /> + <param name="inputType" value="gene" /> + <param name="report" value="diseases" /> + <output name="out_file1" file="ctdBatchOut.txt" /> + </test> + </tests> + <help> + +**Dataset formats** + +The input and output datasets are tabular_. + +----- + +**What it does** + +This tool extracts data related to the provided list of identifiers +from the Comparative Toxicogenomics Database (CTD). The fields +extracted vary with the type of data requested; the first row +of the output identifies the columns. + +For the curated chemical-gene interactions, you can also choose the +interaction type from the search-and-select box. The choices that +start with '-' are a subset of a choice above them; you can chose +either the general interaction type or a more specific one. + +Home page: http://ctdbase.org + +.. _tabular: ${static_path}/formatHelp.html#tab + +----- + +**Examples** + +- input data file: + HBB + +- select column c1, Identifier type = Genes, and Data to extract = All disease relationships + +- output file:: + + #Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs + hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900 + hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741 + etc. + +Another example: + +- same input file: + HBB + +- select column c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY + +- output file:: + + #Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs + hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347 + hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499 + etc. + +----- + +**Reference** + +Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical.gene.disease networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92. + + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ctdBatchInput.txt Wed Sep 25 10:23:26 2013 -0400 @@ -0,0 +1,2 @@ +ABO +LMNA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ctdBatchOut.txt Wed Sep 25 10:23:26 2013 -0400 @@ -0,0 +1,233 @@ +#Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs +abo ABO ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase) 28 Inflammation MESH:D007249 inferred via Flavonoids 17296493 +abo ABO ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase) 28 Pancreatic Neoplasms MESH:D010190 marker/mechanism 19648918 +abo ABO ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase) 28 Prostatic Neoplasms MESH:D011471 marker/mechanism 17013881 +lmna LMNA lamin A/C 4000 Abdominal Neoplasms MESH:D000008 inferred via Tamoxifen 14745880 +lmna LMNA lamin A/C 4000 Acne Vulgaris MESH:D000152 inferred via Ethinyl Estradiol 17505938 +lmna LMNA lamin A/C 4000 Acute-Phase Reaction MESH:D000210 inferred via zoledronic acid 20200999 +lmna LMNA lamin A/C 4000 Adenocarcinoma MESH:D000230 inferred via Ethinyl Estradiol 14692618 +lmna LMNA lamin A/C 4000 Adenoma MESH:D000236 inferred via resveratrol 15688382 +lmna LMNA lamin A/C 4000 Adenoma, Liver Cell MESH:D018248 inferred via Tetrachlorodibenzodioxin 16835633 +lmna LMNA lamin A/C 4000 Alzheimer Disease MESH:D000544 inferred via resveratrol 16162502|16183991 +lmna LMNA lamin A/C 4000 Anemia, Hemolytic MESH:D000743 inferred via Quercetin 17084956 +lmna LMNA lamin A/C 4000 Angioedema MESH:D000799 inferred via Acetaminophen 10982225 +lmna LMNA lamin A/C 4000 Arteriosclerosis MESH:D001161 inferred via Ethinyl Estradiol 11256880 +lmna LMNA lamin A/C 4000 Arthritis, Experimental MESH:D001169 inferred via Ethinyl Estradiol 15885639 +lmna LMNA lamin A/C 4000 Arthritis, Experimental MESH:D001169 inferred via resveratrol 17115116 +lmna LMNA lamin A/C 4000 Asthma MESH:D001249 inferred via Mustard Gas 10378619 +lmna LMNA lamin A/C 4000 Ataxia Telangiectasia MESH:D001260 inferred via Quercetin 15336622 +lmna LMNA lamin A/C 4000 Atherosclerosis MESH:D050197 inferred via resveratrol 17967414|16873680 +lmna LMNA lamin A/C 4000 Autistic Disorder MESH:D001321 inferred via Acetaminophen 18445737 +lmna LMNA lamin A/C 4000 Autistic Disorder MESH:D001321 inferred via Mercury 17497416 +lmna LMNA lamin A/C 4000 Autoimmune Diseases MESH:D001327 inferred via Mercury 16634805 +lmna LMNA lamin A/C 4000 Autoimmune Diseases MESH:D001327 inferred via Quercetin 19761891 +lmna LMNA lamin A/C 4000 Melanoma, Experimental MESH:D008546 inferred via Acetaminophen 19513568 +lmna LMNA lamin A/C 4000 Blister MESH:D001768 inferred via Mustard Gas 19167455 +lmna LMNA lamin A/C 4000 Blood Coagulation Disorders MESH:D001778 inferred via pirinixic acid 19483382 +lmna LMNA lamin A/C 4000 Bone Neoplasms MESH:D001859 inferred via zoledronic acid 16778634|16121404|17312309|11697798|19442620|15867366 +lmna LMNA lamin A/C 4000 Bone Resorption MESH:D001862 inferred via zoledronic acid 18404659|11869084|15845617|18496637|16769263|8053405 +lmna LMNA lamin A/C 4000 Brain Ischemia MESH:D002545 inferred via resveratrol 17600658 +lmna LMNA lamin A/C 4000 Brain Neoplasms MESH:D001932 inferred via KCC 009 16170020 +lmna LMNA lamin A/C 4000 Breast Neoplasms MESH:D001943 inferred via Quercetin 18628248 +lmna LMNA lamin A/C 4000 Breast Neoplasms MESH:D001943 inferred via Tamoxifen 18855134|17049068|16818667|17242785|16202921|15565566|11161223|16873071|17261762|15668708|17440819|17893378|16273361 +lmna LMNA lamin A/C 4000 Breast Neoplasms MESH:D001943 inferred via resveratrol 16393696|17534123|17651959 +lmna LMNA lamin A/C 4000 Breast Neoplasms MESH:D001943 inferred via zoledronic acid 18695136|16096432 +lmna LMNA lamin A/C 4000 Bronchiolitis Obliterans MESH:D001989 inferred via Mustard Gas 15286001 +lmna LMNA lamin A/C 4000 Bronchitis, Chronic MESH:D029481 inferred via Mustard Gas 10378619|17687719 +lmna LMNA lamin A/C 4000 Cadmium Poisoning MESH:D002105 inferred via Quercetin 16962696 +lmna LMNA lamin A/C 4000 Carbon Tetrachloride Poisoning MESH:D002252 inferred via Vitamin E 16050911 +lmna LMNA lamin A/C 4000 Carcinoma MESH:D002277 inferred via Tetrachlorodibenzodioxin 16835633 +lmna LMNA lamin A/C 4000 Carcinoma, Hepatocellular MESH:D006528 inferred via Quercetin 12508355|19519916 +lmna LMNA lamin A/C 4000 Carcinoma, Hepatocellular MESH:D006528 inferred via Tamoxifen 16924424 +lmna LMNA lamin A/C 4000 Carcinoma, Hepatocellular MESH:D006528 inferred via resveratrol 16227395 +lmna LMNA lamin A/C 4000 Carcinoma, Lewis Lung MESH:D018827 inferred via resveratrol 16675471 +lmna LMNA lamin A/C 4000 Carcinoma, Pancreatic Ductal MESH:D021441 inferred via Quercetin 17234771 +lmna LMNA lamin A/C 4000 Carcinoma, Renal Cell MESH:D002292 inferred via zoledronic acid 18507039 +lmna LMNA lamin A/C 4000 Carcinoma, Squamous Cell MESH:D002294 inferred via resveratrol 16227395 +lmna LMNA lamin A/C 4000 Carcinoma, Transitional Cell MESH:D002295 inferred via Tamoxifen 17572228 +lmna LMNA lamin A/C 4000 Cardiomegaly MESH:D006332 inferred via Quercetin 19794523 +lmna LMNA lamin A/C 4000 Cardiomyopathy, Dilated MESH:D002311 marker/mechanism 115200 +lmna LMNA lamin A/C 4000 Cardiovascular Diseases MESH:D002318 inferred via resveratrol 15458977 +lmna LMNA lamin A/C 4000 Cataract MESH:D002386 inferred via Acetaminophen 10977129 +lmna LMNA lamin A/C 4000 CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2B1 OMIM:605588 marker/mechanism 605588 +lmna LMNA lamin A/C 4000 Cholangiocarcinoma MESH:D018281 inferred via Tetrachlorodibenzodioxin 16835633 +lmna LMNA lamin A/C 4000 Cholestasis MESH:D002779 inferred via Ethinyl Estradiol 11677210|17681005|17110522|16919318|17333356|15861022|16105132 +lmna LMNA lamin A/C 4000 Cleft Palate MESH:D002972 inferred via Tetrachlorodibenzodioxin 8697196 +lmna LMNA lamin A/C 4000 Colitis MESH:D003092 inferred via Selenium 17936198 +lmna LMNA lamin A/C 4000 Colitis MESH:D003092 inferred via resveratrol 16474422 +lmna LMNA lamin A/C 4000 Colonic Neoplasms MESH:D003110 inferred via Quercetin 17148506|19440933|19056647|15741050|16640504|17191121|11134977 +lmna LMNA lamin A/C 4000 Colonic Neoplasms MESH:D003110 inferred via resveratrol 16338953 +lmna LMNA lamin A/C 4000 Colorectal Neoplasms MESH:D015179 inferred via Quercetin 18095365|18852136 +lmna LMNA lamin A/C 4000 Colorectal Neoplasms MESH:D015179 inferred via resveratrol 16550006 +lmna LMNA lamin A/C 4000 Coronary Disease MESH:D003327 inferred via fluvastatin 16142594 +lmna LMNA lamin A/C 4000 Coronary Disease MESH:D003327 inferred via resveratrol 16507316 +lmna LMNA lamin A/C 4000 Craniofacial Abnormalities MESH:D019465 inferred via Tetrachlorodibenzodioxin 10048152|20055451 +lmna LMNA lamin A/C 4000 Craniofacial Abnormalities MESH:D019465 inferred via Vitamin E 19769572 +lmna LMNA lamin A/C 4000 Craniofacial Abnormalities MESH:D019465 marker/mechanism 15726408 +lmna LMNA lamin A/C 4000 Diabetes Mellitus, Type 2 MESH:D003924 inferred via Tetrachlorodibenzodioxin 17107852 +lmna LMNA lamin A/C 4000 Diabetes Mellitus, Experimental MESH:D003921 inferred via Quercetin 19496084 +lmna LMNA lamin A/C 4000 Diabetes Mellitus, Experimental MESH:D003921 inferred via resveratrol 16873680 +lmna LMNA lamin A/C 4000 Diabetic Nephropathies MESH:D003928 inferred via resveratrol 16286809 +lmna LMNA lamin A/C 4000 Drug-Induced Liver Injury MESH:D056486 inferred via Acetaminophen 10663392|11529661|12540782|15619225|12705907|19370779|14550746|11421492|19420014|18713872|12153990|11739529|19739265|10915739|17906064|16393943|10774834|16485898|14725611|19416960|11287661|12958197|11834606|11461765|19164858|16081117|17522070|17562736|14986274|16177239|16227642|15968718|11743745|12392966|2444490|16781746|18071297|19085960|12594235 +lmna LMNA lamin A/C 4000 Drug-Induced Liver Injury MESH:D056486 inferred via Selenium 15131321 +lmna LMNA lamin A/C 4000 Drug-Induced Liver Injury, Chronic MESH:D056487 inferred via Acetaminophen 19426721 +lmna LMNA lamin A/C 4000 Edema MESH:D004487 inferred via Mustard Gas 11428647|9260866|11428631|11402378 +lmna LMNA lamin A/C 4000 Edema MESH:D004487 inferred via pirinixic acid 12083418 +lmna LMNA lamin A/C 4000 Edema MESH:D004487 inferred via resveratrol 8985016 +lmna LMNA lamin A/C 4000 EMERY-DREIFUSS MUSCULAR DYSTROPHY, AUTOSOMAL DOMINANT OMIM:181350 marker/mechanism 181350 +lmna LMNA lamin A/C 4000 Encephalomyelitis, Autoimmune, Experimental MESH:D004681 inferred via Ethinyl Estradiol 12538720 +lmna LMNA lamin A/C 4000 Encephalomyelitis, Autoimmune, Experimental MESH:D004681 inferred via resveratrol 17872969 +lmna LMNA lamin A/C 4000 Endometrial Neoplasms MESH:D016889 inferred via Tamoxifen 17893378|16202921 +lmna LMNA lamin A/C 4000 Enterocolitis, Necrotizing MESH:D020345 inferred via resveratrol 17923197 +lmna LMNA lamin A/C 4000 Erythema MESH:D004890 inferred via Mustard Gas 9357497 +lmna LMNA lamin A/C 4000 Eye Abnormalities MESH:D005124 inferred via Tetrachlorodibenzodioxin 11564622 +lmna LMNA lamin A/C 4000 Fatty Liver MESH:D005234 inferred via Ethinyl Estradiol 15345470 +lmna LMNA lamin A/C 4000 Fatty Liver MESH:D005234 inferred via Tamoxifen 14986274 +lmna LMNA lamin A/C 4000 Female Urogenital Diseases MESH:D052776 inferred via Tamoxifen 16709447 +lmna LMNA lamin A/C 4000 Femoral Fractures MESH:D005264 inferred via zoledronic acid 16234978 +lmna LMNA lamin A/C 4000 Fibromatosis, Abdominal MESH:D018221 inferred via Tamoxifen 14745880 +lmna LMNA lamin A/C 4000 Fibromatosis, Aggressive MESH:D018222 inferred via Tamoxifen 19069698 +lmna LMNA lamin A/C 4000 Fibrosis MESH:D005355 inferred via Quercetin 19474275 +lmna LMNA lamin A/C 4000 Glioblastoma MESH:D005909 inferred via KCC 009 16170020 +lmna LMNA lamin A/C 4000 Glioblastoma MESH:D005909 inferred via Quercetin 19804834 +lmna LMNA lamin A/C 4000 Glioma MESH:D005910 inferred via Quercetin 17643826 +lmna LMNA lamin A/C 4000 Heart Defects, Congenital MESH:D006330 inferred via Tetrachlorodibenzodioxin 10048152 +lmna LMNA lamin A/C 4000 Heart Defects, Congenital MESH:D006330 inferred via Vitamin E 16080930 +lmna LMNA lamin A/C 4000 Heart Failure MESH:D006333 inferred via Selenium 17162251 +lmna LMNA lamin A/C 4000 HEART-HAND SYNDROME, SLOVENIAN TYPE OMIM:610140 marker/mechanism 610140 +lmna LMNA lamin A/C 4000 Hernia, Diaphragmatic MESH:D006548 inferred via Vitamin E 16490937|16863852 +lmna LMNA lamin A/C 4000 Herpes Simplex MESH:D006561 inferred via resveratrol 16876885 +lmna LMNA lamin A/C 4000 Hot Flashes MESH:D019584 inferred via Vitamin E 14716179 +lmna LMNA lamin A/C 4000 Hydronephrosis MESH:D006869 inferred via Tetrachlorodibenzodioxin 8697196 +lmna LMNA lamin A/C 4000 Hyperalgesia MESH:D006930 inferred via Acetaminophen 16870215 +lmna LMNA lamin A/C 4000 Hyperalgesia MESH:D006930 inferred via zoledronic acid 16769263 +lmna LMNA lamin A/C 4000 Hypercalcemia MESH:D006934 inferred via zoledronic acid 19622757|18089816 +lmna LMNA lamin A/C 4000 Hypercholesterolemia MESH:D006937 inferred via resveratrol 17188708 +lmna LMNA lamin A/C 4000 Hyperglycemia MESH:D006943 inferred via Quercetin 11834736|18262572 +lmna LMNA lamin A/C 4000 Hyperlipidemias MESH:D006949 inferred via resveratrol 16873680 +lmna LMNA lamin A/C 4000 Hypertension MESH:D006973 inferred via Quercetin 18356687 +lmna LMNA lamin A/C 4000 Hypertrophy, Left Ventricular MESH:D017379 inferred via resveratrol 17488730 +lmna LMNA lamin A/C 4000 Hypocalcemia MESH:D006996 inferred via zoledronic acid 12669777 +lmna LMNA lamin A/C 4000 Hypospadias MESH:D007021 inferred via Ethinyl Estradiol 16945680|16569931 +lmna LMNA lamin A/C 4000 Infarction, Middle Cerebral Artery MESH:D020244 inferred via resveratrol 17600658 +lmna LMNA lamin A/C 4000 Infertility, Female MESH:D007247 inferred via Ethinyl Estradiol 12013081 +lmna LMNA lamin A/C 4000 Infertility, Male MESH:D007248 inferred via Ethinyl Estradiol 17937319 +lmna LMNA lamin A/C 4000 Inflammation MESH:D007249 inferred via Mustard Gas 8975870|11428620|11428631|16001271|17524151|9357497|11402378|11428647|9260866 +lmna LMNA lamin A/C 4000 Inflammation MESH:D007249 inferred via resveratrol 16366677 +lmna LMNA lamin A/C 4000 Influenza, Human MESH:D007251 inferred via Quercetin 16624496 +lmna LMNA lamin A/C 4000 Influenza, Human MESH:D007251 inferred via Selenium 16624496 +lmna LMNA lamin A/C 4000 Influenza, Human MESH:D007251 inferred via Vitamin E 16624496 +lmna LMNA lamin A/C 4000 Influenza, Human MESH:D007251 inferred via resveratrol 16624496 +lmna LMNA lamin A/C 4000 Keloid MESH:D007627 inferred via Quercetin 17086741 +lmna LMNA lamin A/C 4000 Kidney Diseases MESH:D007674 inferred via Quercetin 16962696 +lmna LMNA lamin A/C 4000 Kidney Diseases MESH:D007674 inferred via Vitamin E 12488133 +lmna LMNA lamin A/C 4000 Kidney Failure, Acute MESH:D007675 inferred via resveratrol 16538975 +lmna LMNA lamin A/C 4000 Kidney Failure, Acute MESH:D007675 inferred via zoledronic acid 19715164 +lmna LMNA lamin A/C 4000 Kidney Failure, Chronic MESH:D007676 inferred via Selenium 16518626 +lmna LMNA lamin A/C 4000 Leukemia MESH:D007938 inferred via Quercetin 17468513 +lmna LMNA lamin A/C 4000 Leukemia-Lymphoma, Adult T-Cell MESH:D015459 inferred via zoledronic acid 18089816 +lmna LMNA lamin A/C 4000 Lipidoses MESH:D008064 inferred via Tamoxifen 17567588|15342952 +lmna LMNA lamin A/C 4000 LIPODYSTROPHY, FAMILIAL PARTIAL, TYPE 2 OMIM:151660 marker/mechanism 151660 +lmna LMNA lamin A/C 4000 Liver Cirrhosis, Experimental MESH:D008106 inferred via Quercetin 12741479 +lmna LMNA lamin A/C 4000 Liver Cirrhosis, Experimental MESH:D008106 inferred via Tamoxifen 18564211 +lmna LMNA lamin A/C 4000 Liver Cirrhosis, Experimental MESH:D008106 inferred via Vitamin E 16169303 +lmna LMNA lamin A/C 4000 Liver Cirrhosis, Experimental MESH:D008106 inferred via pirinixic acid 15474484 +lmna LMNA lamin A/C 4000 Liver Diseases MESH:D008107 inferred via Acetaminophen 16610002|19460945|19014921|12969438|16611625|11587558|19784758 +lmna LMNA lamin A/C 4000 Liver Failure, Acute MESH:D017114 inferred via Acetaminophen 17185352|16871587 +lmna LMNA lamin A/C 4000 Liver Neoplasms MESH:D008113 inferred via Mitomycin 15113037 +lmna LMNA lamin A/C 4000 Liver Neoplasms MESH:D008113 inferred via Quercetin 18980244 +lmna LMNA lamin A/C 4000 Liver Neoplasms MESH:D008113 inferred via Tamoxifen 16684651 +lmna LMNA lamin A/C 4000 Liver Neoplasms MESH:D008113 inferred via Tetrachlorodibenzodioxin 16984957 +lmna LMNA lamin A/C 4000 Liver Neoplasms MESH:D008113 inferred via pirinixic acid 15890375 +lmna LMNA lamin A/C 4000 Liver Neoplasms, Experimental MESH:D008114 inferred via Quercetin 19519916 +lmna LMNA lamin A/C 4000 Lung Diseases MESH:D008171 inferred via Mustard Gas 18702808|18161513 +lmna LMNA lamin A/C 4000 Lung Diseases MESH:D008171 inferred via Vitamin E 16863852 +lmna LMNA lamin A/C 4000 Lung Neoplasms MESH:D008175 inferred via Mustard Gas 3148597|8781369 +lmna LMNA lamin A/C 4000 Lung Neoplasms MESH:D008175 inferred via Quercetin 16280456 +lmna LMNA lamin A/C 4000 Lung Neoplasms MESH:D008175 inferred via Vitamin E 11062179 +lmna LMNA lamin A/C 4000 Lymphoma, B-Cell MESH:D016393 inferred via resveratrol 17088997 +lmna LMNA lamin A/C 4000 Mammary Neoplasms, Animal MESH:D015674 inferred via resveratrol 15688416 +lmna LMNA lamin A/C 4000 Mammary Neoplasms, Experimental MESH:D008325 inferred via Selenium 15318939 +lmna LMNA lamin A/C 4000 Mammary Neoplasms, Experimental MESH:D008325 inferred via Tamoxifen 16827153|14580682|11731420 +lmna LMNA lamin A/C 4000 Mammary Neoplasms, Experimental MESH:D008325 inferred via resveratrol 11606380|8985016 +lmna LMNA lamin A/C 4000 Mammary Neoplasms, Experimental MESH:D008325 inferred via zoledronic acid 17312309 +lmna LMNA lamin A/C 4000 MANDIBULOACRAL DYSPLASIA WITH TYPE A LIPODYSTROPHY OMIM:248370 marker/mechanism 248370 17848409|12788894|19764019 +lmna LMNA lamin A/C 4000 Melanoma MESH:D008545 inferred via Tamoxifen 12393984 +lmna LMNA lamin A/C 4000 Melanoma MESH:D008545 inferred via resveratrol 17992120 +lmna LMNA lamin A/C 4000 Melanoma, Amelanotic MESH:D018328 inferred via Tamoxifen 15990972 +lmna LMNA lamin A/C 4000 Mesothelioma MESH:D008654 inferred via Selenium 15107826 +lmna LMNA lamin A/C 4000 Mesothelioma MESH:D008654 inferred via zoledronic acid 16675582 +lmna LMNA lamin A/C 4000 Metabolic Diseases MESH:D008659 inferred via resveratrol 17112576 +lmna LMNA lamin A/C 4000 Multiple Myeloma MESH:D009101 inferred via fluvastatin 16996129 +lmna LMNA lamin A/C 4000 Multiple Myeloma MESH:D009101 inferred via lonafarnib 16996129 +lmna LMNA lamin A/C 4000 Multiple Myeloma MESH:D009101 inferred via resveratrol 16267019|16490592|17049120|14749477|17935668|17164350 +lmna LMNA lamin A/C 4000 Multiple Myeloma MESH:D009101 inferred via zoledronic acid 18089719|16996129|19621390 +lmna LMNA lamin A/C 4000 Muscular Atrophy, Spinal MESH:D009134 inferred via resveratrol 17962980 +lmna LMNA lamin A/C 4000 Muscular Dystrophies, Limb-Girdle MESH:D049288 marker/mechanism 12032588 +lmna LMNA lamin A/C 4000 Muscular Dystrophy, Emery-Dreifuss MESH:D020389 marker/mechanism 12032588 +lmna LMNA lamin A/C 4000 MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 1B OMIM:159001 marker/mechanism 159001 +lmna LMNA lamin A/C 4000 Leukemia, Promyelocytic, Acute MESH:D015473 inferred via resveratrol 16087638 +lmna LMNA lamin A/C 4000 Myocardial Infarction MESH:D009203 inferred via Quercetin 19595682 +lmna LMNA lamin A/C 4000 Myocardial Infarction MESH:D009203 inferred via resveratrol 16317513|17188708|17015251|17125593|16525036|16456233 +lmna LMNA lamin A/C 4000 Myocardial Ischemia MESH:D017202 inferred via resveratrol 17015251|17125593 +lmna LMNA lamin A/C 4000 Myocardial Reperfusion Injury MESH:D015428 inferred via Quercetin 19207477 +lmna LMNA lamin A/C 4000 Myocarditis MESH:D009205 inferred via resveratrol 17322642 +lmna LMNA lamin A/C 4000 Neoplasm Metastasis MESH:D009362 inferred via zoledronic acid 15867366|17312309|19139120 +lmna LMNA lamin A/C 4000 Neoplasms MESH:D009369 inferred via Quercetin 15185748 +lmna LMNA lamin A/C 4000 Neoplasms, Experimental MESH:D009374 inferred via resveratrol 8985016 +lmna LMNA lamin A/C 4000 Neurodegenerative Diseases MESH:D019636 inferred via Acetaminophen 18514411 +lmna LMNA lamin A/C 4000 Neurodegenerative Diseases MESH:D019636 inferred via resveratrol 17652729 +lmna LMNA lamin A/C 4000 Neurogenic Inflammation MESH:D020078 inferred via Quercetin 17929310 +lmna LMNA lamin A/C 4000 Neurogenic Inflammation MESH:D020078 inferred via resveratrol 17929310 +lmna LMNA lamin A/C 4000 Neutropenia MESH:D009503 inferred via Mustard Gas 7688884|16761898 +lmna LMNA lamin A/C 4000 Lymphoma, Non-Hodgkin MESH:D008228 inferred via resveratrol 14749477 +lmna LMNA lamin A/C 4000 Carcinoma, Non-Small-Cell Lung MESH:D002289 inferred via zoledronic acid 19233551 +lmna LMNA lamin A/C 4000 Osteolysis MESH:D010014 inferred via zoledronic acid 15867366 +lmna LMNA lamin A/C 4000 Osteoporosis MESH:D010024 inferred via zoledronic acid 17882678 +lmna LMNA lamin A/C 4000 Osteoporosis, Postmenopausal MESH:D015663 inferred via Quercetin 19495926 +lmna LMNA lamin A/C 4000 Osteoporosis, Postmenopausal MESH:D015663 inferred via resveratrol 17513867 +lmna LMNA lamin A/C 4000 Ovarian Neoplasms MESH:D010051 inferred via Quercetin 19005980 +lmna LMNA lamin A/C 4000 Pain MESH:D010146 inferred via Acetaminophen 16870215 +lmna LMNA lamin A/C 4000 Pain MESH:D010146 inferred via zoledronic acid 16475674 +lmna LMNA lamin A/C 4000 Pancreatic Neoplasms MESH:D010190 inferred via Mitomycin 15113037 +lmna LMNA lamin A/C 4000 Pancreatic Neoplasms MESH:D010190 inferred via Quercetin 16965848 +lmna LMNA lamin A/C 4000 Panic Disorder MESH:D016584 inferred via Ethinyl Estradiol 11578682 +lmna LMNA lamin A/C 4000 Plasmacytoma MESH:D010954 inferred via Selenium 15087411 +lmna LMNA lamin A/C 4000 Poisoning MESH:D011041 inferred via Mustard Gas 15727166 +lmna LMNA lamin A/C 4000 Precancerous Conditions MESH:D011230 inferred via Quercetin 19056647 +lmna LMNA lamin A/C 4000 Prenatal Exposure Delayed Effects MESH:D011297 inferred via resveratrol 16679765 +lmna LMNA lamin A/C 4000 Progeria MESH:D011371 marker/mechanism 176670 15726408|17469202 +lmna LMNA lamin A/C 4000 Prostatic Neoplasms MESH:D011471 inferred via AGN 194204 16000583 +lmna LMNA lamin A/C 4000 Prostatic Neoplasms MESH:D011471 inferred via Quercetin 17292933|14715546 +lmna LMNA lamin A/C 4000 Prostatic Neoplasms MESH:D011471 inferred via Tamoxifen 15067354 +lmna LMNA lamin A/C 4000 Prostatic Neoplasms MESH:D011471 inferred via Vitamin E 15084515 +lmna LMNA lamin A/C 4000 Prostatic Neoplasms MESH:D011471 inferred via resveratrol 17718901|17636462|17804756|15767336|17675339|16731767 +lmna LMNA lamin A/C 4000 Prostatic Neoplasms MESH:D011471 inferred via zoledronic acid 12438248|19103299 +lmna LMNA lamin A/C 4000 Pruritus MESH:D011537 inferred via Ethinyl Estradiol 15861022|16919318 +lmna LMNA lamin A/C 4000 Pruritus MESH:D011537 inferred via Mustard Gas 18058305 +lmna LMNA lamin A/C 4000 Pulmonary Fibrosis MESH:D011658 inferred via Mustard Gas 17620002|17720292|17894541|10334151|17266442 +lmna LMNA lamin A/C 4000 Renal Insufficiency, Chronic MESH:D051436 inferred via resveratrol 16325855 +lmna LMNA lamin A/C 4000 Reperfusion Injury MESH:D015427 inferred via resveratrol 15827377|17520802|17058453|16314181|16317513 +lmna LMNA lamin A/C 4000 RESTRICTIVE DERMOPATHY, LETHAL OMIM:275210 marker/mechanism 275210 +lmna LMNA lamin A/C 4000 Sarcoma, Ewing's MESH:D012512 inferred via zoledronic acid 16121404 +lmna LMNA lamin A/C 4000 Schistosomiasis japonica MESH:D012554 inferred via Quercetin 16862918 +lmna LMNA lamin A/C 4000 Scleroderma, Localized MESH:D012594 marker/mechanism 15726408 +lmna LMNA lamin A/C 4000 Skin Diseases MESH:D012871 inferred via Mustard Gas 16961503|15451306|12880345 +lmna LMNA lamin A/C 4000 Skin Neoplasms MESH:D012878 inferred via resveratrol 8985016|15837718 +lmna LMNA lamin A/C 4000 Spermatocele MESH:D013088 inferred via Ethinyl Estradiol 16709447 +lmna LMNA lamin A/C 4000 Spermatocele MESH:D013088 inferred via Tamoxifen 16709447 +lmna LMNA lamin A/C 4000 Stroke MESH:D020521 inferred via Vitamin E 16517955 +lmna LMNA lamin A/C 4000 STROKE, ISCHEMIC OMIM:601367 inferred via resveratrol 16321402 +lmna LMNA lamin A/C 4000 Thrombophilia MESH:D019851 inferred via Ethinyl Estradiol 11994571 +lmna LMNA lamin A/C 4000 Thrombosis MESH:D013927 inferred via Ethinyl Estradiol 15669648 +lmna LMNA lamin A/C 4000 Tongue Neoplasms MESH:D014062 inferred via resveratrol 16227395 +lmna LMNA lamin A/C 4000 Urinary Bladder Neoplasms MESH:D001749 inferred via Quercetin 16720314 +lmna LMNA lamin A/C 4000 Urinary Bladder Neoplasms MESH:D001749 inferred via Tamoxifen 17572228|16712894 +lmna LMNA lamin A/C 4000 Urticaria MESH:D014581 inferred via Acetaminophen 10982225 +lmna LMNA lamin A/C 4000 Uterine Cervical Neoplasms MESH:D002583 inferred via resveratrol 17473185 +lmna LMNA lamin A/C 4000 Uterine Neoplasms MESH:D014594 inferred via Ethinyl Estradiol 14692618 +lmna LMNA lamin A/C 4000 Uterine Neoplasms MESH:D014594 inferred via resveratrol 17044934 +lmna LMNA lamin A/C 4000 Venous Thrombosis MESH:D020246 inferred via Ethinyl Estradiol 15869587 +lmna LMNA lamin A/C 4000 Ventricular Dysfunction, Left MESH:D018487 inferred via resveratrol 17488730 +lmna LMNA lamin A/C 4000 Werner Syndrome MESH:D014898 marker/mechanism 277700 +