Mercurial > repos > devteam > hgv_fundo
changeset 0:64133669255f draft
Uploaded tool tarball.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 11:22:47 -0400 |
| parents | |
| children | ca3fcd18dc3e |
| files | disease_ontology_gene_fuzzy_selector.pl funDo.xml test-data/funDo_output1.interval tool-data/funDo.loc.sample |
| diffstat | 4 files changed, 659 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/disease_ontology_gene_fuzzy_selector.pl Wed Sep 25 11:22:47 2013 -0400 @@ -0,0 +1,64 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +################################################################## +# Select genes that are associated with the diseases listed in the +# disease ontology. +# ontology: http://do-wiki.nubic.northwestern.edu/index.php/Main_Page +# gene associations by FunDO: http://projects.bioinformatics.northwestern.edu/do_rif/ +# Sept 2010, switch to doLite +# input: build outfile sourceFileLoc.loc term or partial term +################################################################## + +if (!@ARGV or @ARGV < 3) { + print "usage: disease_ontology_gene_selector.pl build outfile.txt sourceFile.loc [list of terms]\n"; + exit; +} + +my $build = shift @ARGV; +my $out = shift @ARGV; +my $in = shift @ARGV; +my $term = shift @ARGV; +$term =~ s/^'//; #remove quotes protecting from shell +$term =~ s/'$//; +my $data; +open(LOC, $in) or die "Couldn't open $in, $!\n"; +while (<LOC>) { + chomp; + if (/^\s*#/) { next; } + my @f = split(/\t/); + if ($f[0] eq $build) { + if ($f[1] eq 'disease associated genes') { + $data = $f[2]; + } + } +} +close LOC or die "Couldn't close $in, $!\n"; +if (!$data) { + print "Error $build not found in $in\n"; + exit; +} +if (!defined $term) { + print "No disease term entered\n"; + exit; +} + +#start with just fuzzy term matches +open(OUT, ">", $out) or die "Couldn't open $out, $!\n"; +open(FH, $data) or die "Couldn't open data file $data, $!\n"; +$term =~ s/\s+/|/g; #use OR between words +while (<FH>) { + chomp; + my @f = split(/\t/); #chrom start end strand geneName geneID disease + if ($f[6] =~ /($term)/i) { + print OUT join("\t", @f), "\n"; + }elsif ($term eq 'disease') { #print all with disease + print OUT join("\t", @f), "\n"; + } +} +close FH or die "Couldn't close data file $data, $!\n"; +close OUT or die "Couldn't close $out, $!\n"; + +exit;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/funDo.xml Wed Sep 25 11:22:47 2013 -0400 @@ -0,0 +1,101 @@ +<tool id="hgv_funDo" name="FunDO" version="1.0.0"> + <description>human genes associated with disease terms</description> + + <command interpreter="perl"> + disease_ontology_gene_fuzzy_selector.pl $build $out_file1 ${GALAXY_DATA_INDEX_DIR}/funDo.loc '$term' + </command> + + <inputs> + <param name="build" type="select" label="Database build"> + <options from_file="funDo.loc"> + <column name="name" index="0"/> + <column name="value" index="0"/> + <filter type="unique_value" column="0"/> + </options> + </param> + <param name="term" size="40" type="text" label="Disease term(s)" /> + </inputs> + + <outputs> + <data format="interval" name="out_file1"> + </data> + </outputs> + + <tests> + <test> + <param name="term" value="lung"/> + <param name="build" value="hg18"/> + <output name="out_file1" file="funDo_output1.interval" /> + </test> + </tests> + + <help> +**Dataset formats** + +There is no input dataset. The output is in interval_ format. + +.. _interval: ${static_path}/formatHelp.html#interval + +----- + +**What it does** + +This tool searches the disease-term field of the DOLite mappings +used by the FunDO project and returns a set of genes that +are associated with terms matching the specified pattern. (This is the +reverse of what FunDO's own server does.) + +The search is case insensitive, and selects terms that contain any of +the given words, either exactly or within a longer word (e.g. "nemia" +selects not only "anemia", but also "hyperglycinemia", "tyrosinemias", +and many other things). Multiple words should be separated by spaces, +not commas. As a special case, entering the word "disease" returns all +genes associated with any disease, even if that word does not actually +appear in the term field. + +Website: http://django.nubic.northwestern.edu/fundo/ + +----- + +**Example** + +Typing:: + + carcinoma + +results in:: + + 1. 2. 3. 4. 5. 6. 7. + chr11 89507465 89565427 + NAALAD2 10003 Adenocarcinoma + chr15 50189113 50192264 - BCL2L10 10017 Carcinoma + chr7 150535855 150555250 - ABCF2 10061 Clear cell carcinoma + chr7 150540508 150555250 - ABCF2 10061 Clear cell carcinoma + chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma + chr10 134925911 134940397 - ADAM8 101 Adenocarcinoma + etc. + +where the column contents are as follows:: + + 1. chromosome name + 2. start position of the gene + 3. end position of the gene + 4. strand + 4. gene name + 6. Entrez Gene ID + 7. disease term + +----- + +**References** + +Du P, Feng G, Flatow J, Song J, Holko M, Kibbe WA, Lin SM. (2009) +From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose +ontology for the test of gene-ontology associations. +Bioinformatics. 25(12):i63-8. + +Osborne JD, Flatow J, Holko M, Lin SM, Kibbe WA, Zhu LJ, Danila MI, Feng G, Chisholm RL. (2009) +Annotating the human genome with Disease Ontology. +BMC Genomics. 10 Suppl 1:S6. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funDo_output1.interval Wed Sep 25 11:22:47 2013 -0400 @@ -0,0 +1,483 @@ +chr5 324735 368089 + PDCD6 10016 Lung cancer +chr10 134925911 134940397 - ADAM8 101 Lung cancer +chr10 134925911 134940397 - ADAM8 101 Lung cancer +chr10 134925911 134940397 - ADAM8 101 Lung cancer +chr17 46294585 46296412 - TOB1 10140 Lung cancer +chr3 50101371 50131396 + RBM5 10181 Lung cancer +chr13 94546025 94751688 - ABCC4 10257 Lung cancer +chr13 94470083 94751688 - ABCC4 10257 Lung cancer +chr17 38166737 38168585 + RAMP2 10266 Lung cancer +chr16 22264757 22293439 - CDR2 1039 Lung disease +chr1 144287344 144297903 + PIAS3 10401 Lung cancer +chr19 38556448 38565432 + CEBPG 1054 Lung cancer +chr16 66153964 66230589 + CTCF 10664 Lung cancer +chr1 11009166 11029872 - MASP2 10747 Infectious lung disease +chr1 11027441 11029872 - MASP2 10747 Infectious lung disease +chrX 133527538 133620179 - PLAC1 10761 Lung cancer +chr8 24207524 24268671 + ADAM28 10863 Lung cancer +chr8 24207524 24249557 + ADAM28 10863 Lung cancer +chr18 9465529 9528106 + RALBP1 10928 Lung cancer +chr2 9641556 9688557 - YWHAQ 10971 Lung cancer +chr14 23875066 23879082 - RIPK3 11035 Lung cancer +chr5 54309452 54317171 - ESM1 11082 Lung cancer +chr5 54309452 54317171 - ESM1 11082 Lung cancer +chr6 167332805 167374056 + FGFR1OP 11116 Lung cancer +chr6 167332805 167374056 + FGFR1OP 11116 Lung cancer +chr11 63098519 63138517 - PLA2G16 11145 Lung cancer +chr11 63098519 63138485 - PLA2G16 11145 Lung cancer +chr4 124033248 124063209 - NUDT6 11162 Lung cancer +chr4 124033248 124063573 - NUDT6 11162 Lung cancer +chr12 26096757 26117073 + RASSF8 11228 Lung cancer +chr12 26017954 26117073 + RASSF8 11228 Lung cancer +chr12 26003230 26117073 + RASSF8 11228 Lung cancer +chr12 26003230 26124091 + RASSF8 11228 Lung cancer +chr3 50337344 50340672 - TUSC2 11334 Lung cancer +chr15 76674701 76700692 - CHRNA3 1136 Lung cancer +chr15 76672451 76700692 - CHRNA3 1136 Lung cancer +chr15 76644960 76673515 + CHRNA5 1138 Lung cancer +chr17 7289129 7301656 + CHRNB1 1140 Lung cancer +chr10 101938113 101979334 - CHUK 1147 Infectious lung disease +chr18 894943 902173 + ADCYAP1 116 Lung cancer +chr18 895296 902173 + ADCYAP1 116 Lung cancer +chr3 46386636 46392701 + CCR5 1234 Lung cancer +chr3_random 664914 670974 + CCR5 1234 Lung cancer +chr3 46386636 46392701 + CCR5 1234 Lung cancer +chr3_random 664914 670974 + CCR5 1234 Lung cancer +chr4 100211152 100228954 - ADH5 128 Lung cancer +chr16 3715056 3870122 - CREBBP 1387 Lung cancer +chr16 3715056 3870122 - CREBBP 1387 Lung cancer +chr4 5873391 5945686 - CRMP1 1400 Lung cancer +chr4 5873391 5941216 - CRMP1 1400 Lung cancer +chr5 131437383 131439758 + CSF2 1437 Lung cancer +chr17 35425213 35427592 + CSF3 1440 Lung cancer +chr17 35425213 35427592 + CSF3 1440 Lung cancer +chr17 35425213 35427592 + CSF3 1440 Lung cancer +chr3 123526700 123543505 + CSTA 1475 Lung cancer +chr21 44018258 44020687 - CSTB 1476 Lung cancer +chr6 132311009 132314211 - CTGF 1490 Lung cancer +chr5 148186348 148188389 + ADRB2 154 Lung cancer +chr16 49333461 49393347 + CYLD 1540 Infectious lung disease +chr16 49333529 49393347 + CYLD 1540 Infectious lung disease +chr16 49333461 49393347 + CYLD 1540 Infectious lung disease +chr19 46041282 46048192 - CYP2A6 1548 Lung cancer +chr19 46286207 46293939 + CYP2A13 1553 Lung cancer +chr12 56442383 56447243 - CYP27B1 1594 Lung cancer +chr17 58908165 58928711 + ACE 1636 Infectious lung disease +chr17 58915908 58928711 + ACE 1636 Infectious lung disease +chr8 6860804 6863226 - DEFA3 1668 Lung disease +chr6 32256723 32260001 - AGER 177 Lung cancer +chr6_cox_hap1 3555933 3559211 - AGER 177 Lung cancer +chr6_qbl_hap2 3363712 3366990 - AGER 177 Lung cancer +chr6 32256723 32260001 - AGER 177 Lung cancer +chr6_cox_hap1 3555933 3559211 - AGER 177 Lung cancer +chr6_qbl_hap2 3363712 3366990 - AGER 177 Lung cancer +chr6 7486868 7531945 + DSP 1832 Lung cancer +chr6 7486868 7531945 + DSP 1832 Lung cancer +chr13 77367616 77447665 - EDNRB 1910 Lung cancer +chr13 77367616 77390967 - EDNRB 1910 Lung cancer +chr13 77367616 77390967 - EDNRB 1910 Lung cancer +chr20 61589809 61600949 - EEF1A2 1917 Lung cancer +chr5 137829079 137832903 + EGR1 1958 Infectious lung disease +chr7 17304800 17352300 + AHR 196 Lung cancer +chr17 7151041 7156504 + EIF5A 1984 Lung cancer +chr17 7152011 7156504 + EIF5A 1984 Lung cancer +chr17 7152417 7156504 + EIF5A 1984 Lung cancer +chr17 7151579 7156504 + EIF5A 1984 Lung cancer +chr19 803290 807246 + ELANE 1991 Infectious lung disease +chr12 6893874 6903120 + ENO2 2026 Lung cancer +chr3 89239363 89613974 + EPHA3 2042 Lung cancer +chr3 89239363 89532185 + EPHA3 2042 Lung cancer +chr1 224079624 224099883 + EPHX1 2052 Lung cancer +chr1 224064419 224099883 + EPHX1 2052 Lung cancer +chr12 129840099 129889764 - STX2 2054 Lung disease +chr12 129840099 129889764 - STX2 2054 Lung disease +chr2 127731335 127768222 - ERCC3 2071 Lung cancer +chr13 102296174 102326346 + ERCC5 2073 Lung cancer +chr10 50334496 50417153 - ERCC6 2074 Lung cancer +chr16 2265879 2330748 - ABCA3 21 Lung disease +chr4 74488835 74505991 + ALB 213 Lung cancer +chr12 110688728 110732167 + ALDH2 217 Lung cancer +chr1 31610686 31618510 - FABP3 2170 Lung cancer +chr17 19581891 19592338 - ALDH3A1 218 Lung cancer +chr17 19581891 19589517 - ALDH3A1 218 Lung cancer +chr17 19581891 19589364 - ALDH3A1 218 Lung cancer +chrX 14771449 14801105 - FANCB 2187 Lung disease +chrX 14771449 14801105 - FANCB 2187 Lung disease +chr2 55946605 56004436 - EFEMP1 2202 Lung cancer +chr2 55946605 56004436 - EFEMP1 2202 Lung cancer +chr2 55946605 56003860 - EFEMP1 2202 Lung cancer +chr11 61316725 61321286 + FEN1 2237 Lung cancer +chr15 47502666 47566814 + FGF7 2252 Infectious lung disease +chr4 155744735 155753352 - FGG 2266 Infectious lung disease +chr4 155745177 155753352 - FGG 2266 Infectious lung disease +chrX 153466611 153468269 + CTAG1A 246100 Lung cancer +chrX 153499058 153500716 - CTAG1A 246100 Lung cancer +chrX 119895375 119898693 - CT47A11 255313 Lung cancer +chrX 119900236 119903554 - CT47A11 255313 Lung cancer +chrX 119905095 119908414 - CT47A11 255313 Lung cancer +chrX 119909957 119913275 - CT47A11 255313 Lung cancer +chrX 119914817 119947319 - CT47A11 255313 Lung cancer +chrX 119924561 119927879 - CT47A11 255313 Lung cancer +chrX 119929421 119932739 - CT47A11 255313 Lung cancer +chrX 119934281 119937599 - CT47A11 255313 Lung cancer +chrX 119939140 119942459 - CT47A11 255313 Lung cancer +chr9 85052126 85343168 - FRMD3 257019 Lung cancer +chr3 101950868 102195024 - ABI3BP 25890 Lung cancer +chr9 115862228 115880573 - AMBP 259 Lung cancer +chr15 73448774 73535177 - SIN3A 25942 Lung cancer +chr15 73448774 73531140 - SIN3A 25942 Lung cancer +chr15 73448774 73530979 - SIN3A 25942 Lung cancer +chr13 20445175 20533722 - LATS2 26524 Lung cancer +chr5 37851509 37875539 - GDNF 2668 Lung cancer +chr5 37851509 37871350 - GDNF 2668 Lung cancer +chr5 37851509 37870655 - GDNF 2668 Lung cancer +chr16 54952864 55016945 - AMFR 267 Lung cancer +chr5 42459782 42757683 + GHR 2690 Lung cancer +chrX 70359780 70361790 + GJB1 2705 Lung cancer +chrX 70351786 70361790 + GJB1 2705 Lung cancer +chr6 53470098 53517790 - GCLC 2729 Lung disease +chr1 94125177 94147600 - GCLM 2730 Lung cancer +chr10 103328630 103338017 - POLL 27343 Lung cancer +chr10 103328630 103338017 - POLL 27343 Lung cancer +chr10 103328630 103338017 - POLL 27343 Lung cancer +chr10 103328630 103338017 - POLL 27343 Lung cancer +chr2 42249993 42413190 + EML4 27436 Lung cancer +chr2 42249993 42413190 + EML4 27436 Lung cancer +chr1 103999663 104008696 + AMY1A 276 Lung disease +chr1 104093801 104102834 + AMY1A 276 Lung disease +chr1 104031562 104040596 - AMY1A 276 Lung disease +chr1 103999824 104008696 + AMY1A 276 Lung disease +chr1 104093962 104102834 + AMY1A 276 Lung disease +chr1 104031562 104040435 - AMY1A 276 Lung disease +chr1 200567408 200577717 - UBE2T 29089 Lung cancer +chr1 110000220 110005853 + GSTM4 2948 Lung cancer +chr1 110000220 110009646 + GSTM4 2948 Lung cancer +chr1 110000220 110005853 + GSTM4 2948 Lung cancer +chr17 32516039 32841015 - ACACA 31 Lung cancer +chr17 32516039 32790172 - ACACA 31 Lung cancer +chr17 32516039 32730805 - ACACA 31 Lung cancer +chr17 32516039 32730805 - ACACA 31 Lung cancer +chr17 32516039 32841015 - ACACA 31 Lung cancer +chr6 31429627 31432968 - HLA-B 3106 Lung cancer +chr6_cox_hap1 2770844 2774184 - HLA-B 3106 Lung cancer +chr6_qbl_hap2 2569111 2572452 - HLA-B 3106 Lung cancer +chr12 108061584 108190413 + ACACB 32 Lung cancer +chr16 70646008 70652456 + HP 3240 Lung cancer +chr16 70646008 70652456 + HP 3240 Lung cancer +chr4 175647902 175680367 - HPGD 3248 Lung cancer +chr4 175647902 175680367 - HPGD 3248 Lung cancer +chr4 175647902 175680619 - HPGD 3248 Lung cancer +chr16 66022536 66028955 + HSD11B2 3291 Infectious lung disease +chr11 116211678 116213548 - APOA1 335 Lung cancer +chr22_random 13497 15367 + APOA1 335 Lung cancer +chr7 47970307 47985771 - HUS1 3364 Lung cancer +chr9 116822625 116920307 - TNC 3371 Lung cancer +chr3 50312324 50316008 - HYAL1 3373 Lung cancer +chr3 50312323 50316008 - HYAL1 3373 Lung cancer +chr3 50312323 50324816 - HYAL1 3373 Lung cancer +chr3 50312323 50316008 - HYAL1 3373 Lung cancer +chr3 50312323 50316008 - HYAL1 3373 Lung cancer +chr3 50312323 50316008 - HYAL1 3373 Lung cancer +chr19 10242516 10258291 + ICAM1 3383 Lung cancer +chr12 66834816 66839788 - IFNG 3458 Lung cancer +chr12 101313774 101398508 - IGF1 3479 Lung cancer +chr12 101313774 101398508 - IGF1 3479 Lung cancer +chr12 101313774 101396559 - IGF1 3479 Lung cancer +chr12 101335583 101398508 - IGF1 3479 Lung cancer +chr19 50100878 50104490 + APOE 348 Infectious lung disease +chr4 57592000 57671296 - IGFBP7 3490 Lung cancer +chr8 42247985 42309122 + IKBKB 3551 Infectious lung disease +chr2 113303807 113310827 - IL1B 3553 Infectious lung disease +chr2 113303807 113310827 - IL1B 3553 Lung cancer +chr2 102136833 102162766 + IL1R1 3554 Lung cancer +chr2 113591940 113608064 + IL1RN 3557 Lung cancer +chr2 113591940 113608064 + IL1RN 3557 Lung cancer +chr2 113601608 113608064 + IL1RN 3557 Lung cancer +chr2 113591940 113608064 + IL1RN 3557 Lung cancer +chr4 123592075 123597100 - IL2 3558 Lung cancer +chr10 6092662 6144339 - IL2RA 3559 Lung cancer +chr1 170894807 170902635 + FASLG 356 Lung cancer +chr5 132037271 132046267 + IL4 3565 Lung cancer +chr5 132037271 132046267 + IL4 3565 Lung cancer +chr7 22733290 22738144 + IL6 3569 Lung cancer +chr5 55272450 55326520 - IL6ST 3572 Infectious lung disease +chr5 55272450 55326520 - IL6ST 3572 Lung cancer +chr5 55272450 55326520 - IL6ST 3572 Infectious lung disease +chr5 55272450 55326520 - IL6ST 3572 Lung cancer +chr4 74825138 74828297 + IL8 3576 Infectious lung disease +chr4 74825138 74828297 + IL8 3576 Lung cancer +chr1 205007570 205012462 - IL10 3586 Lung cancer +chr11 117362315 117377406 + IL10RA 3587 Lung cancer +chr11 117362315 117377406 + IL10RA 3587 Lung cancer +chr5 158674368 158690059 - IL12B 3593 Lung disease +chr9 33431159 33437590 - AQP3 360 Lung cancer +chr4 142777203 142874061 + IL15 3600 Lung disease +chr4 142777203 142874061 + IL15 3600 Lung disease +chr4 184663213 184669243 + ING2 3622 Lung cancer +chr11 2137584 2139015 - INS 3630 Lung disease +chr8 109283147 109330135 - EIF3E 3646 Lung cancer +chr5 52320912 52426366 + ITGA2 3673 Lung cancer +chr2 182029863 182110713 + ITGA4 3676 Lung disease +chr12 53075311 53099317 - ITGA5 3678 Lung cancer +chr17 3564667 3651286 - ITGAE 3682 Lung disease +chr3 52803823 52818065 + ITIH3 3699 Lung cancer +chr2 155263338 155421260 + KCNJ3 3760 Lung cancer +chr11 128266522 128293161 + KCNJ5 3762 Lung cancer +chr21 37918656 38210566 - KCNJ6 3763 Lung cancer +chr1 158317983 158325836 + KCNJ9 3765 Lung cancer +chr11 2422796 2826916 + KCNQ1 3784 Lung disease +chr11 2439259 2826916 + KCNQ1 3784 Lung disease +chr12 9639136 9651764 - KLRB1 3820 Lung cancer +chr14 67156331 67188189 + ARG2 384 Lung cancer +chr12 51577237 51585135 - KRT8 3856 Lung cancer +chr18 19706981 19789027 + LAMA3 3909 Lung cancer +chr18 19523559 19789027 + LAMA3 3909 Lung cancer +chr18 19706981 19789027 + LAMA3 3909 Lung cancer +chr18 19523559 19789027 + LAMA3 3909 Lung cancer +chr1 26083264 26105580 - STMN1 3925 Lung cancer +chr1 26099193 26105580 - STMN1 3925 Lung cancer +chr1 26099193 26105955 - STMN1 3925 Lung cancer +chr1 26099193 26105231 - STMN1 3925 Lung cancer +chr1 32512298 32524353 + LCK 3932 Lung disease +chr1 32489426 32524353 + LCK 3932 Lung disease +chr7 127668566 127684918 + LEP 3952 Lung cancer +chr17 74478930 74487656 - LGALS3BP 3959 Lung cancer +chr8 19840861 19869050 + LPL 4023 Lung cancer +chr3 189425886 190091153 + LPP 4026 Lung disease +chr3 189354356 190091153 + LPP 4026 Lung disease +chr3 189413414 190091153 + LPP 4026 Lung disease +chr6 31648071 31650077 + LTA 4049 Lung cancer +chr6_cox_hap1 2986215 2988221 + LTA 4049 Lung cancer +chr6_qbl_hap2 2787675 2789683 + LTA 4049 Lung cancer +chr6 31647854 31650077 + LTA 4049 Lung cancer +chr6_cox_hap1 2985998 2988221 + LTA 4049 Lung cancer +chr6_qbl_hap2 2787458 2789683 + LTA 4049 Lung cancer +chr3 46452499 46481399 - LTF 4057 Lung cancer +chr9 138684874 138684958 + MIR126 406913 Lung cancer +chr4 146623406 146699775 + SMAD1 4086 Lung cancer +chr4 146622400 146699775 + SMAD1 4086 Lung cancer +chr5 135496434 135546321 + SMAD5 4090 Lung cancer +chr5 135496434 135546321 + SMAD5 4090 Lung cancer +chr5 135496434 135546321 + SMAD5 4090 Lung cancer +chrX 150832016 150844298 + MAGEA4 4103 Lung cancer +chrX 150836052 150844298 + MAGEA4 4103 Lung cancer +chrX 150837415 150844298 + MAGEA4 4103 Lung cancer +chrX 150835364 150844298 + MAGEA4 4103 Lung cancer +chr14 64611597 64638980 - MAX 4149 Lung cancer +chr14 64611597 64638980 - MAX 4149 Lung cancer +chr14 64611597 64638980 - MAX 4149 Lung cancer +chr14 64620214 64638980 - MAX 4149 Lung cancer +chr14 64614273 64638980 - MAX 4149 Lung cancer +chr14 64542644 64638980 - MAX 4149 Lung cancer +chr10 54195145 54201466 - MBL2 4153 Lung cancer +chr22 22566564 22567409 + MIF 4282 Lung cancer +chr7 100325550 100331477 - ACHE 43 Lung cancer +chr7 100325550 100331477 - ACHE 43 Lung cancer +chr11 102211737 102219552 - MMP3 4314 Lung cancer +chr11 102146443 102156554 - MMP10 4319 Lung cancer +chr11 102238674 102250974 - MMP12 4321 Lung cancer +chr14 60271222 60505151 + MNAT1 4331 Lung cancer +chr17 53702215 53713295 - MPO 4353 Lung cancer +chr11 93790114 93866688 - MRE11A 4361 Lung cancer +chr11 93790114 93866688 - MRE11A 4361 Lung cancer +chr7 2248382 2257306 + NUDT1 4521 Lung cancer +chr7 2248382 2257306 + NUDT1 4521 Lung cancer +chr7 2248382 2257306 + NUDT1 4521 Lung cancer +chr7 2248421 2257306 + NUDT1 4521 Lung cancer +chr7 2248421 2257306 + NUDT1 4521 Lung cancer +chr7 2249065 2257306 + NUDT1 4521 Lung cancer +chr7 2249065 2257306 + NUDT1 4521 Lung cancer +chr2 15998133 16004580 + MYCN 4613 Lung disease +chr22 28988818 28992840 - OSM 5008 Lung cancer +chr11 72606991 72625043 + P2RY2 5029 Lung cancer +chr11 72607149 72625043 + P2RY2 5029 Lung cancer +chr11 72606991 72625043 + P2RY2 5029 Lung cancer +chr11 72660894 72687312 + P2RY6 5031 Lung cancer +chr11 72653217 72686498 + P2RY6 5031 Lung cancer +chr11 72653217 72686498 + P2RY6 5031 Lung cancer +chr11 72658586 72686498 + P2RY6 5031 Lung cancer +chr1 45749293 45760196 - PRDX1 5052 Lung cancer +chr1 45749293 45760196 - PRDX1 5052 Lung cancer +chr1 45749293 45760196 - PRDX1 5052 Lung cancer +chr7 100557098 100569266 + SERPINE1 5054 Infectious lung disease +chr7 100557098 100569266 + SERPINE1 5054 Lung cancer +chr7 100557098 100569266 + SERPINE1 5054 Infectious lung disease +chr7 100557098 100569266 + SERPINE1 5054 Lung cancer +chr12 78509875 78608921 - PAWR 5074 Lung cancer +chr2 242440705 242449731 - PDCD1 5133 Lung disease +chr8 42151392 42184351 - PLAT 5327 Lung cancer +chr8 42151392 42184351 - PLAT 5327 Lung cancer +chr6 161043214 161095073 + PLG 5340 Lung cancer +chr6 161043214 161052892 + PLG 5340 Lung cancer +chr12 131710420 131774018 - POLE 5426 Lung cancer +chr20 3011201 3013370 - AVP 551 Lung cancer +chr7 99402287 99411671 - AZGP1 563 Lung cancer +chr2 26924472 27026723 + DPYSL5 56896 Lung cancer +chr2 237143118 237155733 + CXCR7 57007 Lung cancer +chr7 133862883 133876705 + AKR1B10 57016 Lung cancer +chr3 51966511 51976522 - PCBP4 57060 Lung cancer +chr3 51966511 51976490 - PCBP4 57060 Lung cancer +chr3 51966511 51976522 - PCBP4 57060 Lung cancer +chr3 51966511 51971948 - PCBP4 57060 Lung cancer +chr5 357290 491405 + AHRR 57491 Lung cancer +chr12 15366753 15641602 + PTPRO 5800 Lung cancer +chr12 15366753 15641602 + PTPRO 5800 Lung cancer +chr12 15590552 15641602 + PTPRO 5800 Lung cancer +chr12 15590552 15641602 + PTPRO 5800 Lung cancer +chr12 15590552 15641602 + PTPRO 5800 Lung cancer +chr12 15590552 15641602 + PTPRO 5800 Lung cancer +chr20 25176705 25226648 + PYGB 5834 Lung cancer +chr14 67356261 68034351 + RAD51L1 5890 Lung disease +chr14 67356261 68132367 + RAD51L1 5890 Lung disease +chr14 67356261 68014563 + RAD51L1 5890 Lung disease +chr4 99401549 99584035 + RAP1GDS1 5910 Lung cancer +chr4 99401549 99584035 + RAP1GDS1 5910 Lung cancer +chr4 99401549 99584035 + RAP1GDS1 5910 Lung cancer +chr4 99401549 99584035 + RAP1GDS1 5910 Lung cancer +chr4 99401549 99584035 + RAP1GDS1 5910 Lung cancer +chr4 99401549 99584035 + RAP1GDS1 5910 Lung cancer +chr5 86599906 86723489 + RASA1 5921 Lung cancer +chr5 86600521 86723489 + RASA1 5921 Lung cancer +chr17 9741751 9749409 - RCVRN 5957 Lung cancer +chr4 152240203 152245254 + RPS3A 6189 Lung disease +chr14 49113791 49122844 - RPS29 6235 Lung cancer +chr14 49120039 49122844 - RPS29 6235 Lung cancer +chr11 27633017 27698902 - BDNF 627 Lung disease +chr11 27633017 27698902 - BDNF 627 Lung disease +chr11 27633017 27697870 - BDNF 627 Lung disease +chr11 27633017 27679176 - BDNF 627 Lung disease +chr11 27633017 27679176 - BDNF 627 Lung disease +chr11 27633017 27679176 - BDNF 627 Lung disease +chr11 27633017 27679176 - BDNF 627 Lung disease +chr11 27633017 27679023 - BDNF 627 Lung disease +chr11 27633017 27678611 - BDNF 627 Lung disease +chr11 27633017 27678611 - BDNF 627 Lung disease +chr11 27633017 27677790 - BDNF 627 Lung disease +chr11 27633017 27637772 - BDNF 627 Lung disease +chr11 27633017 27678611 - BDNF 627 Lung disease +chr11 27633017 27700181 - BDNF 627 Lung disease +chr11 27633017 27698902 - BDNF 627 Lung disease +chr11 27633017 27679756 - BDNF 627 Lung disease +chr11 27633017 27677790 - BDNF 627 Lung disease +chr11 27633017 27637772 - BDNF 627 Lung disease +chrX 23711195 23714246 + SAT1 6303 Lung cancer +chrX 23711195 23714246 + SAT1 6303 Lung cancer +chr17 31222608 31231490 - CCL5 6352 Lung cancer +chr17 29636799 29639312 + CCL11 6356 Lung disease +chr16 55996179 56007475 + CCL17 6361 Lung disease +chr16 55950218 55957602 + CCL22 6367 Lung cancer +chr1 167958404 167969844 - SELE 6401 Lung cancer +chr1 167824711 167866001 - SELP 6403 Lung cancer +chr3 50167851 50201512 + SEMA3F 6405 Lung cancer +chr15 89061582 89159690 + BLM 641 Lung cancer +chr16 49288550 49324488 + NOD2 64127 Lung cancer +chr16 49288550 49324488 + NOD2 64127 Lung disease +chr2 85737951 85749375 - SFTPB 6439 Lung disease +chr2 85737951 85749375 - SFTPB 6439 Lung disease +chr8 22075128 22077933 + SFTPC 6440 Lung disease +chr8 22075128 22077933 + SFTPC 6440 Lung disease +chr8 22075128 22077936 + SFTPC 6440 Lung disease +chr10 81687475 81698841 - SFTPD 6441 Lung disease +chrX 48252314 48264146 + PORCN 64840 Lung cancer +chrX 48252314 48264146 + PORCN 64840 Lung cancer +chrX 48253115 48264146 + PORCN 64840 Lung cancer +chrX 48253115 48264146 + PORCN 64840 Lung cancer +chrX 48252314 48264146 + PORCN 64840 Lung cancer +chr3 45098772 45162918 - CDCP1 64866 Lung cancer +chr3 45126734 45162918 - CDCP1 64866 Lung cancer +chr12 22237591 22378915 - ST8SIA1 6489 Lung cancer +chr1 32572027 32574421 - MARCKSL1 65108 Lung cancer +chr21 45759056 45786779 - SLC19A1 6573 Lung cancer +chr2 202949294 203140719 + BMPR2 659 Lung cancer +chr20 43314292 43316620 - SLPI 6590 Infectious lung disease +chr20 43314292 43316620 - SLPI 6590 Lung cancer +chr21 31953805 31963114 + SOD1 6647 Lung cancer +chr13 111769913 111774021 + SOX1 6656 Lung cancer +chrX 47326633 47331134 + TIMP1 7076 Lung cancer +chr16 65099407 65141695 - TK2 7084 Lung cancer +chr16 65099407 65141816 - TK2 7084 Lung cancer +chr16 65099407 65141816 - TK2 7084 Lung cancer +chr16 65099407 65141816 - TK2 7084 Lung cancer +chr9 119506280 119519585 + TLR4 7099 Lung cancer +chr9 119506280 119519585 + TLR4 7099 Lung cancer +chr9 119506280 119519585 + TLR4 7099 Lung cancer +chr6 32003244 32021427 + C2 717 Infectious lung disease +chr6_cox_hap1 3341528 3359711 + C2 717 Infectious lung disease +chr6_qbl_hap2 3143005 3161189 + C2 717 Infectious lung disease +chr6 32003244 32021427 + C2 717 Infectious lung disease +chr6_cox_hap1 3341528 3359711 + C2 717 Infectious lung disease +chr6_qbl_hap2 3143005 3161189 + C2 717 Infectious lung disease +chr18 27425727 27432982 + TTR 7276 Lung cancer +chr11 1200871 1239982 + MUC5B 727897 Lung disease +chr6 3098900 3102782 - TUBB2A 7280 Lung cancer +chr10 80985613 80990169 - SFTPA2 729238 Lung disease +chr10 81305559 81310114 - SFTPA2 729238 Lung disease +chr9 112046130 112058599 - TXN 7295 Infectious lung disease +chr9 112046130 112058599 - TXN 7295 Lung cancer +chr4 40953654 40965202 + UCHL1 7345 Lung cancer +chr9 99477011 99499512 - XPA 7507 Lung cancer +chr9 99477012 99499512 - XPA 7507 Lung cancer +chr6 30959839 30975912 + DDR1 780 Lung disease +chr6_cox_hap1 2300465 2316540 + DDR1 780 Lung disease +chr6_qbl_hap2 2098794 2114869 + DDR1 780 Lung disease +chr6 30960305 30975912 + DDR1 780 Lung disease +chr6_cox_hap1 2300931 2316540 + DDR1 780 Lung disease +chr6_qbl_hap2 2099260 2114869 + DDR1 780 Lung disease +chr6 30964443 30975912 + DDR1 780 Lung disease +chr6_cox_hap1 2305069 2316540 + DDR1 780 Lung disease +chr6_qbl_hap2 2103398 2114869 + DDR1 780 Lung disease +chr12 26164227 26169270 - BHLHE41 79365 Lung cancer +chr11 14946625 14950408 - CALCA 796 Infectious lung disease +chr11 14946625 14950408 - CALCA 796 Lung cancer +chr11 14944791 14950408 - CALCA 796 Infectious lung disease +chr11 14944791 14950408 - CALCA 796 Lung cancer +chr11 14946623 14950408 - CALCA 796 Infectious lung disease +chr11 14946623 14950408 - CALCA 796 Lung cancer +chr10 14960904 14986310 + SUV39H2 79723 Lung cancer +chr17 43403427 43414146 + CDK5RAP3 80279 Lung cancer +chr11 104370176 104399105 - CASP5 838 Lung cancer +chr11 104370176 104399105 - CASP5 838 Lung cancer +chr11 104370176 104399105 - CASP5 838 Lung cancer +chr11 104370176 104399105 - CASP5 838 Lung cancer +chr11 104370176 104399105 - CASP5 838 Lung cancer +chr11 104370176 104399105 - CASP5 838 Lung cancer +chr1 15691381 15723377 - CASP9 842 Lung cancer +chr1 15691381 15723377 - CASP9 842 Lung cancer +chr21 43346371 43369109 - CBS 875 Lung cancer +chr10 103103814 103307060 + BTRC 8945 Lung cancer +chr10 103103814 103307060 + BTRC 8945 Lung cancer +chr5 86725837 86744592 - CCNH 902 Lung cancer +chr17 73864456 73867753 - SOCS3 9021 Lung cancer +chr11 1367704 1439904 + BRSK2 9024 Lung cancer +chr12 47373018 47397048 - CCNT1 904 Lung disease +chrX 129091019 129099696 - AIFM1 9131 Lung cancer +chrX 129091019 129127489 - AIFM1 9131 Lung cancer +chrX 129091018 129127489 - AIFM1 9131 Lung cancer +chrX 129091018 129127489 - AIFM1 9131 Lung cancer +chrX 129091018 129127489 - AIFM1 9131 Lung cancer +chr15 57184611 57204536 + CCNB2 9133 Lung cancer +chr11 117680504 117692100 + CD3E 916 Lung cancer +chr3 50375234 50515896 - CACNA2D2 9254 Lung cancer +chr3 50375235 50515896 - CACNA2D2 9254 Lung cancer +chr3 50375234 50515896 - CACNA2D2 9254 Lung cancer +chr6 14225843 14245127 + CD83 9308 Lung cancer +chr6 14225843 14245127 + CD83 9308 Lung cancer +chr3 188043156 188058946 + ADIPOQ 9370 Lung cancer +chr1 87100715 87152695 - SEP15 9403 Lung cancer +chr1 87100715 87152695 - SEP15 9403 Lung cancer +chr19 55553545 55560743 - NAPSA 9476 Lung cancer +chr12 51948349 51973694 + ESPL1 9700 Lung cancer +chr20 4708669 4752291 - RASSF2 9770 Lung cancer +chr20 4708668 4743769 - RASSF2 9770 Lung cancer +chr19 10457795 10474481 - KEAP1 9817 Lung cancer +chr19 10457795 10475054 - KEAP1 9817 Lung cancer +chr1 155171255 155281786 - ARHGEF11 9826 Lung cancer +chr1 155171255 155281786 - ARHGEF11 9826 Lung cancer +chr3 38055699 38139232 + DLEC1 9940 Lung cancer +chr3 38055699 38139232 + DLEC1 9940 Lung cancer +chrX 140819307 140824851 + MAGEC1 9947 Lung cancer +chr7 86619612 86663582 + DMTF1 9988 Lung cancer +chr7 86619612 86663582 + DMTF1 9988 Lung cancer +chr7 86619805 86663582 + DMTF1 9988 Lung cancer +chr7 86619612 86663582 + DMTF1 9988 Lung cancer +chr7 86619612 86663582 + DMTF1 9988 Lung cancer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/funDo.loc.sample Wed Sep 25 11:22:47 2013 -0400 @@ -0,0 +1,11 @@ +#This is a sample file distributed with Galaxy that is used by the FunDO tool. +#The funDo.loc file has this format (white space characters are TAB +#characters): +# +#<build> <description> <path to disease associated genes file> +# +#Your funDo.loc file should include an entry per line for each disease +#associated genes file you have stored. +# +#hg18 disease associated genes /galaxy/data/hg18/misc/funDo/genes-disease.Sept2010.interval +#hg19 disease associated genes /galaxy/data/hg19/misc/funDo/genes-disease.Sept2010.interval