add code to calculate the imprinted genes of mouse

diff --git a/Makefile b/Makefile
index 193e28d99615c78204bc5b738b0c0eb72538da7d..2bac96e06e31b2aacf4e2dfa10bf0938665c1414 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -8,19 +8,33 @@ all: imprinted_genes_information.txt
 geneimprint_human.html:
        wget -O $@ "http://www.geneimprint.com/site/genes-by-species.Homo+sapiens"
 
+geneimprint_mouse.html:
+       wget -O $@ "http://www.geneimprint.com/site/genes-by-species.Mus+musculus"
+
 
 parent_of_origin.html:
        wget -O $@ "http://igc.otago.ac.nz/FMPro?-DB=Catalogue.fm&-error=Error.html&-Format=Record3.html&Genetype=maingene&-SortField=Species&custom=Species&-SortField=Chr&custom=Chromosome&-SortField=Location&-SortOrder=Ascending&-Max=all&-Find"
 
+
 geneimprint_human.txt: geneimprint_human.html parse_geneimprint.pl
        ./parse_geneimprint.pl $< > $@
 
+geneimprint_mouse.txt: geneimprint_mouse.html parse_geneimprint.pl
+       ./parse_geneimprint.pl $< > $@
+
 parent_of_origin.txt: parent_of_origin.html parse_parent_of_origin.pl
        ./parse_parent_of_origin.pl $< > $@
 
+parent_of_origin_mouse.txt: parent_of_origin.html parse_parent_of_origin.pl
+       ./parse_parent_of_origin.pl --taxon Mouse $< > $@
+
 imprinted_genes.txt: combine_imprinted_genes.R geneimprint_human.txt \
        parent_of_origin.txt gene_aliases.txt
        $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@
 
 imprinted_genes_information.txt: imprinted_genes.txt
        ~/projects/chaim/bin/gene_info < $< > $@
+
+imprinted_genes_mouse.txt: combine_imprinted_genes.R geneimprint_mouse.txt \
+       parent_of_origin_mouse.txt gene_aliases_mouse.txt
+       $(R) $(ROPTS) -f $< --args $(wordlist 2,$(words $^),$^) $@

diff --git a/gene_aliases.txt b/gene_aliases.txt
new file mode 100644 (file)
index 0000000..c74bd49
--- /dev/null
+++ b/gene_aliases.txt
@@ -0,0 +1,36 @@
+alias gene
+APS KLK3
+AWT1 WT1
+BRP44L MPC1
+BRUNOL4 CELF4
+CFLJ13639 DHRS12
+GNAS1 GNAS
+IDDM10 IL2RA
+IGF2AS IGF2-AS
+ITUP1 MIMT1
+L3MBTL L3MBTL1
+SCA8 ATXN8OS
+U2AF1L1 ZRSR1
+C10orf93 CFAP46
+C16orf57 USB1
+C20orf20 MRGBP
+C20orf82 ISM1
+C6orf117 MRAP2
+FAM59A GAREM
+FAM70B TMEM255B
+GNASAS GNAS-AS1
+KIAA1530 UVSSA
+KIAA1545 FBRSL1
+FLJ13639 DHRS12
+FLJ20464 LINC01521
+FLJ40296 PRR20A
+FLJ46321 SPATA31D1
+MIM1 MIMT1
+PEG13 KCNK9
+PSIMCT-1 MCTS2P
+PWCR1 SNORD116
+SANG GNAS-AS1
+UPD UROD
+WDR8 WRAP73
+ZNF127AS MKRN3-AS1
+MCTS2 MCTS2P

diff --git a/gene_aliases_mouse.txt b/gene_aliases_mouse.txt
new file mode 100644 (file)
index 0000000..3b7baff
--- /dev/null
+++ b/gene_aliases_mouse.txt
@@ -0,0 +1,3 @@
+alias gene
+Example Example
+

diff --git a/imprinted_genes_mouse.txt b/imprinted_genes_mouse.txt
new file mode 100644 (file)
index 0000000..c4466ca
--- /dev/null
+++ b/imprinted_genes_mouse.txt
@@ -0,0 +1,154 @@
+AF313042
+AF357341
+AF357355
+AF357359
+AF357425
+AF357426
+AF357428
+Air
+AK014392
+AK155734
+Ampd3
+Ano1
+Asb4
+Ascl2
+Atp10a
+B830012L14Rik
+BB077283
+Begain
+Blcap
+BM117114
+Calcr
+Ccdc40
+Cd81
+Cdkn1c
+Commd1
+Copg2
+Cpa4
+Ctnna3
+Dcn
+Ddc
+Dhcr7
+Dio3
+Dlk1
+Dlx5
+DMR
+Ftx
+Gab1
+Gabra5
+Gabrb3
+Gabrg3
+Gatm
+Glis3
+Gnai3
+Gnas
+Gpr1
+Grb10
+Gtl2
+H13
+H19
+Htr2a
+Hymai
+Igf2
+Igf2as
+Igf2r
+Il6
+Impact
+Ins1
+Ins2
+Jpx
+Kcnk9
+Kcnq1
+Kcnq1ot1
+Klf14
+L3mbtl
+Lin28a
+Lin28b
+LOC101055709
+Magel2
+Magi2
+Mcts2
+Mest
+Mir127
+Mir134
+Mir136
+Mir154
+Mir184
+Mir296
+Mir298
+Mir335
+Mir337
+Mir370
+Mir376b
+Mir380
+Mir410
+Mir411
+Mir431
+Mirg
+Mkrn1-ps1
+Mkrn3
+Musd2
+Nap1l4
+Nap1l5
+Nctc1
+Ndn
+Nespas
+Ngfb
+Nnat
+Ntm
+Osbpl5
+Peg10
+Peg12
+Peg13
+Peg3
+Peg3os
+Phlda2
+Plagl1
+Pon1
+Pon2
+Pon3
+Ppp1r9a
+Pwcr1
+Rasgrf1
+Rb1
+Rhox5
+Rian
+Rtl1
+Sdhd
+Sfmbt2
+Sgce
+Slc22a18
+Slc22a2
+Slc22a3
+Slc38a4
+Snrpn
+Snurf
+Snx14
+Tfpi2
+Th
+Tnfrsf22
+Tnfrsf23
+Tnfrsf26
+Trp73
+Trpm5
+Tsix
+Tspan32
+Tssc4
+U2af1-rs1
+U80893
+Ube3a
+UPD
+Usp29
+Wt1
+Xist
+Zc3h12c
+Zcchc13
+Zdbf2
+Zfat
+Zfp127as
+Zfp264
+Zim1
+Zim2
+Zim3
+Znf264
+Zrsr1