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Output Results of CLIME (Clustering by Inferred Models of Evolution)

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Output Results of CLIME (Clustering by Inferred Models of Evolution) Output results of CLIME (CLustering by Inferred Models of Evolution) Dataset: Num of genes in input gene set: 9 Total number of genes: 20834 Prediction LLR threshold: 0 The CLIME PDF output two sections: 1) Overview of Evolutionarily Conserved Modules (ECMs) Top panel shows the predefined species tree. Bottom panel shows the partition of input genes into Evolutionary Conserved Modules (ECMs), ordered by ECM strength (shown at right), and separated by horizontal lines. Each row show one gene, where the phylogenetic profile indicates presence (blue) or absence (gray) of homologs in each species (column). Gene symbols are shown at left. Gray color indicates that the gene is a paralog to a higher scoring gene within the same ECM (based on BLASTP E < 1e-3). 2) Details of each ECM and its expansion ECM+ Top panel shows the inferred evolutionary history on the predefined species tree. Branch color shows the gain event (blue) and loss events (red color, with brighter color indicating higher confidence in loss). Branches before the gain or after a loss are shown in gray. Bottom panel shows the input genes that are within the ECM (blue/white rows) as well as all genes in the expanded ECM+ (green/gray rows). The ECM+ includes genes likely to have arisen under the inferred model of evolution relative to a background model, and scored using a log likelihood ratio (LLR). PG indicates "paralog group" and are labeled alphabetically (i.e., A, B). The first gene within each paralog group is shown in black color. All other genes sharing sequence similarity (BLAST E < 1e-3) are assigned to the same PG label and displayed in gray. ECM 2 ECM 1 Protein CHRNB1 CHRNA1 DPAGT1 CHRND CHRNE RAPSN SCN4A MUSK CHAT Overview ofEvolutionarilyConservedModules(ECMs) Prokaryotes Prokaryotes Last CommonAncestor E.cuniculi E.cuniculi E.histolytica E.histolytica E.dispar E.dispar G.lamblia G.lamblia T.vaginalis T.vaginalis T.brucei T.brucei T.cruzi T.cruzi L.infantum L.infantum L.major L.major L.braziliensis L.braziliensis T.gondii T.gondii Protists C.hominis C.hominis C.parvum C.parvum B.bovis B.bovis T.annulata T.annulata T.parva T.parva P.knowlesi P.knowlesi P.vivax P.vivax P.falciparum P.falciparum P.chabaudi P.chabaudi P.berghei P.berghei P.yoelii P.yoelii P.tetraurelia P.tetraurelia T.thermophila T.thermophila P.infestans P.infestans T.pseudonana T.pseudonana P.tricornutum P.tricornutum C.merolae C.merolae N.gruberi N.gruberi O.lucimarinus O.lucimarinus O.tauri O.tauri C.reinhardtii C.reinhardtii V.carteri V.carteri P.patens P.patens S.moellendorffii Plants S.moellendorffii S.bicolor S.bicolor Z.mays Z.mays O.sativa O.sativa B.distachyon B.distachyon A.lyrata A.lyrata A.thaliana A.thaliana L.japonicus L.japonicus M.truncatula M.truncatula V.vinifera V.vinifera P.trichocarpa P.trichocarpa R.communis R.communis T.trahens T.trahens D.discoideum D.discoideum A.macrogynus A.macrogynus S.punctatus S.punctatus M.globosa M.globosa U.maydis U.maydis C.neoformans C.neoformans P.chrysosporium P.chrysosporium S.commune S.commune C.cinerea C.cinerea L.bicolor L.bicolor S.pombe S.pombe B.fuckeliana B.fuckeliana S.sclerotiorum S.sclerotiorum F.graminearum F.graminearum M.grisea M.grisea N.crassa N.crassa P.anserina P.anserina P.chrysogenum P.chrysogenum A.clavatus A.clavatus A.fumigatus A.fumigatus N.fischeri N.fischeri A.flavus A.flavus A.oryzae A.oryzae A.niger A.niger A.nidulans Fungi A.nidulans U.reesii U.reesii C.immitis C.immitis C.posadasii C.posadasii P.nodorum P.nodorum T.melanosporum T.melanosporum Y.lipolytica Y.lipolytica P.pastoris P.pastoris C.lusitaniae C.lusitaniae D.hansenii D.hansenii M.guilliermondii M.guilliermondii S.stipitis S.stipitis L.elongisporus L.elongisporus C.tropicalis C.tropicalis C.albicans C.albicans C.dubliniensis C.dubliniensis K.lactis K.lactis A.gossypii A.gossypii K.waltii K.waltii L.thermotolerans L.thermotolerans Z.rouxii Z.rouxii V.polyspora V.polyspora C.glabrata C.glabrata S.bayanus S.bayanus S.mikatae S.mikatae S.cerevisiae S.cerevisiae S.paradoxus S.paradoxus S.arctica S.arctica C.owczarzaki C.owczarzaki M.brevicollis M.brevicollis S.rosetta S.rosetta S.mansoni S.mansoni B.malayi B.malayi C.briggsae C.briggsae C.elegans C.elegans D.pulex D.pulex A.pisum A.pisum P.humanus P.humanus A.mellifera A.mellifera N.vitripennis N.vitripennis B.mori B.mori T.castaneum T.castaneum D.melanogaster D.melanogaster D.pseudoobscura D.pseudoobscura A.gambiae A.gambiae A.aegypti A.aegypti C.quinquefasciatus Metazoa C.quinquefasciatus B.floridae B.floridae T.adhaerens T.adhaerens S.purpuratus S.purpuratus H.magnipapillata H.magnipapillata N.vectensis N.vectensis C.intestinalis C.intestinalis D.rerio D.rerio O.latipes O.latipes F.rubripes F.rubripes T.nigroviridis T.nigroviridis X.tropicalis X.tropicalis G.gallus G.gallus M.gallopavo M.gallopavo O.anatinus O.anatinus M.domestica M.domestica S.scrofa S.scrofa M.musculus M.musculus C.familiaris C.familiaris B.taurus B.taurus H.sapiens H.sapiens Strength 5.6 1.0 PG B B C C B B B A B B B B B B B A A A A A B B B B B B B B B B B B A Protein CATSPER2 CATSPER1 100510450 100510158 100294386 SLC16A12 CACNA1G CACNA1H CACNA1C CACNA1B CACNA1A CACNA1S CACNA1E CACNA1I SLC16A1 SDHAF2 SCN11A SCN10A NALCN MFSD6 SCN7A SCN9A SCN5A SCN3A SCN8A SCN2A SCN1A SCN4A CPT1A CPT1B CPT1C CROT CRAT CHAT CPT2 10: Ventricular fibrillation || 1: Myasthenic syndrome || Num ofECMGenes:2.Predicted100.Strength:1.0 ECM 1,Geneset"Myasthenicsyndrome",Page1 Prokaryotes Prokaryotes Last CommonAncestor E.cuniculi E.cuniculi E.histolytica E.histolytica E.dispar E.dispar G.lamblia G.lamblia T.vaginalis T.vaginalis T.brucei T.brucei T.cruzi T.cruzi L.infantum L.infantum L.major L.major L.braziliensis L.braziliensis T.gondii T.gondii Protists C.hominis C.hominis 2: Myotonia congenita|| 11: Insensitivity topain || C.parvum C.parvum B.bovis B.bovis T.annulata T.annulata T.parva T.parva P.knowlesi P.knowlesi P.vivax P.vivax P.falciparum P.falciparum P.chabaudi P.chabaudi P.berghei P.berghei P.yoelii P.yoelii P.tetraurelia P.tetraurelia T.thermophila T.thermophila P.infestans P.infestans T.pseudonana T.pseudonana 3: Epilepsy || P.tricornutum P.tricornutum 12: Spinocerebellar ataxia || C.merolae C.merolae N.gruberi N.gruberi O.lucimarinus O.lucimarinus O.tauri O.tauri C.reinhardtii C.reinhardtii V.carteri V.carteri P.patens P.patens S.moellendorffii Plants S.moellendorffii 4: Epileptic encephalopathy || S.bicolor S.bicolor Z.mays Z.mays O.sativa O.sativa B.distachyon B.distachyon A.lyrata A.lyrata A.thaliana A.thaliana L.japonicus L.japonicus 13: Episodic ataxia || M.truncatula M.truncatula V.vinifera V.vinifera P.trichocarpa P.trichocarpa R.communis R.communis T.trahens T.trahens D.discoideum D.discoideum A.macrogynus A.macrogynus S.punctatus S.punctatus M.globosa M.globosa 5: Cardiomyopathy || U.maydis U.maydis C.neoformans C.neoformans P.chrysosporium P.chrysosporium S.commune S.commune 14: CPT deficiency || C.cinerea C.cinerea L.bicolor L.bicolor S.pombe S.pombe B.fuckeliana B.fuckeliana S.sclerotiorum S.sclerotiorum F.graminearum F.graminearum M.grisea M.grisea N.crassa N.crassa P.anserina P.anserina 6: LongQT syndrome|| P.chrysogenum P.chrysogenum A.clavatus A.clavatus A.fumigatus A.fumigatus 15: Spermatogenic failure || N.fischeri N.fischeri A.flavus A.flavus A.oryzae A.oryzae A.niger A.niger A.nidulans Fungi A.nidulans U.reesii U.reesii C.immitis C.immitis C.posadasii C.posadasii P.nodorum P.nodorum T.melanosporum T.melanosporum 7: Atrialfibrillation || Y.lipolytica Y.lipolytica P.pastoris P.pastoris C.lusitaniae C.lusitaniae D.hansenii D.hansenii M.guilliermondii M.guilliermondii 16: Cataract || S.stipitis S.stipitis L.elongisporus L.elongisporus C.tropicalis C.tropicalis C.albicans C.albicans C.dubliniensis C.dubliniensis K.lactis K.lactis PRESENCE A.gossypii A.gossypii 8: Brugada syndrome|| K.waltii K.waltii L.thermotolerans L.thermotolerans GAIN Z.rouxii Z.rouxii 17: Hyperinsulinemic hypoglycemia || V.polyspora V.polyspora C.glabrata C.glabrata S.bayanus S.bayanus S.mikatae S.mikatae S.cerevisiae S.cerevisiae S.paradoxus S.paradoxus S.arctica S.arctica C.owczarzaki C.owczarzaki M.brevicollis M.brevicollis S.rosetta S.rosetta S.mansoni S.mansoni ABSENCE 9: Sicksinus syndrome || B.malayi B.malayi C.briggsae C.briggsae LOSS C.elegans C.elegans D.pulex D.pulex A.pisum A.pisum P.humanus P.humanus A.mellifera A.mellifera N.vitripennis N.vitripennis B.mori 18: Paragangliomas B.mori T.castaneum T.castaneum D.melanogaster D.melanogaster D.pseudoobscura D.pseudoobscura A.gambiae A.gambiae A.aegypti A.aegypti C.quinquefasciatus Metazoa C.quinquefasciatus B.floridae B.floridae T.adhaerens T.adhaerens 0 Log-likelihood RatioScale S.purpuratus S.purpuratus H.magnipapillata H.magnipapillata 10 N.vectensis N.vectensis C.intestinalis C.intestinalis D.rerio D.rerio 20 O.latipes O.latipes F.rubripes F.rubripes 30 T.nigroviridis T.nigroviridis X.tropicalis X.tropicalis 40 G.gallus G.gallus M.gallopavo M.gallopavo O.anatinus O.anatinus 50 M.domestica M.domestica S.scrofa S.scrofa 60 M.musculus M.musculus C.familiaris C.familiaris B.taurus B.taurus H.sapiens H.sapiens LLR 24.2 24.6 26.7 28.8 29.5 29.7 29.8 30.2 30.3 30.4 31.2 31.2 31.2 31.2 33.8 36.8 37.0 39.5 39.5 39.5 39.6 39.6 40.3 43.1 48.8 49.0 51.0 51.8 51.8 54.0 61.4 62.2 69.0 Notes 18 17 16 14 8 15 14 12 /13 3 /11 5 /678910 4 4 3 1 /2 1 PG H H E E E G G G B D F B F F F F C E D C B B B Protein CATSPER4 CATSPER3 HS3ST3A1 HS3ST3B1 100510228 CACNA1D RNASEH1 CACNA1F SLC16A9 GLT25D2 SLC16A7 CKMT1A CKMT1B DEPDC5 THNSL2 KCNJ15 KCNJ16 HS3ST5 HS3ST1 WWTR1 PAMR1 SLMAP CKMT2 SUMF2 TMED5 KCNJ6 CHIT1 MANF MTAP
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