Paper Title 1: Drosophila NAP-1 is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays. Journal: Ito et al., 1996, Molec. Cell. Biol. 16(6): 3112--3124 FlyBase ID: FBrf0087451 PubMed ID: 8649423 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) Caf1 (dCAF-1) Caf4 (dCAF-4) Nap1 LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- Nap1 P nucleosome assembly ; GO:0006334 | inferred from direct assay F histone binding ; GO:0042393 | inferred from direct assay C cytoplasm ; GO:0005737 | inferred from direct assay C nucleus ; GO:0005634 | inferred from direct assay Internal note: Cellular localization of the Nap1 gene product varies during stages of the cell cycle. LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0015268 Nap1 GO:0005634 FB:FBrf0087451|PMID:8649423 IDA C Nucleosome assembly protein 1 Nap1|NAP1|p56/dCAF-4|dNAP-1|dNap1|dNAP1|Nap-1|NAP-1|CG5330 gene taxon:7227 20040821 FB FB FBgn0015268 Nap1 GO:0005737 FB:FBrf0087451|PMID:8649423 IDA C Nucleosome assembly protein 1 Nap1|NAP1|p56/dCAF-4|dNAP-1|dNap1|dNAP1|Nap-1|NAP-1|CG5330 gene taxon:7227 20040821 FB FB FBgn0015268 Nap1 GO:0006334 FB:FBrf0087451|PMID:8649423 IDA P Nucleosome assembly protein 1 Nap1|NAP1|p56/dCAF-4|dNAP-1|dNap1|dNAP1|Nap-1|NAP-1|CG5330 gene taxon:7227 20040821 FB FB FBgn0015268 Nap1 GO:0042393 FB:FBrf0087451|PMID:8649423 IDA F Nucleosome assembly protein 1 Nap1|NAP1|p56/dCAF-4|dNAP-1|dNap1|dNAP1|Nap-1|NAP-1|CG5330 gene taxon:7227 20040821 FB COMMENTS: --------- The assays performed in this paper with recombinant Nap1 protein demonstrate a role for the Nap1 protein in nucleosome assembly (Pg.3114-3117, Fig.2,3,4), supported by the 'inferred from direct assay' (IDA) evidence code. The authors also performed assays demonstrating binding of the Nap1 protein to core purified histones (Pg.3117-3118, Fig.5,6). IDA was chosen to support this GO annotation because it is not possible to identify which specific histone protein is being bound, and therefore an identifier can not be entered in a 'with column'. It should be noted that when a gene product physically binds to an identifiable protein, the evidence code 'inferred from physical interaction' (IPI) is used and the known protein identifier is added to the 'with column'. The authors here show that the subcellular localization of the Nap1 protein varies between the cytoplasm and the nucleus through the Drosophila embyronic divisions (Pg.3118-3122, Fig.7,8,9). Therefore both 'cytoplasm ; GO:0005737' and 'nucleus ; GO:0005634' GO terms were used for component annotations, and an internal note was added to summarise this subcellular localization pattern. ========================================================================== Paper Title 2: The tomaj mutant alleles of (alpha)Tubulin67C reveal a requirement for the encoded maternal specific tubulin isoform in the sperm aster, the cleavage spindle apparatus and neurogenesis during embryonic development in Drosophila. Journal: Mathe et al., 1998, J. Cell Sci. 111(7): 887--896 FlyBase ID: FBrf0102360 PubMed ID: 9490633 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) &agr;Tub67C cnn Cp190 ovo LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- &agr;Tub67C P central nervous system development ; GO:0007417 | inferred from mutant phenotype P embryonic cleavage ; GO:0040016 | inferred from mutant phenotype P embryonic development ; GO:0009790 | inferred from mutant phenotype P peripheral nervous system development ; GO:0007422 | inferred from mutant phenotype P pronuclear migration ; GO:0035046 | inferred from mutant phenotype P sperm aster formation ; GO:0035044 | inferred from mutant phenotype Internal note: In the absence of a prominent sperm aster the subsequent migration of the female pronucleus does not take place. LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0004236 &agr;Tub67C GO:0007417 FB:FBrf0102360|PMID:9490633 IMP P alphaTub67C|&agr;Tub67C|&agr;-Tub67C|&agr;-Tubulin|Fs(3)Sz22|&agr;4|Tom|D.m.ALPHA-67C|&agr;4-t|&agr;-Tub|T|ALPHA 67C|&agr;tub67C|Fs(3)Tomaj|&agr;Tub4|aTub67C|&mgr;m-tub67C|tubulin|&agr;-tub67C|&agr;4t|&agr;TUB|4t|&agr;-tubulin|&agr;67C|DTA2|Fs(3)Tom|alpha4Tub67C|&agr;Tub67C|alpha tubulin 67C|Tomaj|CG8308|&agr;tubulin|&agr; tubulin|&agr;4-tubulin gene taxon:7227 20040821 FB FB FBgn0004236 &agr;Tub67C GO:0007422 FB:FBrf0102360|PMID:9490633 IMP P alphaTub67C|&agr;Tub67C|&agr;-Tub67C|&agr;-Tubulin|Fs(3)Sz22|&agr;4|Tom|D.m.ALPHA-67C|&agr;4-t|&agr;-Tub|T|ALPHA 67C|&agr;tub67C|Fs(3)Tomaj|&agr;Tub4|aTub67C|&mgr;m-tub67C|tubulin|&agr;-tub67C|&agr;4t|&agr;TUB|4t|&agr;-tubulin|&agr;67C|DTA2|Fs(3)Tom|alpha4Tub67C|&agr;Tub67C|alpha tubulin 67C|Tomaj|CG8308|&agr;tubulin|&agr; tubulin|&agr;4-tubulin gene taxon:7227 20040821 FB FB FBgn0004236 &agr;Tub67C GO:0009790 FB:FBrf0102360|PMID:9490633 IMP P alphaTub67C|&agr;Tub67C|&agr;-Tub67C|&agr;-Tubulin|Fs(3)Sz22|&agr;4|Tom|D.m.ALPHA-67C|&agr;4-t|&agr;-Tub|T|ALPHA 67C|&agr;tub67C|Fs(3)Tomaj|&agr;Tub4|aTub67C|&mgr;m-tub67C|tubulin|&agr;-tub67C|&agr;4t|&agr;TUB|4t|&agr;-tubulin|&agr;67C|DTA2|Fs(3)Tom|alpha4Tub67C|&agr;Tub67C|alpha tubulin 67C|Tomaj|CG8308|&agr;tubulin|&agr; tubulin|&agr;4-tubulin gene taxon:7227 20040821 FB FB FBgn0004236 &agr;Tub67C GO:0035044 FB:FBrf0102360|PMID:9490633 IMP P alphaTub67C|&agr;Tub67C|&agr;-Tub67C|&agr;-Tubulin|Fs(3)Sz22|&agr;4|Tom|D.m.ALPHA-67C|&agr;4-t|&agr;-Tub|T|ALPHA 67C|&agr;tub67C|Fs(3)Tomaj|&agr;Tub4|aTub67C|&mgr;m-tub67C|tubulin|&agr;-tub67C|&agr;4t|&agr;TUB|4t|&agr;-tubulin|&agr;67C|DTA2|Fs(3)Tom|alpha4Tub67C|&agr;Tub67C|alpha tubulin 67C|Tomaj|CG8308|&agr;tubulin|&agr; tubulin|&agr;4-tubulin gene taxon:7227 20040821 FB FB FBgn0004236 &agr;Tub67C GO:0035046 FB:FBrf0102360|PMID:9490633 IMP P alphaTub67C|&agr;Tub67C|&agr;-Tub67C|&agr;-Tubulin|Fs(3)Sz22|&agr;4|Tom|D.m.ALPHA-67C|&agr;4-t|&agr;-Tub|T|ALPHA 67C|&agr;tub67C|Fs(3)Tomaj|&agr;Tub4|aTub67C|&mgr;m-tub67C|tubulin|&agr;-tub67C|&agr;4t|&agr;TUB|4t|&agr;-tubulin|&agr;67C|DTA2|Fs(3)Tom|alpha4Tub67C|&agr;Tub67C|alpha tubulin 67C|Tomaj|CG8308|&agr;tubulin|&agr; tubulin|&agr;4-tubulin gene taxon:7227 20040821 FB FB FBgn0004236 &agr;Tub67C GO:0040016 FB:FBrf0102360|PMID:9490633 IMP P alphaTub67C|&agr;Tub67C|&agr;-Tub67C|&agr;-Tubulin|Fs(3)Sz22|&agr;4|Tom|D.m.ALPHA-67C|&agr;4-t|&agr;-Tub|T|ALPHA 67C|&agr;tub67C|Fs(3)Tomaj|&agr;Tub4|aTub67C|&mgr;m-tub67C|tubulin|&agr;-tub67C|&agr;4t|&agr;TUB|4t|&agr;-tubulin|&agr;67C|DTA2|Fs(3)Tom|alpha4Tub67C|&agr;Tub67C|alpha tubulin 67C|Tomaj|CG8308|&agr;tubulin|&agr; tubulin|&agr;4-tubulin gene taxon:7227 20040821 FB COMMENTS: --------- In Drosophila, the evidence for the role of a gene or gene product in a particular process often comes from analysing processes that are defective in the mutant. The evidence code 'inferred from mutant phenotype' (IMP) is appropriate to support GO annotations in these cases. In this paper, the authors show that mutant alleles of the &agr;Tub67C gene have defects in sperm aster formation (Pg.889, Fig.1). They also show that failure of sperm aster formation leads to the absence of female pronucleus specification and migration toward the male pronucleus in &agr;Tub67C mutants (Pg.889-890). Although this is a secondary effect, &agr;Tub67C has an (indirect) role in pronuclear migration, and therefore was annotated with the GO term 'pronuclear migration ; GO:0035046' in addition to 'sperm aster formation ; GO:0035044' and an internal note added to highlight this. The authors also show highly disorganized neuronal structures in the embryonic central- and peripheral nervous systems in &agr;Tub67C mutants (Pg.890-891, Fig.3), demonstrating a requirement for &agr;Tub67C in embryonic PNS and CNS development. Because there is not a specific term for embryonic nervous system development, concurrent annotations of 'embryonic development ; GO:0009790', 'peripheral nervous system development ; GO:0007422' and 'central nervous system development ; GO:0007417' were used to capture this information. Finally they demonstrate embryonic cleavage spindle apparatus defects for &agr;Tub67C (Pg.892), resulting in the GO annotation 'embryonic cleavage ; GO:0040016'. ========================================================================== Paper Title 3: Mitochondrial small ribosomal RNA is present on polar granules in early cleavage embryos of Drosophila melanogaster. Journal: Kashikawa et al., 1999, Dev., Growth Diffn 41(4): 495--502 FlyBase ID: FBrf0110050 PubMed ID: 10466937 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) mt:ND1 (ND-1) mt:srRNA (mtsrRNA) nos osk tud vas LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- mt:srRNA C colocalizes_with polar granule ; GO:0018994 | inferred from direct assay Internal note: mt:srRNA RNA is found on the surface of polar granules in early cleavage embryos. LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0013688 mt:srRNA colocalizes_with GO:0018994 FB:FBrf0110050|PMID:10466937 IDA C mt:srRNA|anon-EST:fe2A4|12S rRNA|msrRNA|small rRNA|mtrRNA|12S|mtsrRNA gene taxon:7227 20040821 FB COMMENTS: --------- The authors found that 57% of the total mt:srRNA signal in polar plasm was present on the surface of polar granules (Pg.499, Fig.2A,2B). The rest of the signal in the polar plasm and the signal in the lateral region were evenly scattered throughout the cytoplasm (Fig.2A-2D), but the authors conclude that the unlocalized mt:srRNA signal most likely represents background. Because the protein is found on the surface of the polar granule, it is likely it is not an integral part of this cellular organelle. Therefore the qualifier 'colocalizes_with' was used in conjunction with the GO annotation 'polar granule ; GO:0018994'. ========================================================================== Paper Title 4: The genetic control of organ growth: insights from Drosophila. Journal: Weinkove and Leevers, 2000, Curr. Opin. Genet. Dev. 10(1): 75--80 FlyBase ID: FBrf0125443 PubMed ID: 10679387 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) Akt1 (DAkt1) cdc2 chico dm (dmyc) Dp (DP, dDP1) dpp E2f (dE2F) eIF-4a (EiF4A) gig InR (Inr) N Pi3K21B (p60) Pi3K92E (Dp110) pit Pten (PTEN) Ras85D (Ras) Rbf (Rb) S6k (DS6K) wg wts (lats) LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- Akt1 P positive regulation of body size ; GO:0040018 | traceable author statement P positive regulation of cell growth ; GO:0030307 | traceable author statement P regulation of organ size ; GO:0046620 | non-traceable author statement # chico P positive regulation of body size ; GO:0040018 | traceable author statement P positive regulation of cell size ; GO:0045793 | traceable author statement P positive regulation of organ size ; GO:0046622 | traceable author statement # dm P positive regulation of cell growth ; GO:0030307 | traceable author statement # Dp P regulation of cell cycle ; GO:0000074 | non-traceable author statement # dpp P imaginal disc growth ; GO:0007446 | traceable author statement P imaginal disc pattern formation ; GO:0007447 | traceable author statement # E2f P regulation of cell cycle ; GO:0000074 | non-traceable author statement # eIF-4a P imaginal disc growth ; GO:0007446 | traceable author statement P larval development (sensu Insecta) ; GO:0002168 | traceable author statement # gig P negative regulation of cell size ; GO:0045792 | traceable author statement P regulation of cell cycle ; GO:0000074 | traceable author statement # InR P positive regulation of organ size ; GO:0046622 | traceable author statement # N P imaginal disc growth ; GO:0007446 | traceable author statement P imaginal disc pattern formation ; GO:0007447 | traceable author statement # Pi3K21B P insulin receptor signaling pathway ; GO:0008286 | traceable author statement P regulation of organ size ; GO:0046620 | non-traceable author statement # Pi3K92E P positive regulation of organ size ; GO:0046622 | non-traceable author statement # Pten P negative regulation of cell size ; GO:0045792 | traceable author statement P negative regulation of organ size ; GO:0046621 | non-traceable author statement # S6k P positive regulation of body size ; GO:0040018 | traceable author statement P positive regulation of cell growth ; GO:0030307 | traceable author statement P positive regulation of growth ; GO:0045927 | traceable author statement P positive regulation of organ size ; GO:0046622 | traceable author statement # wg P imaginal disc growth ; GO:0007446 | traceable author statement P imaginal disc pattern formation ; GO:0007447 | traceable author statement # LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0010379 Akt1 GO:0046620 FB:FBrf0125443|PMID:10679387 NAS P akt|Akt|AKT|dPKB|DPKB|DAKT1/PKB|DRAC-PK|dAkt|Dakt|PKB/Akt|PKB/AKT|AKT/PKB|Akt/PKB|l(3)04226|PKB/dAKT|dAkt/PKB|RacPK|Akt1|D-Akt|l(3)89Bq|CG4006|DAKT1|DAkt1|Dakt1|dAkt1|dakt1|RAC|DRAC-PK66; DRAC-PK85|PKB gene taxon:7227 20040821 FB FB FBgn0010379 Akt1 GO:0030307 FB:FBrf0125443|PMID:10679387 TAS P akt|Akt|AKT|dPKB|DPKB|DAKT1/PKB|DRAC-PK|dAkt|Dakt|PKB/Akt|PKB/AKT|AKT/PKB|Akt/PKB|l(3)04226|PKB/dAKT|dAkt/PKB|RacPK|Akt1|D-Akt|l(3)89Bq|CG4006|DAKT1|DAkt1|Dakt1|dAkt1|dakt1|RAC|DRAC-PK66; DRAC-PK85|PKB gene taxon:7227 20040821 FB FB FBgn0010379 Akt1 GO:0040018 FB:FBrf0125443|PMID:10679387 TAS P akt|Akt|AKT|dPKB|DPKB|DAKT1/PKB|DRAC-PK|dAkt|Dakt|PKB/Akt|PKB/AKT|AKT/PKB|Akt/PKB|l(3)04226|PKB/dAKT|dAkt/PKB|RacPK|Akt1|D-Akt|l(3)89Bq|CG4006|DAKT1|DAkt1|Dakt1|dAkt1|dakt1|RAC|DRAC-PK66; DRAC-PK85|PKB gene taxon:7227 20040821 FB FB FBgn0024248 chico GO:0040018 FB:FBrf0125443|PMID:10679387 TAS P chico fs(2)4|flipper|dIRS|BcDNA.GH11263|CG5686|chico|CHICO|chic|anon-WO0078940.1|fs(2)ry4|IRS|BcDNA:GH11263 gene taxon:7227 20040821 FB FB FBgn0024248 chico GO:0045793 FB:FBrf0125443|PMID:10679387 TAS P chico fs(2)4|flipper|dIRS|BcDNA.GH11263|CG5686|chico|CHICO|chic|anon-WO0078940.1|fs(2)ry4|IRS|BcDNA:GH11263 gene taxon:7227 20040821 FB FB FBgn0024248 chico GO:0046622 FB:FBrf0125443|PMID:10679387 TAS P chico fs(2)4|flipper|dIRS|BcDNA.GH11263|CG5686|chico|CHICO|chic|anon-WO0078940.1|fs(2)ry4|IRS|BcDNA:GH11263 gene taxon:7227 20040821 FB FB FBgn0000472 dm GO:0030307 FB:FBrf0125443|PMID:10679387 TAS P diminutive EG:BACN5I9.1|dm|l(1)G0139|CG10798|myc|Myc|D-Myc|d-myc|DMYc|Dmyc|dMYC|dMyc|dmyc|dmyc1|dMyc1 gene taxon:7227 20040821 FB FB FBgn0011763 Dp GO:0000074 FB:FBrf0125443|PMID:10679387 NAS P DP transcription factor l(2)vr10|dDp|dDP|vr10|dDP1|Dp|DP|l(2)49Fk|DmDP|CG4654|49Fk gene taxon:7227 20040821 FB FB FBgn0000490 dpp GO:0007446 FB:FBrf0125443|PMID:10679387 TAS P decapentaplegic M(2)LS1|shortvein|Dm-DPP|dpp|Dpp|DPP|CG9885|TGF-beta|TGF-&bgr;|TGF-b|Hin-d|l(2)10638|shv|DPP-C|ho|M(2)23AB|blk|l(2)22Fa|l(2)k17036|Tg|TGF&bgr; gene taxon:7227 20040821 FB FB FBgn0000490 dpp GO:0007447 FB:FBrf0125443|PMID:10679387 TAS P decapentaplegic M(2)LS1|shortvein|Dm-DPP|dpp|Dpp|DPP|CG9885|TGF-beta|TGF-&bgr;|TGF-b|Hin-d|l(2)10638|shv|DPP-C|ho|M(2)23AB|blk|l(2)22Fa|l(2)k17036|Tg|TGF&bgr; gene taxon:7227 20040821 FB FB FBgn0011766 E2f GO:0000074 FB:FBrf0125443|PMID:10679387 NAS P E2F transcription factor l(3)j3B1|CG6376|dE2f|dE2F|l(3)j3C2|drosE2F1|E(Sev-CycE)3A|DmE2F-1|Evar(3)164|DRTF1/E2F|e2f1|E2f1|E2F1|E(var)3-93E|E(var)93E|l(3)rM729|l(3)07172|E2F1/Dp|dE2F1|dE2f1|de2f1|E(var)3-95E|E2F-1|E2F|E2f|e2f gene taxon:7227 20040821 FB FB FBgn0001942 eIF-4a GO:0002168 FB:FBrf0125443|PMID:10679387 TAS P Eukaryotic initiation factor 4a l(2)gdh-4|anon-26Aa|l(2)162|eif4A|eIF4A|Eif4a|EiF4A|l(2)k01501|l(2)02439|2439|l(2L)162|anon26A|EIF-4A|Eif-4a|eIF-4A|eIF-4a|eif-4a|l(2)26Ac|DmRH2|CG9075 gene taxon:7227 20040821 FB FB FBgn0001942 eIF-4a GO:0007446 FB:FBrf0125443|PMID:10679387 TAS P Eukaryotic initiation factor 4a l(2)gdh-4|anon-26Aa|l(2)162|eif4A|eIF4A|Eif4a|EiF4A|l(2)k01501|l(2)02439|2439|l(2L)162|anon26A|EIF-4A|Eif-4a|eIF-4A|eIF-4a|eif-4a|l(2)26Ac|DmRH2|CG9075 gene taxon:7227 20040821 FB FB FBgn0005198 gig GO:0000074 FB:FBrf0125443|PMID:10679387 TAS P gigas dTsc2|dTSC2|l(3)109|Tsc2|TSC2|ME 109|C1|CG6975|gig gene taxon:7227 20040821 FB FB FBgn0005198 gig GO:0045792 FB:FBrf0125443|PMID:10679387 TAS P gigas dTsc2|dTSC2|l(3)109|Tsc2|TSC2|ME 109|C1|CG6975|gig gene taxon:7227 20040821 FB FB FBgn0013984 InR GO:0046622 FB:FBrf0125443|PMID:10679387 TAS P Insulin-like receptor dInsR|insulin/insulin-like growth factor receptor|insulin receptor|dIRH|DIRH|DIHR|l(3)er10|inr|Inr|InR|INR|CG18402|l(3)93Dj|DILR|Dir-a|DInR|DInr|dInR|dInr|dinr|Dir-b|Inr-&agr;|Inr-&bgr;|l(3)05545|er10|IR|DIR&bgr;|DIR|dIR|dir gene taxon:7227 20040821 FB FB FBgn0004647 N GO:0007446 FB:FBrf0125443|PMID:10679387 TAS P Notch dNotch|EG:163A10.2|facet|EG:140G11.1|l(1)3Cb|l(1)Ax|fa|nfah|Abruptex|swb|split|Nintra|N|CT13012|spl|1.1|nd|Co|co|clone 1.12|16-178|Ax|anon-EST:Liang-1.12|Chp|notch|l(1)N|16-55|shd|CG3936 gene taxon:7227 20040821 FB FB FBgn0004647 N GO:0007447 FB:FBrf0125443|PMID:10679387 TAS P Notch dNotch|EG:163A10.2|facet|EG:140G11.1|l(1)3Cb|l(1)Ax|fa|nfah|Abruptex|swb|split|Nintra|N|CT13012|spl|1.1|nd|Co|co|clone 1.12|16-178|Ax|anon-EST:Liang-1.12|Chp|notch|l(1)N|16-55|shd|CG3936 gene taxon:7227 20040821 FB FB FBgn0020622 Pi3K21B GO:0046620 FB:FBrf0125443|PMID:10679387 NAS P PI3-kinase|PI 3-kinase|CG2699|droPIK57|p60|PI3K|dPI 3-kinase|PI(3)K|dPI3K|Pi3K21B|Pi3Kp60 gene taxon:7227 20040821 FB FB FBgn0020622 Pi3K21B GO:0008286 FB:FBrf0125443|PMID:10679387 TAS P PI3-kinase|PI 3-kinase|CG2699|droPIK57|p60|PI3K|dPI 3-kinase|PI(3)K|dPI3K|Pi3K21B|Pi3Kp60 gene taxon:7227 20040821 FB FB FBgn0015279 Pi3K92E GO:0046622 FB:FBrf0125443|PMID:10679387 NAS P p110|p120|Pi3K92D|dp110|Dp110|Pi3K92E|PI3 kinase|PI(3)K|PI3K-92E/Dp110|p110 PI3 kinase|Dp110/PI3K|anon-92Ed|PI-3-K|phosphoinositide 3-kinase.|PI3K-92D|Dmp110|PI3-kinase|CG4141|PI 3-kinase|PI3K|rea|dPI 3-kinase|Pi3Kp110|dPI3K gene taxon:7227 20040821 FB FB FBgn0026379 Pten GO:0046621 FB:FBrf0125443|PMID:10679387 NAS P PTEN3|dPTEN|DPTEN|CG5671|pten|Pten|PTEN gene taxon:7227 20040821 FB FB FBgn0026379 Pten GO:0045792 FB:FBrf0125443|PMID:10679387 TAS P PTEN3|dPTEN|DPTEN|CG5671|pten|Pten|PTEN gene taxon:7227 20040821 FB FB FBgn0015806 S6k GO:0030307 FB:FBrf0125443|PMID:10679387 TAS P RPS6-p70-protein kinase fs(3)07084|S6kinase|p70S6kinase|p70S6 kinase|dS6 kinase|dps6k|p70s6K|p70S6K|p70 S6K|CG10539|Dp70S6k|Dp70s6k|dp70s6k|7084|l(3)07084|S6k|S6K|s6k11|p70S6k|DS6K|dS6K|dS6k|ds6k|dp70S6k|Dp70s6k gene taxon:7227 20040821 FB FB FBgn0015806 S6k GO:0040018 FB:FBrf0125443|PMID:10679387 TAS P RPS6-p70-protein kinase fs(3)07084|S6kinase|p70S6kinase|p70S6 kinase|dS6 kinase|dps6k|p70s6K|p70S6K|p70 S6K|CG10539|Dp70S6k|Dp70s6k|dp70s6k|7084|l(3)07084|S6k|S6K|s6k11|p70S6k|DS6K|dS6K|dS6k|ds6k|dp70S6k|Dp70s6k gene taxon:7227 20040821 FB FB FBgn0015806 S6k GO:0045927 FB:FBrf0125443|PMID:10679387 TAS P RPS6-p70-protein kinase fs(3)07084|S6kinase|p70S6kinase|p70S6 kinase|dS6 kinase|dps6k|p70s6K|p70S6K|p70 S6K|CG10539|Dp70S6k|Dp70s6k|dp70s6k|7084|l(3)07084|S6k|S6K|s6k11|p70S6k|DS6K|dS6K|dS6k|ds6k|dp70S6k|Dp70s6k gene taxon:7227 20040821 FB FB FBgn0015806 S6k GO:0046622 FB:FBrf0125443|PMID:10679387 TAS P RPS6-p70-protein kinase fs(3)07084|S6kinase|p70S6kinase|p70S6 kinase|dS6 kinase|dps6k|p70s6K|p70S6K|p70 S6K|CG10539|Dp70S6k|Dp70s6k|dp70s6k|7084|l(3)07084|S6k|S6K|s6k11|p70S6k|DS6K|dS6K|dS6k|ds6k|dp70S6k|Dp70s6k gene taxon:7227 20040821 FB FB FBgn0004009 wg GO:0007446 FB:FBrf0125443|PMID:10679387 TAS P wingless Sp|DWint-1|spd|CG4889|int-1|I|Wnt1|l(2)wg|Dint-1|fg|Dm-1|l(2)rO727|l(2)02657|Br|Gla|Wnt-1|WNT|Wnt|Wg|wg gene taxon:7227 20040821 FB FB FBgn0004009 wg GO:0007447 FB:FBrf0125443|PMID:10679387 TAS P wingless Sp|DWint-1|spd|CG4889|int-1|I|Wnt1|l(2)wg|Dint-1|fg|Dm-1|l(2)rO727|l(2)02657|Br|Gla|Wnt-1|WNT|Wnt|Wg|wg gene taxon:7227 20040821 FB COMMENTS: --------- In FlyBase reviews, the most common evidence codes used to support GO annotations are traceable author statement (TAS) and non-traceable author statement (NAS). TAS is used where the author references a source for a given statement. NAS is used where no source for the statement is given. If a gene has been extensively characterised and is therefore heavily annotated with a particular GO term, we would not necessarily add in the same GO term attributed to a review; this is left to curator judgement. For each annotation, the most specific GO term possible was chosen. ========================================================================== Paper Title 5: Male-specific IDGF, a novel gene encoding a membrane-bound extracellular signaling molecule expressed exclusively in testis of Drosophila melanogaster. Journal: Matsushita et al., 2000, J. Biol. Chem. 275(47): 36934--36941 FlyBase ID: FBrf0131360 PubMed ID: 10967093 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) aly can mia Msi (MSI, Male-specific insect derived growth factor) sa LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- Msi P spermatid development ; GO:0007286 | inferred from expression pattern F growth factor activity ; GO:0008083 | inferred from sequence similarity with EMBL:D83125; protein_id:BAA11812.1 F growth factor activity ; GO:0008083 | inferred from direct assay C membrane fraction ; GO:0005624 | inferred from direct assay C membrane ; GO:0016020 | inferred from direct assay C integral to membrane ; GO:0016021 | inferred from sequence similarity Internal note: The Msi protein has a transmembrane domain. LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0043025 Msi GO:0005624 FB:FBrf0131360|PMID:10967093 IDA C Male-specific insect derived growth factor Msi|MSI|ADGF-A2|male-specific IDGF|male-specific-imaginal-disc-growth-factor|BcDNA:AT05468|CG32178 gene taxon:7227 20040821 FB FB FBgn0043025 Msi GO:0016020 FB:FBrf0131360|PMID:10967093 IDA C Male-specific insect derived growth factor Msi|MSI|ADGF-A2|male-specific IDGF|male-specific-imaginal-disc-growth-factor|BcDNA:AT05468|CG32178 gene taxon:7227 20040821 FB FB FBgn0043025 Msi GO:0007286 FB:FBrf0131360|PMID:10967093 IEP P Male-specific insect derived growth factor Msi|MSI|ADGF-A2|male-specific IDGF|male-specific-imaginal-disc-growth-factor|BcDNA:AT05468|CG32178 gene taxon:7227 20040821 FB FB FBgn0043025 Msi GO:0008083 FB:FBrf0131360|PMID:10967093 ISS EMBL:D83125; protein_id:BAA11812.1 F Male-specific insect derived growth factor Msi|MSI|ADGF-A2|male-specific IDGF|male-specific-imaginal-disc-growth-factor|BcDNA:AT05468|CG32178 gene taxon:7227 20040821 FB FB FBgn0043025 Msi GO:0008083 FB:FBrf0131360|PMID:10967093 IDA F Male-specific insect derived growth factor Msi|MSI|ADGF-A2|male-specific IDGF|male-specific-imaginal-disc-growth-factor|BcDNA:AT05468|CG32178 gene taxon:7227 20040821 FB FB FBgn0043025 Msi GO:0016021 FB:FBrf0131360|PMID:10967093 ISS C Male-specific insect derived growth factor Msi|MSI|ADGF-A2|male-specific IDGF|male-specific-imaginal-disc-growth-factor|BcDNA:AT05468|CG32178 gene taxon:7227 20040821 FB COMMENTS: --------- COMPONENT: Where sequence/structural similarity is due to a protein domain, the 'with statement' in an 'inferred from sequence similarity' (ISS) line is left blank. For example in this paper, hydropathy analysis revealed that MSI contains a single hydrophobic region (Pg.36935, Fig.1B). ISS is the appropriate evidence code to use, but no 'with statement' can be assigned here. Note that 'transmembrane' is an exact synonym of 'integral to membrane ; GO:0016021'. The fractionation and the immunofluorescence localization assays performed in this paper (Pg.36935-36936) provide evidence for different cellular component GO terms ('membrane fraction ; GO:0005624' and 'membrane ; GO:0016020' respectively). The 'inferred from direct assay' (IDA) evidence code is suitable for both assays. FUNCTION: Msi was predicted to be a growth factor based on similarity to insect-derived growth factor (IDGF) from the flesh fly Sarcophaga peregrina (Pg.36938). In the introduction (Pg.36934, right hand paragraph) the authors refer to Homma et al., JBC 271: 13770-13775 (reference 13) as the source for Sarcophaga IDGF. This link was followed to obtain the EMBL identifier (D83125) for the Sarcophaga protein and therefore the entry in the ISS with statement for the GO annotation 'growth factor activity ; GO:0008083'. The authors also provide direct evidence that MSI exhibits growth factor activity (Pg.36938). Therefore Msi was also annotated to GO:0008083, supported by the IDA evidence code. Where multiple evidence in one paper supports a GO annotation, multiple lines of GO annotation are created in the gene_association.fb file. PROCESS: Note that 'spermiogenesis' is a synonym for 'spermatid development ; GO:0007286'. Based on the expression pattern of Msi in wild type and mutant backgrounds, the authors infer that Msi plays a role in spermiogenesis, the final differentiation step of spermatogenesis; Msi is expressed exclusively in the adult male testes, and the mature primary spermatocytes are the Msi-expressing cells (Pg.36939, Fig.6,7). In addition, similar to other genes that have known roles in spermiogenesis (namely fzo and don juan), expression of Msi is absent in four meiotic arrest mutants (Pg.36939-36940, Fig.8). Based on these expression profiles, Msi was annotated to 'spermatid development ; GO:0007286' supported by the 'inferred from expression pattern' (IEP) evidence code. The IEP evidence code is generally only used in FlyBase when the authors themselves make the inference that a gene is involved in a particular process or has a particular function, based on its expression pattern. (see also FBrf0131360/FBrf0131360). ========================================================================== Paper Title 6: Human and Drosophila UDP-galactose transporters transport UDP-N-acetylgalactosamine in addition to UDP-galactose. Journal: Segawa et al., 2002, Europ. J. Biochem. 269(1): 128--138 FlyBase ID: FBrf0141524 PubMed ID: 11784306 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) Csat (DmUGT, DmNST, D.melanogaster nucleotide sugar transporter) LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- Csat P UDP-galactose transport ; GO:0015785 | inferred from direct assay P UDP-N-acetylgalactosamine transport ; GO:0015789 | inferred from direct assay F NOT CMP-sialic acid transporter activity ; GO:0005456 | inferred from direct assay F NOT UDP-glucuronic acid transporter activity ; GO:0005461 | inferred from direct assay F NOT UDP-xylose transporter activity ; GO:0005464 | inferred from direct assay F UDP-N-acetylgalactosamine transporter activity ; GO:0005463 | inferred from direct assay F UDP-galactose transporter activity ; GO:0005459 | inferred from direct assay LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0024994 Csat GO:0015785 FB:FBrf0141524|PMID:11784306 IDA P ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB FB FBgn0024994 Csat GO:0015789 FB:FBrf0141524|PMID:11784306 IDA P ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB FB FBgn0024994 Csat NOT GO:0005456 FB:FBrf0141524|PMID:11784306 IDA F ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB FB FBgn0024994 Csat NOT GO:0005461 FB:FBrf0141524|PMID:11784306 IDA F ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB FB FBgn0024994 Csat NOT GO:0005464 FB:FBrf0141524|PMID:11784306 IDA F ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB FB FBgn0024994 Csat GO:0005459 FB:FBrf0141524|PMID:11784306 IDA F ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB FB FBgn0024994 Csat GO:0005463 FB:FBrf0141524|PMID:11784306 IDA F ugt|anon-3Bb|DmUGT|EG:100G10.5|UDP-Gal/UDP-GalNAc|DmNST|dNST-1|dNST-2|CSAT|Csat|CG2675 gene taxon:7227 20040821 FB COMMENTS: --------- One of the ways in which we use the 'NOT' qualifier with a GO annotation in FlyBase is when the authors do direct experiments and conclude that the gene product does not posess a specific activity. In this paper for example, the authors perform transport assays and show that the Csat-encoded protein transports UDP-Gal (UDP-galactose) and UDP-GalNAc (UDP-N-acetylgalactosamine), but that is _not_ a xylose, glucuronic acid or sialic acid transporter (Pg.133, Fig.5,6). In addition to the transporter function GO annotations, appropriate process GO annotations were also recorded based on the same assays. ========================================================================== Paper Title 7: Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Journal: Muller et al., 2002, Cell 111(2): 197--208 FlyBase ID: FBrf0151815 PubMed ID: 12408864 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) Abd-B Caf1 (NURF-55) E(z) esc Rpd3 Su(z)12 Ubx LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- Caf1 P histone methylation ; GO:0016571 | inferred from direct assay F contributes_to histone lysine N-methyltransferase activity (H3-K27 specific) ; GO:0046976 | inferred by curator from GO:0035098 C ESC/E(Z) complex ; GO:0035098 | inferred from direct assay Internal note: A recombinant complex of Su(z)12, Caf1, E(z) and esc gene products methylates lysine-27 of histone H3. # E(z) P histone methylation ; GO:0016571 | inferred from direct assay P histone methylation ; GO:0016571 | inferred from mutant phenotype F histone lysine N-methyltransferase activity (H3-K27 specific) ; GO:0046976 | inferred from direct assay F methyltransferase activity ; GO:0008168 ; EC:2.1.1.- | inferred from mutant phenotype C ESC/E(Z) complex ; GO:0035098 | inferred from direct assay Internal note: A recombinant complex of Su(z)12, Caf1, E(z) and esc gene products methylates lysine-27 of histone H3. The E(z) product has catalytic activity. # esc P histone methylation ; GO:0016571 | inferred from direct assay F contributes_to histone lysine N-methyltransferase activity (H3-K27 specific) ; GO:0046976 | inferred by curator from GO:0035098 C ESC/E(Z) complex ; GO:0035098 | inferred from direct assay Internal note: A recombinant complex of Su(z)12, Caf1, E(z) and esc gene products methylates lysine-27 of histone H3. # Su(z)12 P histone methylation ; GO:0016571 | inferred from direct assay F contributes_to histone lysine N-methyltransferase activity (H3-K27 specific) ; GO:0046976 | inferred by curator from GO:0035098 C ESC/E(Z) complex ; GO:0035098 | inferred from direct assay Internal note: A recombinant complex of Su(z)12, Caf1, E(z) and esc gene products methylates lysine-27 of histone H3. LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0015610 Caf1 contributes_to GO:0046976 FB:FBrf0151815|PMID:12408864 IC F Chromatin assembly factor 1 subunit Nurf-55|NURF-55|NURF55|dCAF-1 p55|CAF-1|Caf-1|CG4236|p55|55|p55/NURF-55|NURF|CAF1|Caf1|d-CAF1|dCAF-1|dNURF gene taxon:7227 20040821 FB FB FBgn0015610 Caf1 GO:0016571 FB:FBrf0151815|PMID:12408864 IDA P Chromatin assembly factor 1 subunit Nurf-55|NURF-55|NURF55|dCAF-1 p55|CAF-1|Caf-1|CG4236|p55|55|p55/NURF-55|NURF|CAF1|Caf1|d-CAF1|dCAF-1|dNURF gene taxon:7227 20040821 FB FB FBgn0015610 Caf1 GO:0035098 FB:FBrf0151815|PMID:12408864 IDA C Chromatin assembly factor 1 subunit Nurf-55|NURF-55|NURF55|dCAF-1 p55|CAF-1|Caf-1|CG4236|p55|55|p55/NURF-55|NURF|CAF1|Caf1|d-CAF1|dCAF-1|dNURF gene taxon:7227 20040821 FB FB FBgn0000629 E(z) GO:0016571 FB:FBrf0151815|PMID:12408864 IDA P Enhancer of zeste pco/E(z)|E(z)1|pco|l(3)67Fa|enhancer of zeste|Su(z)301|l(3)ds12|E(Z)|E(z)|l(3)SG17|l(3)B12|CG6502|E[z]|polycombeotic|l(3)1902|Enhancer-of-zeste|Ez|EZ gene taxon:7227 20040821 FB FB FBgn0000629 E(z) GO:0035098 FB:FBrf0151815|PMID:12408864 IDA C Enhancer of zeste pco/E(z)|E(z)1|pco|l(3)67Fa|enhancer of zeste|Su(z)301|l(3)ds12|E(Z)|E(z)|l(3)SG17|l(3)B12|CG6502|E[z]|polycombeotic|l(3)1902|Enhancer-of-zeste|Ez|EZ gene taxon:7227 20040821 FB FB FBgn0000629 E(z) GO:0046976 FB:FBrf0151815|PMID:12408864 IDA F Enhancer of zeste pco/E(z)|E(z)1|pco|l(3)67Fa|enhancer of zeste|Su(z)301|l(3)ds12|E(Z)|E(z)|l(3)SG17|l(3)B12|CG6502|E[z]|polycombeotic|l(3)1902|Enhancer-of-zeste|Ez|EZ gene taxon:7227 20040821 FB FB FBgn0000629 E(z) GO:0008168 FB:FBrf0151815|PMID:12408864 IMP F Enhancer of zeste pco/E(z)|E(z)1|pco|l(3)67Fa|enhancer of zeste|Su(z)301|l(3)ds12|E(Z)|E(z)|l(3)SG17|l(3)B12|CG6502|E[z]|polycombeotic|l(3)1902|Enhancer-of-zeste|Ez|EZ gene taxon:7227 20040821 FB FB FBgn0000629 E(z) GO:0016571 FB:FBrf0151815|PMID:12408864 IMP P Enhancer of zeste pco/E(z)|E(z)1|pco|l(3)67Fa|enhancer of zeste|Su(z)301|l(3)ds12|E(Z)|E(z)|l(3)SG17|l(3)B12|CG6502|E[z]|polycombeotic|l(3)1902|Enhancer-of-zeste|Ez|EZ gene taxon:7227 20040821 FB FB FBgn0000588 esc contributes_to GO:0046976 FB:FBrf0151815|PMID:12408864 IC F extra sexcombs extra sex combs|esc|Esc|ESC|CG14941|L41867 gene taxon:7227 20040821 FB FB FBgn0000588 esc GO:0016571 FB:FBrf0151815|PMID:12408864 IDA P extra sexcombs extra sex combs|esc|Esc|ESC|CG14941|L41867 gene taxon:7227 20040821 FB FB FBgn0000588 esc GO:0035098 FB:FBrf0151815|PMID:12408864 IDA C extra sexcombs extra sex combs|esc|Esc|ESC|CG14941|L41867 gene taxon:7227 20040821 FB FB FBgn0020887 Su(z)12 contributes_to GO:0046976 FB:FBrf0151815|PMID:12408864 IC F l(3)76BDo|Su(z)12|SU(Z)12|CG8013 gene taxon:7227 20040821 FB FB FBgn0020887 Su(z)12 GO:0016571 FB:FBrf0151815|PMID:12408864 IDA P l(3)76BDo|Su(z)12|SU(Z)12|CG8013 gene taxon:7227 20040821 FB FB FBgn0020887 Su(z)12 GO:0035098 FB:FBrf0151815|PMID:12408864 IDA C l(3)76BDo|Su(z)12|SU(Z)12|CG8013 gene taxon:7227 20040821 FB COMMENTS: --------- The authors affinity-purified an ESC-containing complex from Drosophila embryos and identified four subunits, encoded by Su(z)12, E(z), Caf1, and esc (Pg.198-199, Fig.1A-1C). The four gene products were therefore annotated with the cellular component term 'ESC/E(Z) complex ; GO:0035098', supported by the 'inferred from direct assay' (IDA) evidence code. They go on to peform assays that demonstrate that the reconstituted ESC-E(Z) complex has specific histone methyltransferase activity (Pg.199). In FlyBase, we do not currently have identifiers for protein complexes, but because the above four proteins have been shown to be part of the ESC-E(Z) complex, these proteins have a role in histone methylation and therefore each protein was annotated with the GO term 'histone methylation ; GO:0016571', supported by the IDA evidence code. The function situation is slightly more complicated; through direct assays and mutational analyses the authors show that the E(z)-encoded protein has methyltransferase catalytic activity (Fig.3,5). Although the other subunits of the ESC-E(Z) complex do not have this catalytic activity by themselves, the authors show that the complex has greater methyltransferase activity that E(Z) alone. Therefore the Su(z)12, Caf1, and esc proteins contribute to this function and are annotated to 'histone lysine N-methyltransferase activity (H3-K27 specific) ; GO:0046976' with the qualifier 'contributes_to'. The evidence code used in this case is 'inferred by curator' (IC). The GO:ID for the complex (GO:0035098) goes in the 'with column' because it is inferred that these three proteins contribute to this function based on their belonging to the ESC/E(Z) complex. Since the E(z) protein has catalytic activity, this gene product is annotated directly to GO:0046976 without the need for a qualifier. Although the authors do not directly test whether ALL four subunits are essential for methyltransferase activity, 'contributes_to' may be used for any non-catalytic subunit, whether the subunit is essential for the activity of the complex or not. ========================================================================== Paper Title 8: Chromatin loosening by poly(ADP)-ribose polymerase (PARP) at Drosophila puff loci. Journal: Tulin and Spradling, 2003, Science 299(5606): 560--562 FlyBase ID: FBrf0155525 PubMed ID: 12543974 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) h Drs Hsp70Aa (hsp70) Hsp70Ab (hsp70) Hsp70Ba (hsp70) Hsp70Bb (hsp70) Hsp70Bbb (hsp70) Hsp70Bc (hsp70) Parp LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- Parp P antibacterial polypeptide induction ; GO:0006963 | inferred from mutant phenotype P heat shock-mediated polytene chromosome puffing ; GO:0035080 | inferred from expression pattern P heat shock-mediated polytene chromosome puffing ; GO:0035080 | inferred from mutant phenotype P innate immune response ; GO:0045087 | inferred from mutant phenotype C nuclear euchromatin ; GO:0005719 | inferred from direct assay C polytene chromosome ; GO:0005700 | inferred from direct assay C polytene chromosome puff ; GO:0005703 | inferred from direct assay Internal note: Before heat shock, the Parp protein is widely spread along polytene chromosomes. After heat shock, the Parp protein accumulates at newly-formed puffs. LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0010247 Parp GO:0006963 FB:FBrf0155525|PMID:12543974 IMP P PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB FB FBgn0010247 Parp GO:0035080 FB:FBrf0155525|PMID:12543974 IEP P PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB FB FBgn0010247 Parp GO:0035080 FB:FBrf0155525|PMID:12543974 IMP P PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB FB FBgn0010247 Parp GO:0045087 FB:FBrf0155525|PMID:12543974 IMP P PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB FB FBgn0010247 Parp GO:0005719 FB:FBrf0155525|PMID:12543974 IDA C PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB FB FBgn0010247 Parp GO:0005700 FB:FBrf0155525|PMID:12543974 IDA C PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB FB FBgn0010247 Parp GO:0005703 FB:FBrf0155525|PMID:12543974 IDA C PARP-1|LD21673.3prime|CG17718|Parp|PARP|BEST:LD21673|poly(ADP-ribose) polymerase|CG40411|D.PARP|CG17685|CG17696 gene taxon:7227 20040821 FB COMMENTS: --------- 'Inferred from expression pattern' (IEP) is one of the less-commonly used evidence codes in FlyBase. It is only used when an author makes the judgement that a gene product is involved in a particular process or (ocassionally) has a particular function based on when or where it is expressed (See also FBrf0131360/PMID:10967093). A curator does not usually make these inferences. In this paper, the authors say that the location of active Parp protein at site of polytene chromosome puffing following heat shock, strongly suggests that the Parp protein plays a role in this process (Fig.2). Therefore Parp was annotated to 'heat shock-mediated polytene chromosome puffing ; GO:0035080', supported by the IEP evidence code. The authors also confirm a role for PARP in chromosome puffing, by examining Parp-defective larvae (Fig.2). Where multiple sets of evidence within a paper support a GO annotation, all sets of evidence are included; the gene is annotated to the same GO term with multiple evidence codes. The authors show that epitope-tagged Parp protein is found in the euchromatin of diploid and polytene Drosophila nuclei (Pg.560, Fig.1A,1B). They also show that prior to heat shock, the Parp protein is widely spread along polytene chromosomes, and after heat shock, the Parp protein accumulates at newly-formed polytene chromosome puffs (Fig 1). Therefore Parp was annotated with all three component GO terms ('nuclear euchromatin ; GO:0005719', 'polytene chromosome ; GO:0005700' and 'polytene chromosome puff ; GO:0005703'), all supported by the 'inferred from direct assay' (IDA) evidence code. Even though 'polytene chromosome ; GO:0005700' is a parent of 'polytene chromosome puff' ; GO:0005703, it is correct to annotate to both terms because the Parp protein is also localized to sites along the polytene chromosome other than puffs. ========================================================================== Paper Title 9: Cyclin d-cdk4 and cyclin e-cdk2 regulate the Jak/STAT signal transduction pathway in Drosophila. Journal: Chen et al., 2003, Dev. Cell 4(2): 179--190 FlyBase ID: FBrf0155684 PubMed ID: 12586062 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) cdc2c (Cdk2) Cdk4 (l(2)sh0671, l(2)0671) CycD CycE elav (Elav) hop kay (DFOS) mus209 (PCNA) os (upd) RnrS (RNrS) Stat92E (stat92E) LINES OF GO DATA FROM THIS PAPER (ADAPTED FROM FLYBASE FLAT FILES): ------------------------------------------------------------------- cdc2c P JAK-STAT cascade ; GO:0007259 | inferred from physical interaction with FLYBASE:Stat92E; FB:FBgn0016917 F protein binding ; GO:0005515 | inferred from physical interaction with FLYBASE:Stat92E; FB:FBgn0016917 Internal note: CycD-Cdk4 and cdc2c-CycE bind and regulate STAT protein stability. rf040713. # Cdk4 P JAK-STAT cascade ; GO:0007259 | inferred from genetic interaction with FLYBASE:hop; FB:FBgn0004864 P JAK-STAT cascade ; GO:0007259 | inferred from genetic interaction with FLYBASE:os; FB:FBgn0004956, FLYBASE:CycD; FB:FBgn0010315 P JAK-STAT cascade ; GO:0007259 | inferred from mutant phenotype P JAK-STAT cascade ; GO:0007259 | inferred from physical interaction with FLYBASE:Stat92E; FB:FBgn0016917 P JAK-STAT cascade ; GO:0007259 | inferred from physical interaction with FLYBASE:Stat92E; FB:FBgn0016917, FLYBASE:CycD; FB:FBgn0010315 P blastoderm segmentation ; GO:0007350 | inferred from mutant phenotype P tracheal system development (sensu Insecta) ; GO:0007424 | inferred from mutant phenotype F protein binding ; GO:0005515 | inferred from physical interaction with FLYBASE:Stat92E; FB:FBgn0016917 Internal note: CycD-Cdk4 and cdc2c-CycE bind and regulate STAT protein stability. rf040713. # CycD P JAK-STAT cascade ; GO:0007259 | inferred from genetic interaction with FLYBASE:os; FB:FBgn0004956, FLYBASE:Cdk4; FB:FBgn0016131 Internal note: CycD-Cdk4 and cdc2c-CycE bind and regulate STAT protein stability. rf040713. # CycE P JAK-STAT cascade ; GO:0007259 | inferred from genetic interaction with FLYBASE:hop; FB:FBgn0004864 Internal note: CycD-Cdk4 and cdc2c-CycE bind and regulate STAT protein stability. rf040713. # hop P blastoderm segmentation ; GO:0007350 | inferred from mutant phenotype P tracheal system development (sensu Insecta) ; GO:0007424 | inferred from mutant phenotype # Stat92E F protein binding ; GO:0005515 | inferred from physical interaction with FLYBASE:cdc2c; FB:FBgn0004107 F protein binding ; GO:0005515 | inferred from physical interaction with FLYBASE:Cdk4; FB:FBgn0016131 LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0004107 cdc2c GO:0007259 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:Stat92E; FB:FBgn0016917 P cdc2c Dmcdc2c|CG10498|CDK2/CDC2c|Dcdc2c|cdk2|Cdk2|CDK2|DmCdk2|S(Sev-CycE)3A|DmCdc2|CDC2c|Cdc2c|cdc2c gene taxon:7227 20040821 FB FB FBgn0004107 cdc2c GO:0005515 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:Stat92E; FB:FBgn0016917 F cdc2c Dmcdc2c|CG10498|CDK2/CDC2c|Dcdc2c|cdk2|Cdk2|CDK2|DmCdk2|S(Sev-CycE)3A|DmCdc2|CDC2c|Cdc2c|cdc2c gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007259 FB:FBrf0155684|PMID:12586062 IGI FLYBASE:hop; FB:FBgn0004864 P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007259 FB:FBrf0155684|PMID:12586062 IGI FLYBASE:os; FB:FBgn0004956, FLYBASE:CycD; FB:FBgn0010315 P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007259 FB:FBrf0155684|PMID:12586062 IMP P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007350 FB:FBrf0155684|PMID:12586062 IMP P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007424 FB:FBrf0155684|PMID:12586062 IMP P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007259 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:Stat92E; FB:FBgn0016917 P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0007259 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:Stat92E; FB:FBgn0016917, FLYBASE:CycD; FB:FBgn0010315 P Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0016131 Cdk4 GO:0005515 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:Stat92E; FB:FBgn0016917 F Cyclin-dependent kinase 4 Pk?7|l(2)05428|Pk53C|cdk4|Cdk4|CDK4|DmCdk4|l(2)sh0671|l(2)s4639|l(2)k06503|CG5072|8-6|CDK4/6|Cdk4/6|cdk4/6|l(2)0671 gene taxon:7227 20040821 FB FB FBgn0010315 CycD GO:0007259 FB:FBrf0155684|PMID:12586062 IGI FLYBASE:os; FB:FBgn0004956, FLYBASE:Cdk4; FB:FBgn0016131 P CG9096|cycD|CycD|cdi3|Cdi3|CDI3|cyclin D gene taxon:7227 20040821 FB FB FBgn0010382 CycE GO:0007259 FB:FBrf0155684|PMID:12586062 IGI FLYBASE:hop; FB:FBgn0004864 P Cyclin E fondue|CG3938|cycE|CycE|Cyc E|CyeE|fond|cyclinE|cyclin E|Cyclin E|cdi7|Cdi7|CDI7|l(2)05206|l(2)br37|l(2)k02602|D-CycE|DmCycE|DmcycE|l(2)k05007|l(2)k02514|DmcyclinE|BG:DS07108.3|l35Dd|br37|l(2)35Dd gene taxon:7227 20040821 FB FB FBgn0004864 hop GO:0007350 FB:FBrf0155684|PMID:12586062 IMP P hopscotch L4|DmHD-160|msvl|hop|Hop|Dm JAK|l(1)L4|locus 18|HD-160|Hopskotch|Tum-1|4|l(1)hop|Tum|JAK|Jak|l(1)10Be|Hop1|CG1594|l(1)G18|Jak-STAT gene taxon:7227 20040821 FB FB FBgn0004864 hop GO:0007424 FB:FBrf0155684|PMID:12586062 IMP P hopscotch L4|DmHD-160|msvl|hop|Hop|Dm JAK|l(1)L4|locus 18|HD-160|Hopskotch|Tum-1|4|l(1)hop|Tum|JAK|Jak|l(1)10Be|Hop1|CG1594|l(1)G18|Jak-STAT gene taxon:7227 20040821 FB FB FBgn0016917 Stat92E GO:0005515 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:cdc2c; FB:FBgn0004107 F Signal-transducer and activator of transcription protein at 92E SD-stat|dSTAT|Dstat|DSTAT|dSTAT92E/marelle|marelle|D-stat/stat92E|mrl|mrL|l(3)j6C8|stat92E|Stat92E|STAT92E|STAT 92E|DSRC|D-STAT|D-Stat|D-stat|d-STAT|DmSTAT|Dstat 92E|Dstat92E|DRODSRC|l(3)06346|mrl stat92E|Stat1&agr;-like|stat|Stat|STAT|CG4257|Stat92E/marelle gene taxon:7227 20040821 FB FB FBgn0016917 Stat92E GO:0005515 FB:FBrf0155684|PMID:12586062 IPI FLYBASE:Cdk4; FB:FBgn0016131 F Signal-transducer and activator of transcription protein at 92E SD-stat|dSTAT|Dstat|DSTAT|dSTAT92E/marelle|marelle|D-stat/stat92E|mrl|mrL|l(3)j6C8|stat92E|Stat92E|STAT92E|STAT 92E|DSRC|D-STAT|D-Stat|D-stat|d-STAT|DmSTAT|Dstat 92E|Dstat92E|DRODSRC|l(3)06346|mrl stat92E|Stat1&agr;-like|stat|Stat|STAT|CG4257|Stat92E/marelle gene taxon:7227 20040821 FB COMMENTS: --------- Drosophila Janus kinase (JAK) is encoded by the hop (hopscotch) gene, Drosophila STAT is encoded by the Stat92E gene and the os gene (commonly called unpaired/upd) encodes the ligand for the JAK-STAT pathway. In this paper the authors show that Cdk4 mutants have similar phenotypes to those of Stat92E and hop (Pg.180, Fig.1), which they conclude indicates a role for Cdk4 in JAK-STAT signaling. Therefore Cdk4 was annotated with the GO term 'JAK-STAT cascade ; GO:0007259' supported by the 'inferred from mutant phenotype' (IMP) evidence code. The segmentation defects (Fig.1) and tracheal system defects (Fig.2) of hop and Cdk4 mutants allowed these genes to be annotated with the GO terms 'blastoderm segmentation ; GO:0007350' and 'tracheal system development (sensu Insecta) ; GO:0007424' also supported by the IMP evidence code. Genetic interaction between two genes can indicate that they are involved in the same biological process. In this paper, the authors show that Cdk4 functions in the JAK-STAT pathway through genetic interactions between Cdk4 and hop mutations (Pg.181-182, Table 1). Additional genetic interactions between CycE and hop, also places CycE in the JAK-STAT pathway (Pg.182, Fig.3F, Table 1). Cdk4 and CycE were therefore both annotated to 'JAK-STAT cascade ; GO:0007259' with the 'hop' identifier listed in the 'with column' for the 'inferred from genetic interaction' (IGI) evidence code. To test the genetic interaction between upd (os) and Cdk4 in the eye, the authors also expressed UAS-upd and UAS-CycD+UAS-Cdk4 together, and found that driving the expression of UAS-upd and UAS-CycD+UAS-Cdk4 together dramatically enhanced the eye outgrowth phenotype of expressing either UAS-upd or UAS-CycD+Cdk4 alone (Pg.183, Fig.4). This provides further evidence that CycD and Cdk4 act in the JAK-STAT pathway. Since 3 genes are being misexpressed together in this assay, the 'with statements' for the IGI lines contain both interacting genes (upd and CycD, and upd and Cdk4). In a physical interaction assay, the Stat92E protein coimmunoprecipitated with Cdk4 protein and also with Cdk2 (cdc2c) protein (Pg.183-184, Fig.5A,5B). This was the basis for annotating Cdk4 and Cdk2 (cdc2c) to 'JAK-STAT cascade ; GO:0007259', supported by the IPI evidence code. This assay was also used to assign 'protein binding ; GO:0005515' function terms for Stat92E, Cdk4 and Cdk2 (cdc2c). In each case reciprocal annotation lines were created; Cdk4 and Cdk2 bind Stat92E, and therefore Stat92E must bind Cdk4 and Cdk2. ========================================================================== Paper Title 10: Understanding human cancer using Drosophila: Tid47, a cytosolic product of the DnaJ-like tumor suppressor gene l2Tid, is a novel molecular partner of patched related to skin cancer. Journal: Canamasas, 2003, J. Biol. Chem. 278(33): 30952--30960 FlyBase ID: FBrf0173155 PubMed ID: 12783860 DROSOPHILA GENES ANNOTATED IN THIS PAPER: ----------------------------------------- (synonyms used in the paper are indicated in brackets) ci hh Hsp70Aa (Hsp70) Hsp70Ab (Hsp70) Hsp70Ba (Hsp70) Hsp70Bb (Hsp70) Hsp70Bbb (Hsp70) Hsp70Bc (Hsp70) l(2)tid ptc smo LINES OF GO DATA FROM THIS PAPER (TAKEN FROM FLYBASE FLAT FILES): ----------------------------------------------------------------- l(2)tid P smoothened receptor signaling pathway ; GO:0007224 | inferred from genetic interaction with FLYBASE:ptc; FB:FBgn0003892 p smoothened receptor signaling pathway ; GO:0007224 | inferred from physical interaction with FLYBASE:ptc; FB:FBgn0003892 F patched binding ; GO:0005113 | inferred from physical interaction with FLYBASE:ptc; FB:FBgn0003892 C cytosol ; GO:0005829 | inferred from direct assay C mitochondrion ; GO:0005739 | inferred from direct assay Internal note: Different isoforms located in different places - Tid47 is in the cytosol, Tid50 and Tid40 are in the mitochondrion. # ptc F protein binding ; GO:0005515 | inferred from physical interaction with FLYBASE:l(2)tid; FB:FBgn0002174 LINES OF GO DATA FROM THIS PAPER (TAKEN FROM GENE_ASSOCIATION.FB): ------------------------------------------------------------------ FB FBgn0002174 l(2)tid GO:0005113 FB:FBrf0173155 IPI F lethal (2) tumorous imaginal discs l(2)tumorous disc|l(2)tid|tid|l(2)tumorous imaginal discs|l(2)td|l(2)701|CG5504|cDNA 10D|TID56|l(2)tud|DnaJ gene taxon:7227 20040821 FB FB FBgn0002174 l(2)tid GO:0005829 FB:FBrf0173155 IDA C lethal (2) tumorous imaginal discs l(2)tumorous disc|l(2)tid|tid|l(2)tumorous imaginal discs|l(2)td|l(2)701|CG5504|cDNA 10D|TID56|l(2)tud|DnaJ gene taxon:7227 20040821 FB FB FBgn0002174 l(2)tid GO:0005739 FB:FBrf0173155 IDA C lethal (2) tumorous imaginal discs l(2)tumorous disc|l(2)tid|tid|l(2)tumorous imaginal discs|l(2)td|l(2)701|CG5504|cDNA 10D|TID56|l(2)tud|DnaJ gene taxon:7227 20040821 FB FB FBgn0002174 l(2)tid GO:0007224 FB:FBrf0173155 IGI FLYBASE:ptc; FB:FBgn0003892 P lethal (2) tumorous imaginal discs l(2)tumorous disc|l(2)tid|tid|l(2)tumorous imaginal discs|l(2)td|l(2)701|CG5504|cDNA 10D|TID56|l(2)tud|DnaJ gene taxon:7227 20040821 FB FB FBgn0002174 l(2)tid GO:0007224 FB:FBrf0173155 IPI FLYBASE:ptc; FB:FBgn0003892 P lethal (2) tumorous imaginal discs l(2)tumorous disc|l(2)tid|tid|l(2)tumorous imaginal discs|l(2)td|l(2)701|CG5504|cDNA 10D|TID56|l(2)tud|DnaJ gene taxon:7227 20040821 FB FB FBgn0003892 ptc GO:0005515 FB:FBrf0173155 IPI FLYBASE:l(2)tid; FB:FBgn0002174 F patched CG2411|pat|Conf|Ptc_Dm|ptc|Ptc|PTC|l(2)k02507|BcDNA:RH36596|rubr|tuf gene taxon:7227 20040821 FB COMMENTS: --------- The authors present multiple evidence that l(2)tid is involved in the hedgehog (hh) signaling pathway- physical interaction with the patched (ptc) protein, and genetic interaction with the patched gene (Pg.30955-30957). Since multiple lines of GO annotation add to the confidence of that annotation, l(2)tid was annotated to the GO term 'smoothened receptor signaling pathway ; GO:0007224', supported by both the 'inferred from physical interaction' (IPI) and 'inferred from genetic interaction' (IGI) evidence codes. The identifier for patched was included in the with column. The physical interaction between the l(2)tid-encoded protein and the patched-encoded protein (Pg.20955) was also used for GO function annotation. l(2)tid was annotated with the specific GO term 'patched binding ; GO:0005113', using the IPI evidence code. The reciprocal protein binding was captured by annotating ptc with 'protein binding ; GO:0005515', using the IPI evidence code and the identifier for l(2)tid in the with column. (At the time of annotation, gene identifiers were still being used in with statements for the IPI evidence code). In FlyBase, all GO annotations are added to genes. Where two protein isoforms are in different locations in the cell, both cellular_component GO terms are added under the gene, with an internal curator note that the isoforms have different cellular locations. When GO annotations are later transferred to specific protein products, this will allow us to partition the GO data under the correct protein isoforms. In this paper, an immunoblot of subcellular fractions found one protein isoform (Tid47) in the cytosol and two protein isoforms (Tid50 and Tid40) in the mitochondria (Pg.30954. Fig.1). Therefore both 'cytosol ; GO:0005829' 'mitochondrion ; GO:0005739' GO annotations were recorded for l(2)tid. An internal FlyBase note was added to summarize this finding. ========================================================================== Please address any questions to r.foulger@gen.cam.ac.uk