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Add new ubibrowser test files
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@kkaris
kkaris committed Nov 17, 2023
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10 changes: 5 additions & 5 deletions indra/tests/test_sources/resources/ubibrowser_dub.txt
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NUMBER E3ID SUBID E3AC SUBAC E3GENE SUBGENE SOURCE SOURCEID SENTENCE E3TYPE COUNT type species
671 UBP10_HUMAN PTEN_HUMAN Q14694 P60484 USP10 PTEN MEDLINE 28852924 We further demonstrated that USP10 directly interacted with and stabilized PTEN via deubiquitination. USP 1 DUB H.sapiens
673 UBP36_HUMAN SODM_HUMAN Q9P275 P04179 USP36 SOD2 MEDLINE 21268071 we identified a deubiquitinating enzyme USP36 that regulates the protein stability of SOD2 USP 1 DUB H.sapiens
675 UBP13_HUMAN UBL4A_HUMAN Q92995 P11441 USP13 UBL4A MEDLINE 24424410 we identify USP13 as a gp78-associated DUB that eliminates ubiquitin conjugates from Ubl4A to maintain the functionality of Bag6. USP 2 DUB H.sapiens
677 UBP33_HUMAN ARRB1_HUMAN Q8TEY7 P49407 USP33 ARRB1 MEDLINE 19363159 We now report the discovery that the deubiquitinating enzyme ubiquitin-specific protease 33 (USP33) binds beta-arrestin2 and leads to the deubiquitination of beta-arrestins. USP 1 DUB H.sapiens
NUMBER SwissProt ID (DUB) SwissProt ID (Substrate) SwissProt AC (DUB) SwissProt AC (Substrate) Gene Symbol (DUB) Gene Symbol (Substrate) SOURCE SOURCEID SENTENCE DUBTYPE COUNT type species
56 UBP33_HUMAN ARRB1_HUMAN Q8TEY7 P49407 USP33 ARRB1 MEDLINE 19363159 "We now report the discovery that the deubiquitinating enzyme ubiquitin-specific protease 33 (<span class=""match term0"">USP33</span>) binds beta-arrestin2 and leads to the deubiquitination of beta-arrestins" USP 1 Training data H.sapiens
129 UBP13_HUMAN UBL4A_HUMAN Q92995 P11441 USP13 UBL4A MEDLINE 24424410 "we identify <span class=""match term0"">USP13</span> as a gp78-associated DUB that eliminates ubiquitin conjugates from <span class=""match term1"">Ubl4A</span> to maintain the functionality of Bag6" USP 1 Other H.sapiens
388 UBP10_HUMAN PTEN_HUMAN Q14694 P60484 USP10 PTEN MEDLINE 28852924 "We further demonstrated that <span class=""match term0"">USP10</span> directly interacted with and stabilized <span class=""match term1"">PTEN</span> via deubiquitination" USP 1 Training data H.sapiens
726 UBP36_HUMAN SODM_HUMAN Q9P275 P04179 USP36 SOD2 MEDLINE 21268071 "we identified a deubiquitinating enzyme <span class=""match term0"">USP36</span> that regulates the protein stability of <span class=""match term1"">SOD2</span>" USP 1 Other H.sapiens
12 changes: 6 additions & 6 deletions indra/tests/test_sources/resources/ubibrowser_e3.txt
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NUMBER E3ID SUBID E3AC SUBAC E3GENE SUBGENE SOURCE SOURCEID SENTENCE E3TYPE COUNT type species
1 AMFR2_HUMAN A1AT_HUMAN Q9UKV5 P01009 AMFR SERPINA1 MEDLINE 16979136 Here we report that gp78, a ubiquitin ligase (E3) pairing with mammalian Ubc7 for ERAD, ubiquitinates and facilitates degradation of ATZ, the classic deficiency variant of AAT having a Z mutation (Glu 342 Lys) RING 3 E3 H.sapiens
15 AMFR2_HUMAN HMDH_HUMAN Q9UKV5 P04035 AMFR HMGCR MEDLINE 20458442 UBE2G2, a previously known E2 of gp78, is demonstrated to be involved in the sterol-regulated ubiquitination and degradation of HMGCR RING 4 E3 H.sapiens
300 BRCA1_HUMAN BRCA1_HUMAN P38398 P38398 BRCA1 BRCA1 UniProt RNF8_BOVIN Following DNA double-strand breaks (DSBs), it is recruited to the sites of damage by ATM-phosphorylated MDC1, mediates the ubiquitination of histones H2A and H2AX, thereby promoting the formation of TP53BP1 and BRCA1 ionizing radiation-induced foci (IRIF) RING 21 E3 H.sapiens
5642 HRD1_CAEEL Q9BMU4_CAEEL Q20798 Q9BMU4 sel-11 atln-1 MEDLINE 32916628 UbiNet 2.0 RING 1 E3 C.elegans
5644 A0A2I4KBP1_DANRE SHH_DANRE A0A2I4KBP1 Q92008 gan shha MEDLINE 31503551 UbiNet 2.0 other 1 E3 D.rerio
NUMBER SwissProt ID (E3) SwissProt ID (Substrate) SwissProt AC (E3) SwissProt AC (Substrate) Gene Symbol (E3) Gene Symbol (Substrate) SOURCE SOURCEID SENTENCE E3TYPE COUNT type species
109 HRD1_CAEEL Q9BMU4_CAEEL Q20798 Q9BMU4 sel-11 atln-1 MEDLINE 32916628 32916628 RING 1 Other C.elegans
167 A0A2I4KBP1_DANRE SHH_DANRE A0A2I4KBP1 Q92008 gan shha MEDLINE 31503551 31503551 Other 1 Other D.rerio
198 AMFR2_HUMAN A1AT_HUMAN Q9UKV5 P01009 AMFR SERPINA1 MEDLINE 16979136 "Here we report that <span class=""match term0"">gp78</span>, a ubiquitin ligase (E3) pairing with mammalian Ubc7 for ERAD, ubiquitinates and facilitates degradation of ATZ, the classic deficiency variant of <span class=""match term1"">AAT</span> having a Z mutation (Glu 342 Lys)" RING 1 Training data H.sapiens
1040 GAN_HUMAN SHH_HUMAN Q9H2C0 Q15465 GAN SHH MEDLINE 31503551 31503551 BTB_3 1 Other H.sapiens
2631 SYVN1_HUMAN ATLA1_HUMAN Q86TM6 Q8WXF7 SYVN1 ATL1 MEDLINE 32916628 "The E3 Ubiquitin Ligase <span class=""match term0"">SYVN1</span> Ubiquitinates Atlastins to Remodel the Endoplasmic Reticulum Network." RING 1 Other H.sapiens

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