Root organelle term usage in gene reviews
Generated by scripts/root_organelle_usage.py; do not edit by hand.
A gene is counted as having a specific sub-compartment when its review
also carries (not REMOVEd), proposes, or lists as a core location an
is_a/part_of descendant of the same organelle.
| organelle | rows | genes | genes w/ sub-compartment | % | rows w/o sub-compartment |
|---|---|---|---|---|---|
| mitochondrion (GO:0005739) | 3585 | 1230 | 810 | 66 | 864 |
| nucleus (GO:0005634) | 6972 | 2525 | 1040 | 41 | 3087 |
| endoplasmic reticulum (GO:0005783) | 1325 | 715 | 483 | 68 | 356 |
| Golgi apparatus (GO:0005794) | 640 | 389 | 215 | 55 | 250 |
| lysosome (GO:0005764) | 333 | 136 | 87 | 64 | 80 |
| peroxisome (GO:0005777) | 363 | 140 | 59 | 42 | 153 |
| endosome (GO:0005768) | 254 | 165 | 104 | 63 | 92 |
| chloroplast (GO:0009507) | 263 | 160 | 54 | 34 | 125 |
| vacuole (GO:0005773) | 46 | 35 | 13 | 37 | 26 |
| autophagosome (GO:0005776) | 92 | 53 | 17 | 32 | 51 |
mitochondrion (GO:0005739)
- Actions (all rows): {'ACCEPT': 2389, 'KEEP_AS_NON_CORE': 725, 'MARK_AS_OVER_ANNOTATED': 188, 'MODIFY': 174, 'REMOVE': 55, 'UNDECIDED': 38, 'TOO_GENERAL': 11, 'NEW': 5}
- Evidence (all rows): {'IDA': 839, 'HDA': 695, 'IEA': 625, 'IBA': 514, 'HTP': 437, 'ISS': 112, 'EXP': 82, 'TAS': 69, 'ISO': 61, 'NAS': 47, 'IMP': 34, 'ISM': 28, 'RCA': 23, 'IC': 9, 'IPI': 7, 'IGI': 2, 'ISA': 1}
- Sub-compartment kinds, by gene: {'membrane': 327, 'lumen': 322, 'lumen+membrane': 125, 'lumen+other': 16, 'membrane+other': 16, 'lumen+membrane+other': 2, 'other': 2}
- Rows with no sub-compartment, actions: {'ACCEPT': 394, 'KEEP_AS_NON_CORE': 264, 'MARK_AS_OVER_ANNOTATED': 117, 'REMOVE': 54, 'UNDECIDED': 30, 'NEW': 5}
- Rows with no sub-compartment, evidence: {'HDA': 247, 'IEA': 187, 'IDA': 132, 'IBA': 123, 'ISS': 43, 'HTP': 37, 'ISO': 22, 'EXP': 21, 'ISM': 15, 'TAS': 12, 'IMP': 9, 'NAS': 9, 'RCA': 2, 'IPI': 2, 'IGI': 1, 'ISA': 1, 'IC': 1}
- Example genes with only the root term: ARATH/ABCG36, ARATH/AGT1, ARATH/ALAAT1, ARATH/ASP2, ARATH/BIK1, ARATH/CAT2, ARATH/CER1, ARATH/CLV3, ARATH/CRN, ARATH/CUT1, ARATH/CYP71A13, ARATH/ERECTA, ARATH/FLD, ARATH/FPS1, ARATH/FTSH12__Q9SAJ3, ARATH/FVE, ARATH/GGAT2, ARATH/GIP1, ARATH/GLN2, ARATH/GLYK, ARATH/GSTF6, ARATH/GSTU20, ARATH/HKT1, ARATH/HPR, ARATH/HPR2
nucleus (GO:0005634)
- Actions (all rows): {'ACCEPT': 4939, 'KEEP_AS_NON_CORE': 1500, 'MODIFY': 205, 'MARK_AS_OVER_ANNOTATED': 140, 'UNDECIDED': 85, 'REMOVE': 63, 'NEW': 33, 'TOO_GENERAL': 7}
- Evidence (all rows): {'IDA': 2064, 'IEA': 1886, 'IBA': 1037, 'EXP': 556, 'HDA': 451, 'ISS': 248, 'ISO': 200, 'ISM': 171, 'NAS': 170, 'TAS': 97, 'IC': 43, 'IMP': 32, 'IPI': 13, 'IGI': 3, 'IEP': 1}
- Sub-compartment kinds, by gene: {'lumen': 595, 'lumen+other': 232, 'other': 156, 'membrane': 19, 'lumen+membrane+other': 16, 'lumen+membrane': 13, 'membrane+other': 9}
- Rows with no sub-compartment, actions: {'ACCEPT': 1800, 'KEEP_AS_NON_CORE': 1003, 'MARK_AS_OVER_ANNOTATED': 121, 'UNDECIDED': 69, 'REMOVE': 62, 'NEW': 29, 'MODIFY': 3}
- Rows with no sub-compartment, evidence: {'IEA': 961, 'IDA': 658, 'IBA': 577, 'HDA': 341, 'EXP': 148, 'ISM': 141, 'ISS': 120, 'ISO': 59, 'TAS': 37, 'NAS': 23, 'IC': 11, 'IMP': 5, 'IPI': 3, 'IGI': 2, 'IEP': 1}
- Example genes with only the root term: 9POAL/NCGR_LOCUS1765, 9POAL/NCGR_LOCUS27674, ABRPR/A0A8B8L1Z3, ARATH/ABCB1, ARATH/ABCB19, ARATH/ABCB4, ARATH/ABF2, ARATH/ABI1, ARATH/ABI5, ARATH/AFB2, ARATH/AG, ARATH/AGO1, ARATH/AHK3, ARATH/AHK4, ARATH/AHP1, ARATH/ALAAT1, ARATH/AP1, ARATH/AP2, ARATH/AP3, ARATH/ARF19, ARATH/ARF5, ARATH/ARF7, ARATH/ARR1, ARATH/ARR12, ARATH/ARR5
endoplasmic reticulum (GO:0005783)
- Actions (all rows): {'ACCEPT': 918, 'KEEP_AS_NON_CORE': 276, 'MODIFY': 69, 'MARK_AS_OVER_ANNOTATED': 27, 'UNDECIDED': 23, 'NEW': 6, 'TOO_GENERAL': 4, 'REMOVE': 2}
- Evidence (all rows): {'IDA': 423, 'IEA': 303, 'IBA': 202, 'HDA': 194, 'ISS': 60, 'ISO': 40, 'EXP': 39, 'TAS': 37, 'NAS': 13, 'IMP': 8, 'IC': 3, 'IGI': 2, 'IPI': 1}
- Sub-compartment kinds, by gene: {'membrane': 372, 'membrane+other': 39, 'lumen': 33, 'lumen+other': 17, 'lumen+membrane': 9, 'lumen+membrane+other': 7, 'other': 6}
- Rows with no sub-compartment, actions: {'KEEP_AS_NON_CORE': 173, 'ACCEPT': 134, 'MARK_AS_OVER_ANNOTATED': 21, 'UNDECIDED': 20, 'NEW': 6, 'REMOVE': 2}
- Rows with no sub-compartment, evidence: {'IEA': 119, 'IDA': 93, 'IBA': 46, 'HDA': 28, 'ISS': 23, 'ISO': 19, 'EXP': 18, 'TAS': 8, 'IGI': 1, 'IC': 1}
- Example genes with only the root term: ARATH/ABCB1, ARATH/AGO1, ARATH/CSLD3, ARATH/FAE1, ARATH/FKBP42, ARATH/FT, ARATH/GA3, ARATH/GDCH, ARATH/MNS1, ARATH/MVP1, ARATH/PIN2, ARATH/PIN3, ARATH/UGT73C5, ASPRC/fogD, CANAL/ERG6, CANAL/JEM1, DANRE/prom1a, DANRE/tlr21, DANRE/tomt, DANRE/ufsp2, DERPT/Derp23, DESRO/K9J287, DICDI/acrA, DICDI/pdsA, DICDI/tlcd4b
Golgi apparatus (GO:0005794)
- Actions (all rows): {'ACCEPT': 286, 'KEEP_AS_NON_CORE': 224, 'MODIFY': 71, 'MARK_AS_OVER_ANNOTATED': 29, 'UNDECIDED': 18, 'NEW': 10, 'REMOVE': 2}
- Evidence (all rows): {'IDA': 234, 'IEA': 202, 'IBA': 60, 'ISS': 36, 'HDA': 34, 'EXP': 22, 'ISO': 20, 'TAS': 18, 'NAS': 7, 'ISM': 3, 'IMP': 3, 'IPI': 1}
- Sub-compartment kinds, by gene: {'membrane': 125, 'membrane+other': 49, 'other': 34, 'lumen': 4, 'lumen+membrane+other': 1, 'lumen+membrane': 1, 'lumen+other': 1}
- Rows with no sub-compartment, actions: {'KEEP_AS_NON_CORE': 144, 'ACCEPT': 52, 'MARK_AS_OVER_ANNOTATED': 26, 'UNDECIDED': 17, 'NEW': 9, 'REMOVE': 2}
- Rows with no sub-compartment, evidence: {'IEA': 84, 'IDA': 80, 'ISO': 17, 'IBA': 15, 'TAS': 14, 'ISS': 13, 'EXP': 13, 'HDA': 10, 'NAS': 2, 'IMP': 1, 'IPI': 1}
- Example genes with only the root term: ARATH/AT5G02500, ARATH/AUX1, ARATH/BIK1, ARATH/MLO2, ARATH/RBOHD, ARATH/RCA, DANRE/tomt, DORPE/AP180, DROME/BicD, DROME/CG33116, DROME/CG3631, DROME/Fer1HCH, DROME/Fer2LCH, DROME/NTPase, DROME/park, EQUAS/APP, HORSE/APP, PANPA/A0A2R9CAF4, SALRS/jumble, SCHPO/ade3, SCHPO/alg6, SCHPO/ayr1, SCHPO/bgs4, SCHPO/dca7, SCHPO/erg26
lysosome (GO:0005764)
- Actions (all rows): {'ACCEPT': 256, 'KEEP_AS_NON_CORE': 50, 'MODIFY': 21, 'NEW': 3, 'MARK_AS_OVER_ANNOTATED': 2, 'UNDECIDED': 1}
- Evidence (all rows): {'IDA': 136, 'IEA': 86, 'IBA': 31, 'ISO': 21, 'EXP': 16, 'TAS': 15, 'ISS': 12, 'NAS': 7, 'IMP': 7, 'IPI': 2}
- Sub-compartment kinds, by gene: {'membrane': 35, 'lumen': 22, 'lumen+membrane': 10, 'other': 10, 'lumen+other': 6, 'membrane+other': 4}
- Rows with no sub-compartment, actions: {'ACCEPT': 40, 'KEEP_AS_NON_CORE': 34, 'NEW': 3, 'MARK_AS_OVER_ANNOTATED': 1, 'MODIFY': 1, 'UNDECIDED': 1}
- Rows with no sub-compartment, evidence: {'IEA': 28, 'IDA': 22, 'ISO': 9, 'IBA': 7, 'ISS': 6, 'EXP': 5, 'TAS': 2, 'NAS': 1}
- Example genes with only the root term: ANOGA/psidin, DANRE/fgf8a, DANRE/tpp1, DROME/N, HETGA/Has2, HETGA/Hyal2, human/ADA, human/ADRB2, human/ANK2, human/AP5Z1, human/APP, human/ARRDC3, human/ARSI, human/BACE1, human/BCL10, human/CRYAB, human/CXCR4, human/GABARAP, human/IL4I1, human/LRIG1, human/MYO5A, human/NBR1, human/PLD4, human/RAB7B, human/RAB8A
peroxisome (GO:0005777)
- Actions (all rows): {'ACCEPT': 262, 'KEEP_AS_NON_CORE': 44, 'MARK_AS_OVER_ANNOTATED': 20, 'MODIFY': 15, 'REMOVE': 13, 'UNDECIDED': 8, 'NEW': 1}
- Evidence (all rows): {'IDA': 159, 'IEA': 73, 'IBA': 52, 'ISS': 20, 'EXP': 17, 'HDA': 17, 'ISO': 9, 'ISM': 6, 'IMP': 5, 'NAS': 4, 'TAS': 1}
- Sub-compartment kinds, by gene: {'lumen': 30, 'membrane': 24, 'lumen+membrane': 5}
- Rows with no sub-compartment, actions: {'ACCEPT': 79, 'KEEP_AS_NON_CORE': 32, 'MARK_AS_OVER_ANNOTATED': 20, 'REMOVE': 13, 'UNDECIDED': 8, 'NEW': 1}
- Rows with no sub-compartment, evidence: {'IDA': 45, 'IBA': 33, 'IEA': 32, 'HDA': 16, 'ISS': 11, 'ISM': 5, 'ISO': 5, 'EXP': 4, 'TAS': 1, 'IMP': 1}
- Example genes with only the root term: ARATH/AGT1, ARATH/BGLU18, ARATH/GGAT1, ARATH/GGAT2, ARATH/GLO1, ARATH/GLO2, ARATH/HPR, ARATH/PLP2, ARATH/TGG1, ARATH/TGG2, ARATH/UGT74C1, ASPFU/erg8, CANAL/ERG8, CANAL/GND1, DANRE/agxta, DANRE/agxtb, DANRE/uox, DANRE/urad, DROME/Acat1, DROME/Ccs, DROME/Ech1, DROME/Got1, DROME/Idh, DROME/Mdh1, DROME/Mtpalpha
endosome (GO:0005768)
- Actions (all rows): {'ACCEPT': 148, 'KEEP_AS_NON_CORE': 72, 'MODIFY': 26, 'UNDECIDED': 5, 'MARK_AS_OVER_ANNOTATED': 2, 'NEW': 1}
- Evidence (all rows): {'IDA': 93, 'IEA': 82, 'IBA': 25, 'ISS': 20, 'ISO': 14, 'EXP': 10, 'HDA': 5, 'TAS': 5}
- Sub-compartment kinds, by gene: {'membrane+other': 44, 'membrane': 35, 'other': 20, 'lumen+membrane': 2, 'lumen+other': 1, 'lumen+membrane+other': 1, 'lumen': 1}
- Rows with no sub-compartment, actions: {'KEEP_AS_NON_CORE': 50, 'ACCEPT': 34, 'UNDECIDED': 5, 'MARK_AS_OVER_ANNOTATED': 2, 'NEW': 1}
- Rows with no sub-compartment, evidence: {'IEA': 29, 'IDA': 28, 'IBA': 11, 'ISS': 8, 'ISO': 7, 'HDA': 4, 'TAS': 3, 'EXP': 2}
- Example genes with only the root term: ARATH/AUX1, ARATH/CASPL1D1, ARATH/CBL10, ARATH/CSLD3, ARATH/IRX10L, ARATH/MNS1, ARATH/STM, DICDI/ptpC, DROME/AMPKalpha, DROME/Lkb1, DROME/Vps26, DROME/hbs, DROME/hh, DROME/neur, SCHPO/apl2, SCHPO/lsb6, SCHPO/pik3, SCHPO/vas2, human/ABCA1, human/ANKRD50, human/AP4E1, human/ARRDC5, human/ASTN1, human/ATP1A2, human/ATP6V1E1
chloroplast (GO:0009507)
- Actions (all rows): {'ACCEPT': 147, 'MODIFY': 44, 'REMOVE': 37, 'MARK_AS_OVER_ANNOTATED': 20, 'KEEP_AS_NON_CORE': 9, 'UNDECIDED': 6}
- Evidence (all rows): {'IEA': 84, 'ISM': 82, 'HDA': 59, 'IDA': 21, 'IBA': 9, 'ISS': 4, 'TAS': 4}
- Sub-compartment kinds, by gene: {'other': 42, 'membrane+other': 7, 'membrane': 5}
- Rows with no sub-compartment, actions: {'ACCEPT': 66, 'REMOVE': 37, 'MARK_AS_OVER_ANNOTATED': 13, 'UNDECIDED': 5, 'KEEP_AS_NON_CORE': 4}
- Rows with no sub-compartment, evidence: {'IEA': 55, 'ISM': 48, 'HDA': 9, 'IDA': 6, 'IBA': 4, 'ISS': 2, 'TAS': 1}
- Example genes with only the root term: 9POAL/NCGR_LOCUS29329, ARATH/ABCG36, ARATH/APO1, ARATH/ARR1, ARATH/AT5G02500, ARATH/At1g67980, ARATH/BES1, ARATH/BGLU18, ARATH/CYP79B2, ARATH/CYP79B3, ARATH/CYP79F1, ARATH/CYP79F2, ARATH/DELTA-OAT, ARATH/EBF2, ARATH/EDS1, ARATH/ESP, ARATH/F4JLB7, ARATH/FAE1, ARATH/FLD, ARATH/GA1, ARATH/GGAT1, ARATH/GSTF6, ARATH/GSTU20, ARATH/HPR, ARATH/IAMH1
vacuole (GO:0005773)
- Actions (all rows): {'KEEP_AS_NON_CORE': 14, 'MARK_AS_OVER_ANNOTATED': 10, 'ACCEPT': 7, 'TOO_GENERAL': 7, 'MODIFY': 3, 'REMOVE': 3, 'UNDECIDED': 2}
- Evidence (all rows): {'IEA': 19, 'IBA': 7, 'NAS': 6, 'IDA': 5, 'EXP': 4, 'HDA': 2, 'ISS': 2, 'TAS': 1}
- Sub-compartment kinds, by gene: {'membrane': 4, 'lumen+other': 3, 'other': 3, 'membrane+other': 2, 'lumen+membrane+other': 1}
- Rows with no sub-compartment, actions: {'KEEP_AS_NON_CORE': 11, 'MARK_AS_OVER_ANNOTATED': 10, 'REMOVE': 3, 'UNDECIDED': 1, 'ACCEPT': 1}
- Rows with no sub-compartment, evidence: {'IEA': 11, 'NAS': 6, 'IDA': 3, 'HDA': 2, 'ISS': 2, 'EXP': 2}
- Example genes with only the root term: ARATH/GLDP2, ARATH/JAR1, ARATH/TFL1, EMENI/mstE, GADMO/A0A8C5FPT8, NICAT/NaBBL1_candidate_FOX1_0, NICAT/NaBBL2_candidate_FOX1_2, NICAT/NaBBL_candidate_FOX1_4, NICAT/NaBBL_candidate_FOX2_2, NICAT/NaBBL_candidate_FOX2_4, SCHPO/ayr1, SOLTU/PATB1, yeast/ERG10, yeast/ERG19, yeast/ERG20, yeast/ERG8, yeast/GLG1, yeast/GLG2, yeast/ICL1, yeast/IDI1, yeast/MVD1, yeast/PAH1
autophagosome (GO:0005776)
- Actions (all rows): {'ACCEPT': 61, 'KEEP_AS_NON_CORE': 27, 'MARK_AS_OVER_ANNOTATED': 2, 'REMOVE': 1, 'NEW': 1}
- Evidence (all rows): {'IEA': 32, 'IDA': 30, 'IBA': 22, 'ISS': 5, 'NAS': 2, 'ISO': 1}
- Sub-compartment kinds, by gene: {'membrane': 15, 'other': 2}
- Rows with no sub-compartment, actions: {'ACCEPT': 25, 'KEEP_AS_NON_CORE': 23, 'MARK_AS_OVER_ANNOTATED': 2, 'REMOVE': 1}
- Rows with no sub-compartment, evidence: {'IEA': 23, 'IBA': 15, 'IDA': 7, 'ISS': 3, 'NAS': 2, 'ISO': 1}
- Example genes with only the root term: DICDI/atg1, DROME/Sting, PARTE/A0BFB4, SCHPO/atg13, SCHPO/atg5, SOLTU/JOKA2, human/AMBRA1, human/ATG13, human/ATG5, human/ATG9A, human/ATG9B, human/AUP1, human/BECN1, human/C9orf72, human/CLN3, human/FTH1, human/FTL, human/GRAMD1A, human/HTT, human/MEFV, human/NBR1, human/NCOA4, human/OPTN, human/PIK3C3, human/PIK3R4