SAS; refined (All Genes in which Alternative Splicing Events were located)

Genes541
GO terms1227
Edges:4123
Max GO term frequency:197
Average annotation per gene:7
Generic GO terms (BLUE):60
GO terms not selected in topics (MAGENTA):1092
Count of eliminated edges:982
GO terms occurring in topics:75
Topics threshold:0.03


GO terms occurring in more than one topic and having score >= the threshold at least in one topic (21):

GOGO frequencyTopics
GO:0009507--chloroplast 14015   (0, 2, 6, 7, 10, 11, 13, 14, 15, 20, 21, 25, 26, 27, 28)
GO:0005829--cytosol 8214   (0, 3, 4, 6, 9, 11, 15, 17, 18, 19, 23, 25, 28, 29)
GO:0005524--atp binding 709   (1, 4, 8, 9, 17, 18, 19, 22, 24)
GO:0005886--plasma membrane 858   (0, 1, 3, 11, 15, 22, 24, 28)
GO:0005739--mitochondrion 727   (6, 15, 16, 17, 20, 26, 28)
GO:0046872--metal ion binding 407   (0, 7, 9, 11, 22, 25, 27)
GO:0003677--dna binding 345   (4, 9, 23, 27, 29)
GO:0008270--zinc ion binding 293   (2, 7, 21)
GO:0009570--chloroplast stroma 463   (13, 14, 20)
GO:0055114--oxidation-reduction process 363   (15, 17, 21)
GO:0003729--mrna binding 312   (3, 11)
GO:0006351--transcription, dna-templated 382   (4, 23)
GO:0006355--regulation of transcription, dna-templated 342   (4, 23)
GO:0006468--protein phosphorylation 152   (8, 24)
GO:0009506--plasmodesma 322   (3, 18)
GO:0009535--chloroplast thylakoid membrane 212   (20, 27)
GO:0009793--embryo development ending in seed dormancy 92   (13, 16)


Frequency of GO terms that are eliminated (BLUE 60) or not selected in topics (MAGENTA 79 with frequency >=4):

GOGO frequency
GO:0005634--nucleus 197
GO:0005737--cytoplasm 100
GO:0005515--protein binding 92
GO:0016021--integral component of membrane 78
GO:0003674--molecular_function 73
GO:0008150--biological_process 73
GO:0016020--membrane 50
GO:0005576--extracellular region 38
GO:0003723--RNA binding 36
GO:0003700--transcription factor activity, sequence-specific DNA binding 26
GO:0016301--kinase activity 22
GO:0003676--nucleic acid binding 17
GO:0048046--apoplast 17
GO:0009536--plastid 16
GO:0009409--response to cold 13
GO:0016491--oxidoreductase activity 13
GO:0005575--cellular_component 12
GO:0005507--copper ion binding 11
GO:0009534--chloroplast thylakoid 11
GO:0016787--hydrolase activity 11
GO:0005525--GTP binding 10
GO:0009737--response to abscisic acid 10
GO:0030154--cell differentiation 10
GO:0042742--defense response to bacterium 10
GO:0006397--mRNA processing 9
GO:0008380--RNA splicing 9
GO:0009414--response to water deprivation 9
GO:0009735--response to cytokinin 9
GO:0042802--identical protein binding 9
GO:0005622--intracellular 8
GO:0006457--protein folding 8
GO:0009505--plant-type cell wall 8
GO:0010468--regulation of gene expression 8
GO:0022626--cytosolic ribosome 8
GO:0000166--nucleotide binding 7
GO:0003824--catalytic activity 7
GO:0005681--spliceosomal complex 7
GO:0005802--trans-Golgi network 7
GO:0005840--ribosome 7
GO:0007275--multicellular organism development 7
GO:0009611--response to wounding 7
GO:0009790--embryo development 7
GO:0016740--transferase activity 7
GO:0032259--methylation 7
GO:0003735--structural constituent of ribosome 6
GO:0003924--GTPase activity 6
GO:0005975--carbohydrate metabolic process 6
GO:0006886--intracellular protein transport 6
GO:0007049--cell cycle 6
GO:0009555--pollen development 6
GO:0009753--response to jasmonic acid 6
GO:0015031--protein transport 6
GO:0016607--nuclear speck 6
GO:0030170--pyridoxal phosphate binding 6
GO:0030246--carbohydrate binding 6
GO:0045892--negative regulation of transcription, DNA-templated 6
GO:0048364--root development 6
GO:0000785--chromatin 5
GO:0003682--chromatin binding 5
GO:0005215--transporter activity 5
GO:0005768--endosome 5
GO:0005789--endoplasmic reticulum membrane 5
GO:0006281--DNA repair 5
GO:0006413--translational initiation 5
GO:0006810--transport 5
GO:0006974--cellular response to DNA damage stimulus 5
GO:0008289--lipid binding 5
GO:0008565--protein transporter activity 5
GO:0009553--embryo sac development 5
GO:0009617--response to bacterium 5
GO:0009626--plant-type hypersensitive response 5
GO:0009637--response to blue light 5
GO:0009909--regulation of flower development 5
GO:0043531--ADP binding 5
GO:0045454--cell redox homeostasis 5
GO:0045893--positive regulation of transcription, DNA-templated 5
GO:0001666--response to hypoxia 4
GO:0003746--translation elongation factor activity 4
GO:0003755--peptidyl-prolyl cis-trans isomerase activity 4
GO:0004519--endonuclease activity 4
GO:0004871--signal transducer activity 4
GO:0005578--proteinaceous extracellular matrix 4
GO:0005747--mitochondrial respiratory chain complex I 4
GO:0006099--tricarboxylic acid cycle 4
GO:0006334--nucleosome assembly 4
GO:0006378--mRNA polyadenylation 4
GO:0006629--lipid metabolic process 4
GO:0006813--potassium ion transport 4
GO:0009058--biosynthetic process 4
GO:0009501--amyloplast 4
GO:0009624--response to nematode 4
GO:0009744--response to sucrose 4
GO:0009965--leaf morphogenesis 4
GO:0010073--meristem maintenance 4
GO:0010228--vegetative to reproductive phase transition of meristem 4
GO:0010287--plastoglobule 4
GO:0015297--antiporter activity 4
GO:0015979--photosynthesis 4
GO:0016887--ATPase activity 4
GO:0022625--cytosolic large ribosomal subunit 4
GO:0031225--anchored component of membrane 4
GO:0042626--ATPase activity, coupled to transmembrane movement of substances 4
GO:0048366--leaf development 4
GO:0050897--cobalt ion binding 4
GO:0051082--unfolded protein binding 4
GO:0071555--cell wall organization 4
GO:0080008--Cul4-RING E3 ubiquitin ligase complex 4
GO:0005198--structural molecule activity 3
GO:0005623--cell 3
GO:0008152--metabolic process 3
GO:0008283--cell proliferation 3
GO:0019898--extrinsic component of membrane 3
GO:0022857--transmembrane transporter activity 3
GO:0005199--structural constituent of cell wall 2
GO:0005200--structural constituent of cytoskeleton 2
GO:0007017--microtubule-based process 2
GO:0007623--circadian rhythm 2
GO:0008265--Mo-molybdopterin cofactor sulfurase activity 2
GO:0009055--electron carrier activity 2
GO:0016853--isomerase activity 2
GO:0016874--ligase activity 2
GO:0030234--enzyme regulator activity 2
GO:0031012--extracellular matrix 2
GO:0045735--nutrient reservoir activity 2
GO:0000156--phosphorelay response regulator activity 1
GO:0000384--first spliceosomal transesterification activity 1
GO:0000386--second spliceosomal transesterification activity 1
GO:0003006--developmental process involved in reproduction 1
GO:0004872--receptor activity 1
GO:0005615--extracellular space 1
GO:0006807--nitrogen compound metabolic process 1
GO:0009295--nucleoid 1
GO:0015976--carbon utilization 1
GO:0019239--deaminase activity 1
GO:0019825--oxygen binding 1
GO:0030527--structural constituent of chromatin 1
GO:0031409--pigment binding 1
GO:0040008--regulation of growth 1
GO:0071944--cell periphery 1


All Topics:

Topic #0:
Score: 0.0494GO:0005773--vacuole
Score: 0.0307GO:0005829--cytosol
Score: 0.0304GO:0046872--metal ion binding
Score: 0.0300GO:0005886--plasma membrane
Score: 0.0286GO:0009507--chloroplast
GO terms cooccurrence

Topic #1:
Score: 0.2387GO:0005886--plasma membrane
Score: 0.0704GO:0005524--atp binding
Score: 0.0616GO:0006952--defense response
Score: 0.0343GO:0007165--signal transduction
Score: 0.0318GO:0005774--vacuolar membrane
GO terms cooccurrence

Topic #2:
Score: 0.0309GO:0009507--chloroplast
Score: 0.0301GO:0003743--translation initiation factor activity
Score: 0.0226GO:0008270--zinc ion binding
Score: 0.0226GO:0005618--cell wall
Score: 0.0226GO:0009416--response to light stimulus
GO terms cooccurrence

Topic #3:
Score: 0.0790GO:0003729--mrna binding
Score: 0.0720GO:0005829--cytosol
Score: 0.0546GO:0009506--plasmodesma
Score: 0.0340GO:0005886--plasma membrane
Score: 0.0281GO:0006412--translation
GO terms cooccurrence

Topic #4:
Score: 0.0280GO:0003677--dna binding
Score: 0.0200GO:0005524--atp binding
Score: 0.0188GO:0006351--transcription, dna-templated
Score: 0.0188GO:0006355--regulation of transcription, dna-templated
Score: 0.0124GO:0005829--cytosol
GO terms cooccurrence

Topic #5:
Score: 0.0395GO:0050832--defense response to fungus
Score: 0.0384GO:0055085--transmembrane transport
Score: 0.0265GO:0019538--protein metabolic process
Score: 0.0135GO:0031969--chloroplast membrane
Score: 0.0135GO:0042803--protein homodimerization activity
GO terms cooccurrence

Topic #6:
Score: 0.0281GO:0005739--mitochondrion
Score: 0.0281GO:0009507--chloroplast
Score: 0.0281GO:0046686--response to cadmium ion
Score: 0.0192GO:0005829--cytosol
Score: 0.0188GO:0031969--chloroplast membrane
GO terms cooccurrence

Topic #7:
Score: 0.0609GO:0008270--zinc ion binding
Score: 0.0177GO:0009507--chloroplast
Score: 0.0165GO:0005730--nucleolus
Score: 0.0156GO:0046872--metal ion binding
Score: 0.0156GO:0009826--unidimensional cell growth
GO terms cooccurrence

Topic #8:
Score: 0.0605GO:0005509--calcium ion binding
Score: 0.0570GO:0005524--atp binding
Score: 0.0371GO:0016310--phosphorylation
Score: 0.0272GO:0006468--protein phosphorylation
Score: 0.0249GO:0004672--protein kinase activity
GO terms cooccurrence

Topic #9:
Score: 0.0228GO:0003677--dna binding
Score: 0.0225GO:0005524--atp binding
Score: 0.0225GO:0000790--nuclear chromatin
Score: 0.0220GO:0005829--cytosol
Score: 0.0215GO:0046872--metal ion binding
GO terms cooccurrence

Topic #10:
Score: 0.0519GO:0008168--methyltransferase activity
Score: 0.0402GO:0009507--chloroplast
Score: 0.0210GO:0006508--proteolysis
Score: 0.0210GO:0009658--chloroplast organization
Score: 0.0210GO:0010206--photosystem ii repair
GO terms cooccurrence

Topic #11:
Score: 0.0405GO:0005886--plasma membrane
Score: 0.0271GO:0005829--cytosol
Score: 0.0234GO:0009507--chloroplast
Score: 0.0204GO:0003729--mrna binding
Score: 0.0195GO:0046872--metal ion binding
GO terms cooccurrence

Topic #12:
Score: 0.0353GO:0016567--protein ubiquitination
Score: 0.0265GO:0019005--scf ubiquitin ligase complex
Score: 0.0265GO:0080167--response to karrikin
Score: 0.0178GO:0000139--golgi membrane
Score: 0.0178GO:0016811--hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO terms cooccurrence

Topic #13:
Score: 0.0414GO:0009793--embryo development ending in seed dormancy
Score: 0.0326GO:0009507--chloroplast
Score: 0.0150GO:0009570--chloroplast stroma
Score: 0.0141GO:0005759--mitochondrial matrix
Score: 0.0141GO:0000287--magnesium ion binding
GO terms cooccurrence

Topic #14:
Score: 0.0631GO:0009579--thylakoid
Score: 0.0501GO:0009507--chloroplast
Score: 0.0491GO:0009543--chloroplast thylakoid lumen
Score: 0.0330GO:0009570--chloroplast stroma
Score: 0.0282GO:0031977--thylakoid lumen
GO terms cooccurrence

Topic #15:
Score: 0.0274GO:0005739--mitochondrion
Score: 0.0274GO:0005886--plasma membrane
Score: 0.0267GO:0005829--cytosol
Score: 0.0234GO:0009507--chloroplast
Score: 0.0219GO:0055114--oxidation-reduction process
GO terms cooccurrence

Topic #16:
Score: 0.0365GO:0005794--golgi apparatus
Score: 0.0245GO:0005739--mitochondrion
Score: 0.0152GO:0005654--nucleoplasm
Score: 0.0124GO:0048316--seed development
Score: 0.0124GO:0009793--embryo development ending in seed dormancy
GO terms cooccurrence

Topic #17:
Score: 0.0246GO:0005829--cytosol
Score: 0.0226GO:0005739--mitochondrion
Score: 0.0212GO:0055114--oxidation-reduction process
Score: 0.0159GO:0005524--atp binding
Score: 0.0152GO:0005874--microtubule
GO terms cooccurrence

Topic #18:
Score: 0.0444GO:0005524--atp binding
Score: 0.0242GO:0005829--cytosol
Score: 0.0239GO:0004386--helicase activity
Score: 0.0239GO:0008026--atp-dependent helicase activity
Score: 0.0179GO:0009506--plasmodesma
GO terms cooccurrence

Topic #19:
Score: 0.0269GO:0005829--cytosol
Score: 0.0202GO:0009733--response to auxin
Score: 0.0158GO:0005524--atp binding
Score: 0.0135GO:0009751--response to salicylic acid
Score: 0.0135GO:0000398--mrna splicing, via spliceosome
GO terms cooccurrence

Topic #20:
Score: 0.2374GO:0009507--chloroplast
Score: 0.1031GO:0009570--chloroplast stroma
Score: 0.0944GO:0009941--chloroplast envelope
Score: 0.0582GO:0005739--mitochondrion
Score: 0.0445GO:0009535--chloroplast thylakoid membrane
GO terms cooccurrence

Topic #21:
Score: 0.0788GO:0055114--oxidation-reduction process
Score: 0.0304GO:0009507--chloroplast
Score: 0.0297GO:0008270--zinc ion binding
Score: 0.0297GO:0006511--ubiquitin-dependent protein catabolic process
Score: 0.0199GO:0005777--peroxisome
GO terms cooccurrence

Topic #22:
Score: 0.0321GO:0005886--plasma membrane
Score: 0.0321GO:0005516--calmodulin binding
Score: 0.0309GO:0046872--metal ion binding
Score: 0.0258GO:0005524--atp binding
Score: 0.0194GO:0004722--protein serine/threonine phosphatase activity
GO terms cooccurrence

Topic #23:
Score: 0.1001GO:0006355--regulation of transcription, dna-templated
Score: 0.0957GO:0006351--transcription, dna-templated
Score: 0.0803GO:0003677--dna binding
Score: 0.0309GO:0005829--cytosol
Score: 0.0286GO:0043565--sequence-specific dna binding
GO terms cooccurrence

Topic #24:
Score: 0.0794GO:0005524--atp binding
Score: 0.0460GO:0005886--plasma membrane
Score: 0.0450GO:0006468--protein phosphorylation
Score: 0.0420GO:0004674--protein serine/threonine kinase activity
Score: 0.0267GO:0004672--protein kinase activity
GO terms cooccurrence

Topic #25:
Score: 0.0284GO:0005829--cytosol
Score: 0.0240GO:0009507--chloroplast
Score: 0.0196GO:0009908--flower development
Score: 0.0194GO:0046872--metal ion binding
Score: 0.0143GO:0005777--peroxisome
GO terms cooccurrence

Topic #26:
Score: 0.1774GO:0005739--mitochondrion
Score: 0.0565GO:0005783--endoplasmic reticulum
Score: 0.0357GO:0006979--response to oxidative stress
Score: 0.0286GO:0016757--transferase activity, transferring glycosyl groups
Score: 0.0235GO:0009507--chloroplast
GO terms cooccurrence

Topic #27:
Score: 0.0387GO:0009507--chloroplast
Score: 0.0275GO:0046983--protein dimerization activity
Score: 0.0189GO:0003677--dna binding
Score: 0.0184GO:0046872--metal ion binding
Score: 0.0184GO:0009535--chloroplast thylakoid membrane
GO terms cooccurrence

Topic #28:
Score: 0.0300GO:0005739--mitochondrion
Score: 0.0238GO:0005886--plasma membrane
Score: 0.0183GO:0009507--chloroplast
Score: 0.0173GO:0005730--nucleolus
Score: 0.0173GO:0005829--cytosol
GO terms cooccurrence

Topic #29:
Score: 0.0222GO:0003677--dna binding
Score: 0.0195GO:0005829--cytosol
Score: 0.0195GO:0009651--response to salt stress
Score: 0.0195GO:0030042--actin filament depolymerization
Score: 0.0195GO:0003779--actin binding
GO terms cooccurrence