81-SAR-SAS; refined (List of inflorescence SAR genes with identified alternative splicing events)

Genes81
GO terms316
Edges:594
Max GO term frequency:43
Average annotation per gene:7
Generic GO terms (BLUE):32
GO terms not selected in topics (MAGENTA):203
Count of eliminated edges:160
GO terms occurring in topics:81
Topics threshold:0.045

GO terms occurring in more than one topic and having score >= the threshold at least in one topic (23):

GOGO frequencyTopics
Interest Eliminate   |    GO:0006952--defense response 57   (5, 6, 7, 11, 12, 13, 15)
Interest Eliminate   |    GO:0009507--chloroplast 117   (0, 1, 2, 4, 16, 18, 20)
Interest Eliminate   |    GO:0006355--regulation of transcription, dna-templated 106   (3, 18, 21, 24, 26, 28)
Interest Eliminate   |    GO:0005524--atp binding 125   (11, 14, 17, 23, 27)
Interest Eliminate   |    GO:0006351--transcription, dna-templated 105   (3, 4, 18, 21, 24)
Interest Eliminate   |    GO:0005886--plasma membrane 104   (0, 10, 23, 27)
Interest Eliminate   |    GO:0005829--cytosol 93   (9, 14, 19)
Interest Eliminate   |    GO:0006468--protein phosphorylation 43   (14, 17, 23)
Interest Eliminate   |    GO:0046872--metal ion binding 73   (3, 4, 8)
Interest Eliminate   |    GO:0000398--mrna splicing, via spliceosome 42   (8, 29)
Interest Eliminate   |    GO:0003677--dna binding 62   (8, 21)
Interest Eliminate   |    GO:0003729--mrna binding 32   (18, 22)
Interest Eliminate   |    GO:0004674--protein serine/threonine kinase activity 32   (14, 17)
Interest Eliminate   |    GO:0005509--calcium ion binding 42   (0, 23)
Interest Eliminate   |    GO:0005654--nucleoplasm 42   (9, 29)
Interest Eliminate   |    GO:0005739--mitochondrion 72   (1, 9)
Interest Eliminate   |    GO:0005794--golgi apparatus 52   (2, 22)

Frequency of GO terms that are eliminated (BLUE 32) or not selected in topics (MAGENTA 11 with frequency >=2):

GOGO frequency
Interest    Eliminate   |    GO:0005634--nucleus 43
Interest    Eliminate   |    GO:0005737--cytoplasm 19
Interest    Eliminate   |    GO:0008150--biological_process 15
Interest    Eliminate   |    GO:0003723--RNA binding 12
Interest    Eliminate   |    GO:0005515--protein binding 12
Interest    Eliminate   |    GO:0003674--molecular_function 10
Interest    Eliminate   |    GO:0003676--nucleic acid binding 6
Interest    Eliminate   |    GO:0016021--integral component of membrane 6
Interest    Eliminate   |    GO:0016301--kinase activity 5
Interest    Eliminate   |    GO:0003700--transcription factor activity, sequence-specific DNA binding 4
Interest    Eliminate   |    GO:0016787--hydrolase activity 3
Interest    Eliminate   |    GO:0003824--catalytic activity 2
Interest    Eliminate   |    GO:0005576--extracellular region 2
Interest    Eliminate   |    GO:0005622--intracellular 2
Interest    Eliminate   |    GO:0006979--response to oxidative stress 2
Interest    Eliminate   |    GO:0008565--protein transporter activity 2
Interest    Eliminate   |    GO:0009414--response to water deprivation 2
Interest    Eliminate   |    GO:0009553--embryo sac development 2
Interest    Eliminate   |    GO:0009555--pollen development 2
Interest    Eliminate   |    GO:0009617--response to bacterium 2
Interest    Eliminate   |    GO:0009658--chloroplast organization 2
Interest    Eliminate   |    GO:0009733--response to auxin 2
Interest    Eliminate   |    GO:0009965--leaf morphogenesis 2
Interest    Eliminate   |    GO:0010073--meristem maintenance 2
Interest    Eliminate   |    GO:0016020--membrane 2
Interest    Eliminate   |    GO:0045893--positive regulation of transcription, DNA-templated 2
Interest    Eliminate   |    GO:0000156--phosphorelay response regulator activity 1
Interest    Eliminate   |    GO:0000384--first spliceosomal transesterification activity 1
Interest    Eliminate   |    GO:0003682--chromatin binding 1
Interest    Eliminate   |    GO:0004871--signal transducer activity 1
Interest    Eliminate   |    GO:0004872--receptor activity 1
Interest    Eliminate   |    GO:0005198--structural molecule activity 1
Interest    Eliminate   |    GO:0005575--cellular_component 1
Interest    Eliminate   |    GO:0005623--cell 1
Interest    Eliminate   |    GO:0006457--protein folding 1
Interest    Eliminate   |    GO:0007017--microtubule-based process 1
Interest    Eliminate   |    GO:0007623--circadian rhythm 1
Interest    Eliminate   |    GO:0008152--metabolic process 1
Interest    Eliminate   |    GO:0008289--lipid binding 1
Interest    Eliminate   |    GO:0016740--transferase activity 1
Interest    Eliminate   |    GO:0019898--extrinsic component of membrane 1
Interest    Eliminate   |    GO:0030246--carbohydrate binding 1
Interest    Eliminate   |    GO:0048046--apoplast 1

All Topics:

Topic #0: Interesting topic
Score: 0.1027GO:0005886--plasma membrane
Score: 0.0350GO:0005509--calcium ion binding
Score: 0.0350GO:0016042--lipid catabolic process
Score: 0.0350GO:0009507--chloroplast
Score: 0.0350GO:0046470--phosphatidylcholine metabolic process
GO terms cooccurrence

Topic #1: Interesting topic
Score: 0.1346GO:0005739--mitochondrion
Score: 0.0902GO:0009507--chloroplast
Score: 0.0459GO:0005783--endoplasmic reticulum
Score: 0.0459GO:0010584--pollen exine formation
Score: 0.0459GO:0019200--carbohydrate kinase activity
GO terms cooccurrence

Topic #2: Interesting topic
Score: 0.0665GO:0005794--golgi apparatus
Score: 0.0665GO:0005802--trans-golgi network
Score: 0.0665GO:0005768--endosome
Score: 0.0665GO:0009011--starch synthase activity
Score: 0.0665GO:0009507--chloroplast
GO terms cooccurrence

Topic #3: Interesting topic
Score: 0.0318GO:0046872--metal ion binding
Score: 0.0318GO:0006355--regulation of transcription, dna-templated
Score: 0.0318GO:0006351--transcription, dna-templated
Score: 0.0318GO:0009908--flower development
Score: 0.0318GO:0000785--chromatin
GO terms cooccurrence

Topic #4: Interesting topic
Score: 0.0395GO:0009507--chloroplast
Score: 0.0395GO:0009790--embryo development
Score: 0.0395GO:0046872--metal ion binding
Score: 0.0395GO:0006351--transcription, dna-templated
Score: 0.0201GO:0009941--chloroplast envelope
GO terms cooccurrence

Topic #8: Interesting topic
Score: 0.0902GO:0016607--nuclear speck
Score: 0.0459GO:0046872--metal ion binding
Score: 0.0459GO:0003677--dna binding
Score: 0.0459GO:0000398--mrna splicing, via spliceosome
Score: 0.0459GO:0006406--mrna export from nucleus
GO terms cooccurrence

Topic #9: Interesting topic
Score: 0.1242GO:0005829--cytosol
Score: 0.0255GO:0004519--endonuclease activity
Score: 0.0255GO:0005739--mitochondrion
Score: 0.0255GO:0005654--nucleoplasm
Score: 0.0255GO:0005730--nucleolus
GO terms cooccurrence

Topic #10: Interesting topic
Score: 0.0375GO:0005773--vacuole
Score: 0.0375GO:0009505--plant-type cell wall
Score: 0.0375GO:0005886--plasma membrane
Score: 0.0375GO:0006013--mannose metabolic process
Score: 0.0375GO:0004559--alpha-mannosidase activity
GO terms cooccurrence

Topic #11: Interesting topic
Score: 0.1644GO:0006952--defense response
Score: 0.1236GO:0005524--atp binding
Score: 0.1236GO:0043531--adp binding
Score: 0.0829GO:0007165--signal transduction
Score: 0.0421GO:2000071--regulation of defense response by callose deposition
GO terms cooccurrence

Topic #14: Interesting topic
Score: 0.0503GO:0005829--cytosol
Score: 0.0503GO:0005524--atp binding
Score: 0.0503GO:0000139--golgi membrane
Score: 0.0503GO:0004674--protein serine/threonine kinase activity
Score: 0.0503GO:0006468--protein phosphorylation
GO terms cooccurrence

Topic #16: Interesting topic
Score: 0.0764GO:0009507--chloroplast
Score: 0.0764GO:0048316--seed development
Score: 0.0764GO:0000373--group ii intron splicing
Score: 0.0025GO:0006611--protein export from nucleus
Score: 0.0025GO:0006629--lipid metabolic process
GO terms cooccurrence

Topic #17: Interesting topic
Score: 0.0503GO:0005524--atp binding
Score: 0.0503GO:0004674--protein serine/threonine kinase activity
Score: 0.0503GO:0006468--protein phosphorylation
Score: 0.0503GO:0004672--protein kinase activity
Score: 0.0503GO:0055028--cortical microtubule
GO terms cooccurrence

Topic #18: Interesting topic
Score: 0.0738GO:0003729--mrna binding
Score: 0.0375GO:0009507--chloroplast
Score: 0.0375GO:0006355--regulation of transcription, dna-templated
Score: 0.0375GO:0071482--cellular response to light stimulus
Score: 0.0375GO:0006351--transcription, dna-templated
GO terms cooccurrence

Topic #19: Interesting topic
Score: 0.0428GO:0005829--cytosol
Score: 0.0217GO:0008536--ran gtpase binding
Score: 0.0217GO:0005525--gtp binding
Score: 0.0217GO:0009846--pollen germination
Score: 0.0217GO:0009860--pollen tube growth
GO terms cooccurrence

Topic #20: Interesting topic
Score: 0.0542GO:0009507--chloroplast
Score: 0.0542GO:0071555--cell wall organization
Score: 0.0275GO:0016310--phosphorylation
Score: 0.0275GO:0015969--guanosine tetraphosphate metabolic process
Score: 0.0275GO:0008728--gtp diphosphokinase activity
GO terms cooccurrence

Topic #21: Interesting topic
Score: 0.0529GO:0006355--regulation of transcription, dna-templated
Score: 0.0529GO:0006351--transcription, dna-templated
Score: 0.0529GO:0003677--dna binding
Score: 0.0529GO:0000082--g1/s transition of mitotic cell cycle
Score: 0.0529GO:0000981--rna polymerase ii transcription factor activity, sequence-specific dna binding
GO terms cooccurrence

Topic #22: Interesting topic
Score: 0.1309GO:0008270--zinc ion binding
Score: 0.0665GO:0005794--golgi apparatus
Score: 0.0665GO:0003729--mrna binding
Score: 0.0665GO:0009920--cell plate formation involved in plant-type cell wall biogenesis
Score: 0.0021GO:2000280--regulation of root development
GO terms cooccurrence

Topic #23: Interesting topic
Score: 0.0480GO:0005886--plasma membrane
Score: 0.0480GO:0005524--atp binding
Score: 0.0480GO:0005509--calcium ion binding
Score: 0.0480GO:0006468--protein phosphorylation
Score: 0.0480GO:0004683--calmodulin-dependent protein kinase activity
GO terms cooccurrence

Topic #24: Interesting topic
Score: 0.0606GO:0006355--regulation of transcription, dna-templated
Score: 0.0606GO:0006351--transcription, dna-templated
Score: 0.0308GO:0030154--cell differentiation
Score: 0.0308GO:0009908--flower development
Score: 0.0308GO:0046983--protein dimerization activity
GO terms cooccurrence

Topic #25: Interesting topic
Score: 0.0275GO:0030154--cell differentiation
Score: 0.0275GO:0006378--mrna polyadenylation
Score: 0.0275GO:0010087--phloem or xylem histogenesis
Score: 0.0275GO:0080060--integument development
Score: 0.0275GO:0010075--regulation of meristem growth
GO terms cooccurrence

Topic #26: Interesting topic
Score: 0.0490GO:0006355--regulation of transcription, dna-templated
Score: 0.0249GO:0045944--positive regulation of transcription from rna polymerase ii promoter
Score: 0.0249GO:0016538--cyclin-dependent protein serine/threonine kinase regulator activity
Score: 0.0249GO:0009637--response to blue light
Score: 0.0249GO:0051726--regulation of cell cycle
GO terms cooccurrence

Topic #27: Interesting topic
Score: 0.0589GO:0005886--plasma membrane
Score: 0.0589GO:0005524--atp binding
Score: 0.0589GO:0005774--vacuolar membrane
Score: 0.0589GO:0000325--plant-type vacuole
Score: 0.0589GO:0055085--transmembrane transport
GO terms cooccurrence

Topic #28: Interesting topic
Score: 0.0209GO:0009909--regulation of flower development
Score: 0.0209GO:0030154--cell differentiation
Score: 0.0209GO:0006355--regulation of transcription, dna-templated
Score: 0.0209GO:0009908--flower development
Score: 0.0209GO:0045892--negative regulation of transcription, dna-templated
GO terms cooccurrence

Topic #29: Interesting topic
Score: 0.0625GO:0005654--nucleoplasm
Score: 0.0625GO:0009793--embryo development ending in seed dormancy
Score: 0.0625GO:0000398--mrna splicing, via spliceosome
Score: 0.0625GO:0006397--mrna processing
Score: 0.0625GO:0044030--regulation of dna methylation
GO terms cooccurrence