SR45-upregulated; refined

Genes89
GO terms247
Edges:491
Max GO term frequency:32
Average annotation per gene:5
Generic GO terms (BLUE):25
GO terms not selected in topics (MAGENTA):136
Count of eliminated edges:152
GO terms occurring in topics:88
Topics threshold:0.05

GO terms occurring in more than one topic and having score >= the threshold at least in one topic (25):

GOGO frequencyTopics
GO:0009507--chloroplast 155   (7, 14, 15, 25, 26)
GO:0005886--plasma membrane 94   (4, 12, 19, 22)
GO:0005739--mitochondrion 93   (0, 6, 23)
GO:0005794--golgi apparatus 43   (5, 25, 29)
GO:0046872--metal ion binding 83   (0, 9, 15)
GO:0055114--oxidation-reduction process 73   (8, 15, 25)
GO:0003677--dna binding 82   (9, 17)
GO:0005507--copper ion binding 22   (9, 22)
GO:0005524--atp binding 72   (12, 21)
GO:0006355--regulation of transcription, dna-templated 72   (17, 21)
GO:0006810--transport 52   (6, 19)
GO:0016757--transferase activity, transferring glycosyl groups 32   (16, 29)

Frequency of GO terms that are eliminated (BLUE 25) or not selected in topics (MAGENTA 0 with frequency >=4):

GOGO frequency
GO:0005634--nucleus 32
GO:0008150--biological_process 23
GO:0003674--molecular_function 17
GO:0005737--cytoplasm 12
GO:0016021--integral component of membrane 10
GO:0005576--extracellular region 7
GO:0016020--membrane 7
GO:0003700--sequence-specific DNA binding transcription factor activity 6
GO:0003723--RNA binding 6
GO:0003676--nucleic acid binding 5
GO:0005215--transporter activity 5
GO:0005515--protein binding 4
GO:0003824--catalytic activity 2
GO:0005575--cellular_component 2
GO:0016491--oxidoreductase activity 2
GO:0022857--transmembrane transporter activity 2
GO:0048046--apoplast 2
GO:0003682--chromatin binding 1
GO:0003735--structural constituent of ribosome 1
GO:0007017--microtubule-based process 1
GO:0008152--metabolic process 1
GO:0016740--transferase activity 1
GO:0016787--hydrolase activity 1
GO:0016829--lyase activity 1
GO:0045177--apical part of cell 1

All Topics:

Topic #0:
Score: 0.0845GO:0005739--mitochondrion
Score: 0.0845GO:0046872--metal ion binding
Score: 0.0845GO:0009164--nucleoside catabolic process
Score: 0.0845GO:0016818--hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Score: 0.0027GO:2000024--regulation of leaf development
GO terms cooccurrence

Topic #2:
Score: 0.0567GO:0000139--golgi membrane
Score: 0.0567GO:0006486--protein glycosylation
Score: 0.0567GO:0005789--endoplasmic reticulum membrane
Score: 0.0567GO:0005783--endoplasmic reticulum
Score: 0.0567GO:0004571--mannosyl-oligosaccharide 1,2-alpha-mannosidase activity
GO terms cooccurrence

Topic #3:
Score: 0.0537GO:0015031--protein transport
Score: 0.0537GO:0030150--protein import into mitochondrial matrix
Score: 0.0537GO:0009527--plastid outer membrane
Score: 0.0537GO:0005744--mitochondrial inner membrane presequence translocase complex
Score: 0.0537GO:0015171--amino acid transmembrane transporter activity
GO terms cooccurrence

Topic #5:
Score: 0.0537GO:0042742--defense response to bacterium
Score: 0.0537GO:0005794--golgi apparatus
Score: 0.0537GO:0045824--negative regulation of innate immune response
Score: 0.0537GO:0003680--at dna binding
Score: 0.0537GO:0045087--innate immune response
GO terms cooccurrence

Topic #6:
Score: 0.1598GO:0005739--mitochondrion
Score: 0.0410GO:0009941--chloroplast envelope
Score: 0.0410GO:0006810--transport
Score: 0.0410GO:0009536--plastid
Score: 0.0410GO:0009658--chloroplast organization
GO terms cooccurrence

Topic #7:
Score: 0.0920GO:0009506--plasmodesma
Score: 0.0920GO:0005773--vacuole
Score: 0.0920GO:0009507--chloroplast
Score: 0.0030GO:2000024--regulation of leaf development
Score: 0.0030GO:0006857--oligopeptide transport
GO terms cooccurrence

Topic #8:
Score: 0.0941GO:0055114--oxidation-reduction process
Score: 0.0321GO:0005975--carbohydrate metabolic process
Score: 0.0321GO:0050661--nadp binding
Score: 0.0321GO:0006006--glucose metabolic process
Score: 0.0321GO:0006096--glycolytic process
GO terms cooccurrence

Topic #11:
Score: 0.0775GO:0000166--nucleotide binding
Score: 0.0775GO:0080008--cul4-ring e3 ubiquitin ligase complex
Score: 0.0394GO:0009941--chloroplast envelope
Score: 0.0394GO:0009536--plastid
Score: 0.0394GO:0006886--intracellular protein transport
GO terms cooccurrence

Topic #12:
Score: 0.1662GO:0005524--atp binding
Score: 0.0845GO:0005886--plasma membrane
Score: 0.0845GO:0004702--receptor signaling protein serine/threonine kinase activity
Score: 0.0027GO:0005983--starch catabolic process
Score: 0.0027GO:0006006--glucose metabolic process
GO terms cooccurrence

Topic #14:
Score: 0.0651GO:0000724--double-strand break repair via homologous recombination
Score: 0.0651GO:0009507--chloroplast
Score: 0.0331GO:0009853--photorespiration
Score: 0.0331GO:0043879--glycolate transmembrane transporter activity
Score: 0.0331GO:0005774--vacuolar membrane
GO terms cooccurrence

Topic #15:
Score: 0.0594GO:0009507--chloroplast
Score: 0.0594GO:0009733--response to auxin
Score: 0.0302GO:0055114--oxidation-reduction process
Score: 0.0302GO:0046872--metal ion binding
Score: 0.0302GO:1901601--strigolactone biosynthetic process
GO terms cooccurrence

Topic #16:
Score: 0.0537GO:0052689--carboxylic ester hydrolase activity
Score: 0.0537GO:0016298--lipase activity
Score: 0.0537GO:0016757--transferase activity, transferring glycosyl groups
Score: 0.0537GO:0015020--glucuronosyltransferase activity
Score: 0.0537GO:0043231--intracellular membrane-bounded organelle
GO terms cooccurrence

Topic #17:
Score: 0.1993GO:0003677--dna binding
Score: 0.1993GO:0006351--transcription, dna-templated
Score: 0.1993GO:0006355--regulation of transcription, dna-templated
Score: 0.0016GO:2000024--regulation of leaf development
Score: 0.0016GO:0006886--intracellular protein transport
GO terms cooccurrence

Topic #19:
Score: 0.0958GO:0005886--plasma membrane
Score: 0.0958GO:0006810--transport
Score: 0.0487GO:0006979--response to oxidative stress
Score: 0.0487GO:0009636--response to toxic substance
Score: 0.0487GO:0004364--glutathione transferase activity
GO terms cooccurrence

Topic #20:
Score: 0.0379GO:0008508--bile acid:sodium symporter activity
Score: 0.0379GO:0006814--sodium ion transport
Score: 0.0379GO:0009753--response to jasmonic acid
Score: 0.0379GO:0019761--glucosinolate biosynthetic process
Score: 0.0379GO:0006098--pentose-phosphate shunt
GO terms cooccurrence

Topic #21:
Score: 0.1005GO:0006355--regulation of transcription, dna-templated
Score: 0.0511GO:0005524--atp binding
Score: 0.0511GO:0006260--dna replication
Score: 0.0511GO:0010385--double-stranded methylated dna binding
Score: 0.0511GO:0008270--zinc ion binding
GO terms cooccurrence

Topic #22:
Score: 0.0747GO:0005886--plasma membrane
Score: 0.0379GO:0005507--copper ion binding
Score: 0.0379GO:0005975--carbohydrate metabolic process
Score: 0.0379GO:0004556--alpha-amylase activity
Score: 0.0379GO:0005983--starch catabolic process
GO terms cooccurrence

Topic #23:
Score: 0.0487GO:0005739--mitochondrion
Score: 0.0487GO:0005654--nucleoplasm
Score: 0.0487GO:0048768--root hair cell tip growth
Score: 0.0487GO:0008526--phosphatidylinositol transporter activity
Score: 0.0487GO:0009932--cell tip growth
GO terms cooccurrence

Topic #24:
Score: 0.0245GO:0048868--pollen tube development
Score: 0.0245GO:0006096--glycolytic process
Score: 0.0245GO:0009409--response to cold
Score: 0.0245GO:0035024--negative regulation of rho protein signal transduction
Score: 0.0245GO:0004396--hexokinase activity
GO terms cooccurrence

Topic #25:
Score: 0.0561GO:0009507--chloroplast
Score: 0.0285GO:0055114--oxidation-reduction process
Score: 0.0285GO:0005794--golgi apparatus
Score: 0.0285GO:0005829--cytosol
Score: 0.0285GO:2000024--regulation of leaf development
GO terms cooccurrence

Topic #29:
Score: 0.1364GO:0006952--defense response
Score: 0.0915GO:0009807--lignan biosynthetic process
Score: 0.0465GO:0005794--golgi apparatus
Score: 0.0465GO:0016757--transferase activity, transferring glycosyl groups
Score: 0.0465GO:0008378--galactosyltransferase activity
GO terms cooccurrence