CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Contig9642_at

Gene name
Homology with Arabidopsis Similar to At4g27960: UBC9 (UBIQUITIN CONJUGATING ENZYME 9) (HF=1e-13)

Module size 6 genes

NF 0.56

%ile 77.1

Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. Ev AGI code Arabidopsis gene name O.I. H.G. S.X. Other DB
0.50 66.9 0.95 Contig9642_at Contig9642 - - 1e-13 At4g27960 UBC9 (UBIQUITIN CONJUGATING ENZYME 9) O.I. H.G. S.X.
0.71 87.1 0.96 Contig9200_at Contig9200 - - 6e-1 At5g10230 ANNAT7 (ANNEXIN ARABIDOPSIS 7) O.I. H.G. S.X.
0.61 78.7 0.96 Contig1056_s_at Contig1056 - - 5e-140 At4g05050 UBQ11 (UBIQUITIN 11) O.I. H.G. S.X.
0.46 61.0 0.96 Contig6616_at Contig6616 - - 1e-57 At4g35260 IDH1 (ISOCITRATE DEHYDROGENASE 1) O.I. H.G. S.X.
0.46 61.0 0.96 Contig12434_at Contig12434 - - 2e-6 At4g30930 NFD1 (NUCLEAR FUSION DEFECTIVE 1) O.I. H.G. S.X.
0.44 58.9 0.95 Contig13988_at Contig13988 - - 5e-4 At4g24020 NLP7 (NIN LIKE PROTEIN 7) O.I. H.G. S.X.

Click More genes

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
9.5 99.0 GSM261045 after 3 days in mannitol medium rep1 GSE10330 Transcriptome analysis of barley anthers: effect of mannitol treatment on microspore embryogenesis
8.4 98.8 GSM215732 gibberellin plus Yariv-reagent treatment rep2 GSE8712 The effects of Yariv-reagent on barley aleurone GA signaling
7.5 98.6 GSM419980 Awn_Rep3 GSE16754 Comparative transcriptional profiling of organs of the barley spike
7.5 98.6 GSM440971 Control awn_Rep3 GSE17669 Gene expression in the barley spike during drought stress
7.5 98.6 GSM261046 after 3 days in mannitol medium rep2 GSE10330 Transcriptome analysis of barley anthers: effect of mannitol treatment on microspore embryogenesis
6.3 98.1 GSM419979 Awn_Rep2 GSE16754 Comparative transcriptional profiling of organs of the barley spike
6.3 98.1 GSM440970 Control awn_Rep2 GSE17669 Gene expression in the barley spike during drought stress
6.1 98.0 GSM146379 Maythorpe shoot Salt, biological rep 2 GSE6325 Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise
5.9 97.9 GSM419978 Awn_Rep1 GSE16754 Comparative transcriptional profiling of organs of the barley spike
5.9 97.9 GSM440969 Control awn_Rep1 GSE17669 Gene expression in the barley spike during drought stress

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At4g27960, orthologous to the query gene, Contig9642_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
0.55 70.6 At4g27960 828909 UBC9 (UBIQUITIN CONJUGATING ENZYME 9) ubiquitin conjugating enzyme O.I. H.G. S.X.
0.41 52.4 At1g78040 844139 pollen Ole e 1 allergen and extensin family protein F:molecular_function unknown;P:in 10 processes;C:endomembrane system;P O.I. H.G. S.X.
0.39 48.4 At3g48140 823969 senescence-associated protein, putative F:molecular_function unknown;P:leaf senescence;C:endomembrane system;P O.I. H.G. S.X.
0.39 48.4 At3g08580 820005 AAC1 (ADP/ATP CARRIER 1) mitochondrial ADP/ATP carrier O.I. H.G. S.X.
0.38 46.7 At3g16640 820916 TCTP (TRANSLATIONALLY CONTROLLED TUMOR PROTEIN) Encodes a protein homologous to translationally controlled tumor protein (TCTP) from Drosophila. In flies, TCTP functions guanine nucleotide exchange factor in the TOR signaling pathway. TCTP is expressed throughout the plant with highest levels seen in meristematic regions of the shoot and root. Loss of function alleles are not transmitted through the male gametophyte due to defects in pollen tube growth. Hypomorphs, generated through RNAi, are dwarf and have smaller cells. These plants also have defects in lateral and primary root growth as well as root hair growth. The phenotypes are similar to TOR mutants suggesting that TCTP functions in the is pathway in Arabidopsis as well. O.I. H.G. S.X.
0.38 46.7 At4g29350 829056 PFN2 (PROFILIN 2) Encodes profilin2, a low-molecular weight, actin monomer-binding protein that regulates the organization of actin cytoskeleton. Expressed in vegetative organs. The first intron of PRF2 enhances gene expression. O.I. H.G. S.X.
0.36 43.6 At5g64400 836561 - F:molecular_function unknown;P:biological_process unknown;C:unknown;MFPOB O.I. H.G. S.X.
0.35 41.6 At1g04410 839527 malate dehydrogenase, cytosolic, putative F:in 6 functions;P:response to cadmium ion, response to salt stress;C:in 7 components;BOMPFA O.I. H.G. S.X.
0.32 35.7 At1g13440 837904 GAPC2 (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C2) F:NAD or NADH binding, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity, binding, catalytic activity, glyceraldehyde-3-phosphate dehydrogenase activity;P:response to oxidative stress, response to cadmium ion, gluconeogenesis, defense response to bacterium, glycolysis;C:in 8 components;BOPFMA O.I. H.G. S.X.
0.29 30.3 At1g26630 839203 FBR12 (FUMONISIN B1-RESISTANT12) Eukaryotic translation initiation factor 5A-2. Involved in programmed cell death triggered as a response to pseudomonas syringae infection. Loss of function mutants are more resistant to infection. O.I. H.G. S.X.
0.29 30.3 At4g37830 829939 cytochrome c oxidase-related F:cytochrome-c oxidase activity;P:unknown;C:mitochondrion;MPO O.I. H.G. S.X.
0.29 30.3 At5g48810 834939 CB5-D (CYTOCHROME B5 ISOFORM D) Encodes a cytochrome b5 isoform that localizes to the ER. The C-terminal portion of the protein appears to be capable of inserting into a plant microsomal membrane in vitro and the protein appears to be subject to glycosylation. O.I. H.G. S.X.
0.28 30.3 At2g38130 818391 ATMAK3 Encodes the Arabidopsis homolog of the yeast protein MAK3, a component of the N-terminal acetyltransferase complex C. In mutant plants, synthesis of plastome-encoded photosystem II core proteins D1 and CP47 is affected resulting in fewer thylakoid multiprotein complexes. O.I. H.G. S.X.
0.27 26.2 At1g49140 841337 NADH-ubiquinone oxidoreductase-related F:unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPM O.I. H.G. S.X.
0.26 24.4 At4g22310 828326 unknown protein F:unknown;P:biological_process unknown;C:mitochondrion;MFPO O.I. H.G. S.X.
0.24 20.7 At2g47170 819330 ARF1A1C Gene encoding ADP-ribosylation factor and similar to other ARFs and ARF-like proteins. Members of this family are known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct. O.I. H.G. S.X.
0.23 19.3 At4g13940 827028 MEE58 (MATERNAL EFFECT EMBRYO ARREST 58) Encodes a S-adenosyl-L-homocysteine hydrolase required for DNA methylation-dependent gene silencing. O.I. H.G. S.X.
0.21 15.8 At5g53560 835438 CB5-E (CYTOCHROME B5 ISOFORM E) Encodes a cytochrome b5 isoform that can be reduced by AtCBR, a cytochrome b5 reductase. O.I. H.G. S.X.

Select a plant to compare co-expressed genes between species.
Glycine_max
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays

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