Co-expression analysis

Gene ID At1g32610
Gene name hydroxyproline-rich glycoprotein family protein
Module size 5 genes
NF 0.49
%ile 69.2



Co-expression network

pink confeito: Transcription factor, green bicone: Binding protein, red cone: Enzyme protein, blue sphere: Other protein
large node: VF over 0.50, middle node: over 0.25, small node: below 0.25



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. O.I. H.G. S.X. Other DB
0.6781.61.00At1g32610840156hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOVBO.I.H.G.S.X.
0.6781.60.92At4g14590827107emb2739 (embryo defective 2739)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.5773.80.92At4g29560829077unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO.I.H.G.S.X.
0.5065.30.91At2g33760817942pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3235.70.91At1g30010839880intron maturase, type II family proteinF:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:unknown;BPOFAMVO.I.H.G.S.X.

VF%ileCCGene IDRepr. IDGene nameFunc.O.I.H.G.S.X.Other DB
0.6781.60.90At3g06600819839unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6781.60.87At3g45440823682lectin protein kinase family proteinF:carbohydrate binding, kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.6781.60.85At1g12630837819DNA binding / transcription activator/ transcription factorencodes a member of the DREB subfamily A-4 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 17 members in this subfamily including TINY.O.I.H.G.S.X.
0.6176.70.86At3g05480819713RAD9Involved in the regulation of DNA damage repair and homologous recombination.O.I.H.G.S.X.
0.6075.70.85At1g31840840074-F:unknown;P:unknown;C:endomembrane system;POFMBAO.I.H.G.S.X.
0.6075.70.85At1g31240840012DNA bindingF:DNA binding;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X.
0.5773.80.88At4g39440830099unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMO.I.H.G.S.X.
0.5773.80.87At1g642503767631transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.5673.00.89At1g74350843776intron maturase, type II family proteinF:RNA binding, RNA-directed DNA polymerase activity;P:RNA-dependent DNA replication, RNA splicing;C:cellular_component unknown;BPOFAMO.I.H.G.S.X.
0.5570.60.91At1g55970842048HAC4 (HISTONE ACETYLTRANSFERASE OF THE CBP FAMILY 4)HAC4 is most likely to be an expressed pseudogene that lacks HAT function. there is a single nucleotide deletion in both the HAC4 genomic and cDNA sequences relative to its homologs. The resulting frameshift within the open reading frame causes a stop codon to occur within the predicted acetyltransferase catalytic domain.O.I.H.G.S.X.
0.5570.60.87At5g12280831103RNA bindingF:RNA binding;P:protein modification process, RNA processing;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.5368.60.90At4g13330826963unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMBOO.I.H.G.S.X.
0.5065.30.88At4g25270828630pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBO.I.H.G.S.X.
0.5065.30.89At2g47820819394unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBFPVO.I.H.G.S.X.
0.5065.30.89At4g21880828277-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POMFBAO.I.H.G.S.X.
0.5065.30.84At5g290403770873-F:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.4659.80.90At1g25360839121pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFAO.I.H.G.S.X.
0.4659.80.89At5g05350830417unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PFO.I.H.G.S.X.
0.4659.80.87At4g08840826455APUM11 (Arabidopsis Pumilio 11)F:RNA binding, binding;P:biological_process unknown;C:cellular_component unknown;FMOPO.I.H.G.S.X.
0.4457.20.86At4g25540828659MSH3 (Arabidopsis homolog of DNA mismatch repair protein MSH3)encodes a DNA mismatch repair homolog of human MutS gene, MSH6. There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2*MSH3 heterodimers bound 'insertion-deletion' DNA with three nucleotides (+AAG) or one nucleotide (+T) looped out much better than they bound DNA with a base/base mispair (T/G).O.I.H.G.S.X.
0.4457.20.87At3g18840821417--O.I.H.G.S.X.
0.4457.20.84At3g14640820692CYP72A10putative cytochrome P450O.I.H.G.S.X.
0.4457.20.84At5g28310832915oxidoreductase-relatedF:oxidoreductase activity, binding, oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, catalytic activity, cofactor binding;P:metabolic process;C:cellular_component unknown;BOPFAMO.I.H.G.S.X.
0.4355.30.90At3g49740824136pentatricopeptide (PPR) repeat-containing proteinF:binding;P:biological_process unknown;C:unknown;POFMBO.I.H.G.S.X.
0.4355.30.88At2g16260816122-pseudogene of glycine-rich RNA-binding proteinO.I.H.G.S.X.
0.4253.90.90At5g08230830719PWWP domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.4253.90.89At1g61210842414WD-40 repeat family protein / katanin p80 subunit, putativeF:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOPBVAO.I.H.G.S.X.
0.4050.80.91At1g63730842677disease resistance protein (TIR-NBS-LRR class), putativeF:protein binding, transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:defense response;C:intrinsic to membrane;PMBOAFO.I.H.G.S.X.
0.4050.80.92At2g20210816540leucine-rich repeat family proteinF:protein binding;P:unknown;C:endomembrane system;MOPBFO.I.H.G.S.X.
0.4050.80.90At1g52620841694pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.4050.80.88At5g24980832568unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.4050.80.88At4g19650827709-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMBO.I.H.G.S.X.
0.4050.80.84At1g25250839108AtIDD16 (Arabidopsis thaliana Indeterminate(ID)-Domain 16)F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MOPFBVAO.I.H.G.S.X.
0.4050.80.85At3g53840824551protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.3846.70.84At1g74200843760AtRLP16 (Receptor Like Protein 16)F:protein binding;P:signal transduction;C:cellular_component unknown;PMOBFAO.I.H.G.S.X.
0.3846.70.92At1g50260841448NTMC2T5.1 (N-TERMINAL-TRANSMEMBRANE-C2 DOMAIN TYPE 5.1)F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMFOBO.I.H.G.S.X.
0.3643.60.90At5g19830832103aminoacyl-tRNA hydrolaseF:aminoacyl-tRNA hydrolase activity;P:translation;C:mitochondrion;BOPFMO.I.H.G.S.X.
0.3643.60.88At5g16420831503pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3643.60.85At5g04610830338spermidine synthase-related / putrescine aminopropyltransferase-relatedF:catalytic activity;P:unknown;C:unknown;BPMOFAO.I.H.G.S.X.
0.3541.60.89At4g39380830093-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.3541.60.84At1g31430840033pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:unknown;POMFBO.I.H.G.S.X.
0.3541.60.90At1g23980839010zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVBO.I.H.G.S.X.
0.3541.60.89At1g50910841513unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.3338.10.89At2g40720818667pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMFBO.I.H.G.S.X.
0.3338.10.88At4g16570827358PRMT7 (PROTEIN ARGININE METHYLTRANSFERASE 7)F:methyltransferase activity;P:protein amino acid methylation;C:chloroplast;MFOPBAO.I.H.G.S.X.
0.3338.10.90At4g30700829193pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.3338.10.89At1g74400843781pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMBO.I.H.G.S.X.
0.3338.10.89At3g20730821621pentatricopeptide (PPR) repeat-containing proteinF:binding;P:biological_process unknown;C:endomembrane system;POMFBO.I.H.G.S.X.
0.3338.10.85At5g417103771395transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.3338.10.85At2g36980818272pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFABO.I.H.G.S.X.

Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
22.499.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
22.299.6E-MEXP-285-raw-cel-440782725
21.299.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
20.899.6E-MEXP-285-raw-cel-440782791
18.799.5GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
17.399.5E-ATMX-35-raw-cel-1574334880
15.999.5GSM239253CaMV::DME pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
15.699.5E-ATMX-35-raw-cel-1574334848
15.499.5GSM239251Columbia glabrous (C24) wild type pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
13.099.4GSM131638ATGE_73_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
12.799.3GSM131636ATGE_73_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
11.999.3E-ATMX-1-raw-cel-1112746154
11.499.3GSM131637ATGE_73_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
10.699.2GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.599.2GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.599.1E-ATMX-35-raw-cel-1574334864
9.599.1GSM131698ATGE_81_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.599.1GSM131699ATGE_81_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
9.299.1GSM133957Fukuda_1-2_0B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
8.899.0E-ATMX-1-raw-cel-1112746267

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1671GO:0006278The process whereby new strands of DNA are synthesized, using RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strands.Link to AmiGO
0.0451GO:0008380The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

Inter-species module comparison

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



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