CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID Ta.7506.2.S1_a_at

Gene name
Homology with Arabidopsis Similar to At1g27650: ATU2AF35A (HF=5e-15)

Module size 6 genes

NF 0.63

%ile 88.0

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
0.83 93.4 0.97 Ta.7506.2.S1_a_at BJ267303 - - 5e-15 At1g27650 ATU2AF35A O.I. H.G. S.X.
0.60 81.0 0.97 TaAffx.87003.1.S1_s_at CA597427 - - 4e-3 At4g19150 ankyrin repeat family protein O.I. H.G. S.X.
0.56 78.6 0.96 Ta.28206.3.S1_a_at CA661286 - - 2e-2 At3g02220 unknown protein O.I. H.G. S.X.
0.55 76.8 0.97 Ta.8142.1.S1_at BQ752849 - - 3e-15 At1g61620 phosphoinositide binding O.I. H.G. S.X.
0.50 72.4 0.97 Ta.2207.2.S1_a_at CA612248 - - 5e-25 At5g05780 RPN8A (RP NON-ATPASE SUBUNIT 8A) O.I. H.G. S.X.
0.40 58.4 0.97 TaAffx.77390.1.S1_at CD893386 histone deacetylase - 1e-19 At5g63110 HDA6 (HISTONE DEACETYLASE 6) O.I. H.G. S.X.

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Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
4.4 96.8 GSM250900 TcLr34_3dpi_inoculated_rep3 GSE9915 Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat
4.1 96.4 GSM314258 tissue type: germinating seed, embryo - rep2 GSE12508 Transcription patterns during wheat development
3.9 96.1 GSM298064 Crown tissue of Harnesk at 9 weeks post germination, biological rep 2 GSE11774 Expression data from cold treated wheat cultivars
3.4 95.2 GSM298092 Crown tissue of Solstice at 3 weeks post germination GSE11774 Expression data from cold treated wheat cultivars
3.2 94.8 GSM314259 tissue type: germinating seed, embryo - rep3 GSE12508 Transcription patterns during wheat development
3.2 94.8 GSM298063 Crown tissue of Harnesk at 9 weeks post germination, biological rep 1 GSE11774 Expression data from cold treated wheat cultivars
3.1 94.5 GSM298076 Crown tissue of Paragon at 9 weeks post germination, biological rep 2 GSE11774 Expression data from cold treated wheat cultivars
3.0 94.3 GSM298062 Crown tissue of Harnesk at 5 weeks post germination, biological rep 2 GSE11774 Expression data from cold treated wheat cultivars
3.0 94.3 GSM250899 TcLr34_3dpi_mock_rep3 GSE9915 Transcript profiling of Lr1- and Lr34-mediated leaf rust resistance in wheat
3.0 94.3 GSM298061 Crown tissue of Harnesk at 5 weeks post germination, biological rep 1 GSE11774 Expression data from cold treated wheat cultivars

Inter-species module comparison

A co-expression module including the Arabidopsis gene, At1g27650, orthologous to the query gene, Ta.7506.2.S1_a_at

VF %ile Gene ID Repr. ID Gene Name Func. O.I. H.G. S.X. Other DB
1.00 100.0 At1g27650 839657 ATU2AF35A U2 auxiliary factor small subunit. The atU2AF35a protein and its homolog, atU2AF35b, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions. O.I. H.G. S.X.
0.43 55.3 At3g13460 820548 ECT2 Physically interacts with CIPK1. O.I. H.G. S.X.
0.42 53.9 At5g19330 832053 armadillo/beta-catenin repeat family protein / BTB/POZ domain-containing protein F:protein binding, binding;P:unknown;C:plasma membrane;MPOFVBA O.I. H.G. S.X.
0.41 52.4 At4g27000 828808 ATRBP45C F:RNA binding;P:unknown;C:unknown;MPFOBAV O.I. H.G. S.X.
0.33 38.1 At1g02100 837541 leucine carboxyl methyltransferase family protein F:methyltransferase activity;P:biological_process unknown;C:cellular_component unknown;FMOP O.I. H.G. S.X.
0.32 35.7 At5g06140 830501 SNX1 (SORTING NEXIN 1) Homolog of yeast retromer subunit VPS5. Part of a retromer-like protein complex involved in endosome to lysosome protein transport. In roots it co-localizes with the PIN2 auxin efflux carrier. Involved in endocytic sorting of membrane proteins including PIN2, BOR1 and BRI1. O.I. H.G. S.X.
0.26 24.4 At1g33680 840259 RNA binding / nucleic acid binding F:RNA binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MFOBPVA O.I. H.G. S.X.
0.24 20.7 At5g42820 834293 U2AF35B U2 auxiliary factor small subunit. The atU2AF35b protein and its homolog, atU2AF35a, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions. O.I. H.G. S.X.
0.24 20.7 At2g37410 818317 ATTIM17-2 Mitochondrial inner membrane translocase. Together with AtTIM17-1, TIM17-2 has a long C-terminal extension not present in other TIMs. The extension is located in the outer membrane and so TIM17-2 links the inner and outer mitochondrial membranes. The C-terminal region is essential for protein import into mitochondria via the general import pathway but is not necessary for import via the carrier pathway. O.I. H.G. S.X.
0.22 17.5 At4g24520 828554 ATR1 (ARABIDOPSIS P450 REDUCTASE 1) Encodes a cyp450 reductase likely to be involved in phenylpropanoid metabolism. O.I. H.G. S.X.
0.16 8.8 At4g11240 826726 TOPP7 encodes a type I serine/threonine protein phosphatase expressed in expressed in roots, rosettes and flowers. O.I. H.G. S.X.
0.14 6.8 At5g42080 834213 ADL1 (ARABIDOPSIS DYNAMIN-LIKE PROTEIN) Encodes a dynamin-like protein related to phragmoplastin. Mutations in this gene, in combination with mutation in ADL1E, result in defects in embryogenesis, cell plate formation and trichome branching. Also controls vascular patterning in combination with VAN3 and GNOM. O.I. H.G. S.X.
0.12 4.9 At2g32600 817820 hydroxyproline-rich glycoprotein family protein F:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:nucleus, intracellular, spliceosome;MPOFBVA O.I. H.G. S.X.
0.11 4.1 At4g05420 825890 DDB1A (DAMAGED DNA BINDING PROTEIN 1A) Structurally similar to damaged DNA binding proteins.DDB1a is part of a 350 KDa nuclear localized DET1 protein complex. This complex may physically interact with histone tails and while bound to chromatin- repress transcription of genes involved in photomorphogenesis. O.I. H.G. S.X.

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

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