CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g57920

Gene name SPL15 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 15)

Module size 7 genes

NF 0.55

%ile 76.5

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : 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
1.00 100.0 1.00 At3g57920 824961 SPL15 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 15) Encodes a putative transcriptional regulator that is involved in the vegetative to reproductive phase transition. Expression is regulated by MIR156b. O.I. H.G. S.X.
0.77 88.0 0.84 At2g42200 818820 SPL9 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9) Encodes a putative transcriptional regulator that is involved in the vegetative to reproductive phase transition. Expresssion is regulated by MIR156b. O.I. H.G. S.X.
0.67 81.6 0.80 At3g06160 819790 transcriptional factor B3 family protein F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;PO O.I. H.G. S.X.
0.55 70.6 0.84 At2g42800 818880 AtRLP29 (Receptor Like Protein 29) F:protein binding;P:unknown;C:anchored to membrane, plant-type cell wall;PMOBFA O.I. H.G. S.X.
0.44 57.2 0.83 At4g30130 829136 unknown protein F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PMF O.I. H.G. S.X.
0.38 46.7 0.80 At1g10980 837641 - F:unknown;P:biological_process unknown;C:vacuole;MFPO O.I. H.G. S.X.
0.33 38.1 0.81 At1g27370 839626 squamosa promoter-binding protein-like 10 (SPL10) F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PM O.I. H.G. S.X.

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Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
24.9 99.6 GSM311288 Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
21.5 99.6 GSM311287 Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
16.7 99.5 E-MEXP-509-raw-cel-829148456
16.1 99.5 E-MEXP-509-raw-cel-829148525
16.0 99.5 E-MEXP-509-raw-cel-829148597
14.1 99.4 E-MEXP-509-raw-cel-829148808
12.8 99.3 E-MEXP-509-raw-cel-829148348
12.8 99.3 E-MEXP-509-raw-cel-829148420
11.1 99.2 E-MEXP-509-raw-cel-829148842
10.6 99.2 E-MEXP-509-raw-cel-829148632
10.1 99.2 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
9.7 99.1 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 E-MEXP-509-raw-cel-829148385
9.3 99.1 E-MEXP-509-raw-cel-829148913
9.2 99.1 E-MEXP-509-raw-cel-829148877
9.0 99.1 E-MEXP-509-raw-cel-829148561
8.7 99.0 E-MEXP-509-raw-cel-829148276
8.6 99.0 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.182 1 GO:0008361 Any process that modulates the size of a cell.
0.100 1 GO:0042127 Any process that modulates the frequency, rate or extent of cell proliferation.
0.093 2 GO:0010228 The process involved in transforming a meristem that produces vegetative structures, such as leaves, into a meristem that produces reproductive structures, such as a flower or an inflorescence.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link 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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