Co-expression analysis

Gene ID At5g03150
Gene name JKD (JACKDAW)
Module size 5 genes
NF 0.36
%ile 48.2



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
0.1811.41.00At5g03150831919JKD (JACKDAW)JKD is a nuclear-localized putative transcription factor with three zinc finger domains. jkd mutants show a number of root patterning defects including ectopic periclinal divisions in the cortex, increased cell numbers in the cortical and epidermal layers, a disrupted QC marker expression pattern, and disorganized QC and columella cells. jkd mutants also have a reduced number of meristematic cells in their roots. JKD can interact with the SCR and SHR proteins implicated in root patterning, as well as another zinc finger transcription factor, MAGPIE. All of these interactions require the first zinc finger in JKD according to a Y2H assay. There are also transcriptional interactions among these proteins. The initiation of JKD transcription does not appear to depend on SCR and SHR, but later expression in the post-embryonic QC cells and ground tissue initials is reduced in scr and shr mutants. JKD also appears to be required for SCR transcription beginning in the embryo. There is also some evidence that JKD plays a role in promoting the movement of SHR into the nucleus, particularly in QC cells, but this may be indirect.O.I.H.G.S.X.
0.7586.90.70At2g19660816485DC1 domain-containing proteinF:molecular_function unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.6075.70.73At1g27670839659unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4659.80.71At5g37790833757protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.2014.40.73At5g10430830907AGP4 (ARABINOGALACTAN PROTEIN 4)Encodes arabinogalactan-protein (AGP4).O.I.H.G.S.X.

Click More genes

Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
82.699.9GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
29.799.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.099.5GSM133779Lindsey_1-5_globular-basal_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.399.5GSM133758Lindsey_1-11_heart-stage-root_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.499.3GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.499.2GSM133761Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.199.2GSM133952Murray_2-8_T14-APH_Rep1_ATH1GSE5747Genome-wide cell cycle studiesLink to GEO
9.299.1GSM133756Lindsey_1-10_heart-stage-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.699.0GSM133953Murray_2-9_T16-APH_Rep1_ATH1GSE5747Genome-wide cell cycle studiesLink to GEO
8.499.0GSM134204Murray_3-2_D3-GROWTH_Rep1_ATH1GSE5750Growth of suspension-cultured cellsLink to GEO
8.198.9GSM133951Murray_2-7_T12-APH_Rep1_ATH1GSE5747Genome-wide cell cycle studiesLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1541GO:0051302Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.Link to AmiGO
0.1111GO:0010075Any process involved in maintaining the size and shape of a meristem.Link to AmiGO
0.0231GO:0048364The process whose specific outcome is the progression of the root over time, from its formation to the mature structure. The root is the water- and mineral-absorbing part of a plant which is usually underground, does not bear leaves, tends to grow downwards and is typically derived from the radicle of the embryo.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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