Phatr_bicluster_0056 Residual: 0.30
Phaeodactylum tricornutum

Module Page Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.
Title Residual Model version Organism
Phatr_bicluster_0056 0.30 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_14177 neural precursor celldevelopmentally down-regulated 4 (HECTc)

PHATRDRAFT_14177 - neural precursor celldevelopmentally down-regulated 4 (HECTc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14177
PHATRDRAFT_15207 wd repeat domain 45 (COG2319)

PHATRDRAFT_14477 - wd repeat domain 45 (COG2319)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14477
PHATRDRAFT_1534 at5g47240 mql5_10 (Nudix_Hydrolase superfamily)

PHATRDRAFT_15207 - at5g47240 mql5_10 (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15207
PHATRDRAFT_15341 anion exchange family protein (HCO3_cotransp superfamily)

PHATRDRAFT_1534 - anion exchange family protein (HCO3_cotransp superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1534
PHATRDRAFT_15929 at5g19750 t29j13_170 (Mpv17_PMP22)

PHATRDRAFT_15341 - at5g19750 t29j13_170 (Mpv17_PMP22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15341
PHATRDRAFT_16014 protein kinase domain containingexpressed (S_TKc)

PHATRDRAFT_15929 - protein kinase domain containingexpressed (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15929
PHATRDRAFT_16105 rna binding trna methyltransferase (tRNA_m1G_MT)

PHATRDRAFT_16014 - rna binding trna methyltransferase (tRNA_m1G_MT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16014
PHATRDRAFT_16471 transmembrane proteinisoform cra_a (Solute_trans_a)

PHATRDRAFT_16105 - transmembrane proteinisoform cra_a (Solute_trans_a)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16105
PHATRDRAFT_16693

PHATRDRAFT_16471 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16471
PHATRDRAFT_21996 iron-sulfur cluster assembly protein (COG0694)

PHATRDRAFT_16693 - iron-sulfur cluster assembly protein (COG0694)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16693
PHATRDRAFT_3834 nonsense-mediated mrna decay protein (NMD3)

PHATRDRAFT_21996 - nonsense-mediated mrna decay protein (NMD3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21996
PHATRDRAFT_39303 protein phosphatase 2c containing protein (PP2Cc)

PHATRDRAFT_3834 - protein phosphatase 2c containing protein (PP2Cc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3834
PHATRDRAFT_39615

PHATRDRAFT_39303 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39303
PHATRDRAFT_40322

PHATRDRAFT_39615 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39615
PHATRDRAFT_41807

PHATRDRAFT_40322 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40322
PHATRDRAFT_44112 serinelong chain base subunit 1 (PLN03227)

PHATRDRAFT_41807 - serinelong chain base subunit 1 (PLN03227)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41807
PHATRDRAFT_46277 enhanced disease susceptibility salicylic acid induction deficient (MATE_like superfamily)

PHATRDRAFT_44112 - enhanced disease susceptibility salicylic acid induction deficient (MATE_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44112
PHATRDRAFT_4634

PHATRDRAFT_46277 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46277
PHATRDRAFT_46830 dhhc zinc finger domain containing protein (zf-DHHC)

PHATRDRAFT_4634 - dhhc zinc finger domain containing protein (zf-DHHC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4634
PHATRDRAFT_47669 delta 5 fatty acid desaturase d5 (Delta6-FADS-like)

PHATRDRAFT_46830 - delta 5 fatty acid desaturase d5 (Delta6-FADS-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46830
PHATRDRAFT_48117 (zf-MYND)

PHATRDRAFT_47669 - (zf-MYND)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47669
PHATRDRAFT_48267 ntp7b_xenlasodium bile acid cotransporter 7-b (na(+) bile acid cotransporter 7-b) (solute carrier family 10 member 7-b) (DUF4137)

PHATRDRAFT_48117 - ntp7b_xenlasodium bile acid cotransporter 7-b (na(+) bile acid cotransporter 7-b) (solute carrier family 10 member 7-b) (DUF4137)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48117
PHATRDRAFT_49296

PHATRDRAFT_48267 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48267
PHATRDRAFT_49514

PHATRDRAFT_49296 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49296
PHATRDRAFT_49592 (MFS)

PHATRDRAFT_49514 - (MFS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49514
PHATRDRAFT_49601 (LmjF365940-deam)

PHATRDRAFT_49592 - (LmjF365940-deam)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49592
PHATRDRAFT_49646 serine-pyruvate aminotransferase (COG0075)

PHATRDRAFT_49601 - serine-pyruvate aminotransferase (COG0075)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49601
PHATRDRAFT_49877

PHATRDRAFT_49646 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49646
PHATRDRAFT_50078

PHATRDRAFT_49877 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49877
PHATRDRAFT_7780

PHATRDRAFT_50078 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50078

PHATRDRAFT_7780 - iron-sulfur cluster assembly accessory protein (Fe-S_biosyn superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7780
GO ID Go Term p-value q-value Cluster
GO:0006636 fatty acid desaturation 0.0220309 1 Phatr_bicluster_0056
GO:0006820 anion transport 0.026385 1 Phatr_bicluster_0056
GO:0006470 protein amino acid dephosphorylation 0.0414888 1 Phatr_bicluster_0056
GO:0006512 ubiquitin cycle 0.0814404 1 Phatr_bicluster_0056
GO:0009058 biosynthesis 0.095782 1 Phatr_bicluster_0056
GO:0006464 protein modification 0.13175 1 Phatr_bicluster_0056
GO:0008152 metabolism 0.134877 1 Phatr_bicluster_0056
GO:0006468 protein amino acid phosphorylation 0.323667 1 Phatr_bicluster_0056
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