Phatr_bicluster_0034 Residual: 0.35
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_0034 0.35 Phaeodactylum tricornutum
Displaying 1 - 38 of 38
PHATRDRAFT_10518 5-adenylylsulfate reductase (Thioredoxin_like superfamily)

PHATRDRAFT_10518 - 5-adenylylsulfate reductase (Thioredoxin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10518
PHATRDRAFT_13107 peptide methionine sulfoxide reductase (MsrA)

PHATRDRAFT_13107 - peptide methionine sulfoxide reductase (MsrA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13107
PHATRDRAFT_14478 adrenodoxin-type ferredoxin (fer2)

PHATRDRAFT_14478 - adrenodoxin-type ferredoxin (fer2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14478
PHATRDRAFT_1884 leucine aminopeptidase (PRK00913)

PHATRDRAFT_1884 - leucine aminopeptidase (PRK00913)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_1884
PHATRDRAFT_23444 gtp-binding protein typa (TypA)

PHATRDRAFT_23444 - gtp-binding protein typa (TypA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23444
PHATRDRAFT_23717 chloroplast ferredoxin nadp(+) reductase (PLN03116)

PHATRDRAFT_23717 - chloroplast ferredoxin nadp(+) reductase (PLN03116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23717
PHATRDRAFT_23850 at1g34430 f7p12_2 (PRK11856)

PHATRDRAFT_23850 - at1g34430 f7p12_2 (PRK11856)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23850
PHATRDRAFT_27323 tyrosyl-trna synthetase (PRK05912)

PHATRDRAFT_27323 - tyrosyl-trna synthetase (PRK05912)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27323
PHATRDRAFT_32597

PHATRDRAFT_32597 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32597
PHATRDRAFT_34010 alanine aminotransferase (PTZ00377)

PHATRDRAFT_34010 - alanine aminotransferase (PTZ00377)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34010
PHATRDRAFT_35416

PHATRDRAFT_35416 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35416
PHATRDRAFT_36529

PHATRDRAFT_36529 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36529
PHATRDRAFT_37727

PHATRDRAFT_37727 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37727
PHATRDRAFT_37835 (Dynamitin)

PHATRDRAFT_37835 - (Dynamitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37835
PHATRDRAFT_40467 m-like protein

PHATRDRAFT_40467 - m-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40467
PHATRDRAFT_43560 2-nitropropane dioxygenase npd (NPD_like)

PHATRDRAFT_43560 - 2-nitropropane dioxygenase npd (NPD_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43560
PHATRDRAFT_43939

PHATRDRAFT_43939 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43939
PHATRDRAFT_44384 4-hydroxyphenylpyruvate dioxygenase (4HPPD)

PHATRDRAFT_44384 - 4-hydroxyphenylpyruvate dioxygenase (4HPPD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44384
PHATRDRAFT_45240 gcn5-related n-acetyltransferase

PHATRDRAFT_45240 - gcn5-related n-acetyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45240
PHATRDRAFT_45457

PHATRDRAFT_45457 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45457
PHATRDRAFT_45840 c-type u1 snrnp

PHATRDRAFT_45840 - c-type u1 snrnp

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45840
PHATRDRAFT_46690

PHATRDRAFT_46690 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46690
PHATRDRAFT_47395 thylakoid ascorbate peroxidase (ascorbate_peroxidase)

PHATRDRAFT_47395 - thylakoid ascorbate peroxidase (ascorbate_peroxidase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47395
PHATRDRAFT_47449 lsu ribosomal protein l9p (rplI)

PHATRDRAFT_47449 - lsu ribosomal protein l9p (rplI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47449
PHATRDRAFT_47505 (Exostosin superfamily)

PHATRDRAFT_47505 - (Exostosin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47505
PHATRDRAFT_47922

PHATRDRAFT_47922 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47922
PHATRDRAFT_48078 carnitine acetyl transferase (Carn_acyltransf superfamily)

PHATRDRAFT_48078 - carnitine acetyl transferase (Carn_acyltransf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48078
PHATRDRAFT_48683 ankyrin unc44 (ANK)

PHATRDRAFT_48683 - ankyrin unc44 (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48683
PHATRDRAFT_49127 (RanBD_family)

PHATRDRAFT_49127 - (RanBD_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49127
PHATRDRAFT_49494 zinc finger (c3hc4-type ring finger) family protein (RING)

PHATRDRAFT_49494 - zinc finger (c3hc4-type ring finger) family protein (RING)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49494
PHATRDRAFT_49896

PHATRDRAFT_49896 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49896
PHATRDRAFT_49965 cg9520-isoform b

PHATRDRAFT_49965 - cg9520-isoform b

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49965
PHATRDRAFT_50489 agc family protein kinase (S_TKc)

PHATRDRAFT_50489 - agc family protein kinase (S_TKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50489
PHATRDRAFT_50561

PHATRDRAFT_50561 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50561
PHATRDRAFT_54738 triosephosphate isomerase (TIM)

PHATRDRAFT_54738 - triosephosphate isomerase (TIM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54738
PHATRDRAFT_8024 ribosomal protein l22 (Ribosomal_L22)

PHATRDRAFT_8024 - ribosomal protein l22 (Ribosomal_L22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8024
PHATRDRAFT_9400 peptidyl-prolyl cis-transfkbp-type (FkpA)

PHATRDRAFT_9400 - peptidyl-prolyl cis-transfkbp-type (FkpA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9400
PHATRDRAFT_9701 rna binding motifx-linked 2 (RRM_ist3_like)

PHATRDRAFT_9701 - rna binding motifx-linked 2 (RRM_ist3_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9701
GO ID Go Term p-value q-value Cluster
GO:0006437 tyrosyl-tRNA aminoacylation 0.00444554 1 Phatr_bicluster_0034
GO:0006118 electron transport 0.0162729 1 Phatr_bicluster_0034
GO:0006412 protein biosynthesis 0.032453 1 Phatr_bicluster_0034
GO:0006979 response to oxidative stress 0.101687 1 Phatr_bicluster_0034
GO:0019538 protein metabolism 0.148789 1 Phatr_bicluster_0034
GO:0009058 biosynthesis 0.182574 1 Phatr_bicluster_0034
GO:0006418 tRNA aminoacylation for protein translation 0.207972 1 Phatr_bicluster_0034
GO:0006464 protein modification 0.246382 1 Phatr_bicluster_0034
GO:0016567 protein ubiquitination 0.276493 1 Phatr_bicluster_0034
GO:0006457 protein folding 0.410758 1 Phatr_bicluster_0034
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