Phatr_bicluster_0064 Residual: 0.31
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_0064 0.31 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_12267 uracil-dna glycosylase (UDG_F1)

PHATRDRAFT_12267 - uracil-dna glycosylase (UDG_F1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12267
PHATRDRAFT_12294 (Rotamase)

PHATRDRAFT_12294 - (Rotamase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12294
PHATRDRAFT_12451 metal-dependent phosphohydrolase hd domain-containing protein (HD_3)

PHATRDRAFT_12451 - metal-dependent phosphohydrolase hd domain-containing protein (HD_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12451
PHATRDRAFT_13395 molybdenum cofactor biosynthesis enzyme (MogA_MoaB)

PHATRDRAFT_13395 - molybdenum cofactor biosynthesis enzyme (MogA_MoaB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13395
PHATRDRAFT_16698 transaldolase (Transaldolase_TalAB)

PHATRDRAFT_16698 - transaldolase (Transaldolase_TalAB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16698
PHATRDRAFT_23077 wdr5 protein (WD40)

PHATRDRAFT_23077 - wdr5 protein (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_23077
PHATRDRAFT_25495 dna-directed polymerase kappa (PolY_Pol_IV_kappa)

PHATRDRAFT_25495 - dna-directed polymerase kappa (PolY_Pol_IV_kappa)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25495
PHATRDRAFT_33480 ac010924_18 ests gb

PHATRDRAFT_33480 - ac010924_18 ests gb

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33480
PHATRDRAFT_33631 oxidoreductase-like protein (MviM)

PHATRDRAFT_33631 - oxidoreductase-like protein (MviM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33631
PHATRDRAFT_36095

PHATRDRAFT_36095 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36095
PHATRDRAFT_38475

PHATRDRAFT_38475 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38475
PHATRDRAFT_38518 (DUF3067 superfamily)

PHATRDRAFT_38518 - (DUF3067 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38518
PHATRDRAFT_39079 avrrpt2-induced aig2 protein (GGCT_like)

PHATRDRAFT_39079 - avrrpt2-induced aig2 protein (GGCT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39079
PHATRDRAFT_39127

PHATRDRAFT_39127 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39127
PHATRDRAFT_39578 2-dehydropantoate 2-reductase (PRK06249)

PHATRDRAFT_39578 - 2-dehydropantoate 2-reductase (PRK06249)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39578
PHATRDRAFT_40967 fa86a_human protein fam86a (Methyltransf_16 superfamily)

PHATRDRAFT_40967 - fa86a_human protein fam86a (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40967
PHATRDRAFT_43720 (START)

PHATRDRAFT_43720 - (START)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43720
PHATRDRAFT_44063 (SGNH_hydrolase superfamily)

PHATRDRAFT_44063 - (SGNH_hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44063
PHATRDRAFT_44507

PHATRDRAFT_44507 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44507
PHATRDRAFT_44952 transcription factor protein (Rtt106)

PHATRDRAFT_44952 - transcription factor protein (Rtt106)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44952
PHATRDRAFT_45522

PHATRDRAFT_45522 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45522
PHATRDRAFT_46668 glycoside hydrolase family 28 protein polygalacturonasefamily protein (Pectate_lyase_3 superfamily)

PHATRDRAFT_46668 - glycoside hydrolase family 28 protein polygalacturonasefamily protein (Pectate_lyase_3 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46668
PHATRDRAFT_47113 riken cdnaisoform cra_a

PHATRDRAFT_47113 - riken cdnaisoform cra_a

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47113
PHATRDRAFT_47585 (DUF2064 superfamily)

PHATRDRAFT_47585 - (DUF2064 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47585
PHATRDRAFT_4821 histone deacetylase superfamily (HDAC_classIV)

PHATRDRAFT_4821 - histone deacetylase superfamily (HDAC_classIV)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_4821
PHATRDRAFT_49037 af205360_1recombinant ubiquitin-somatotropin fusion protein (Ubiquitin)

PHATRDRAFT_49037 - af205360_1recombinant ubiquitin-somatotropin fusion protein (Ubiquitin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49037
PHATRDRAFT_49876 (Fasciclin superfamily)

PHATRDRAFT_49876 - (Fasciclin superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49876
PHATRDRAFT_49987 and mbr-like protein (TspO_MBR)

PHATRDRAFT_49987 - and mbr-like protein (TspO_MBR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49987
PHATRDRAFT_50625 cobyrinic acid-diamide synthase family protein (AAA_26)

PHATRDRAFT_50625 - cobyrinic acid-diamide synthase family protein (AAA_26)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50625
PHATRDRAFT_54577 deah (asp-glu-ala-his) box polypeptidepartial (HrpA)

PHATRDRAFT_54577 - deah (asp-glu-ala-his) box polypeptidepartial (HrpA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54577
PHATRDRAFT_6528 zinc transporter (Zip superfamily)

PHATRDRAFT_6528 - zinc transporter (Zip superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6528
PHATRDRAFT_7562 thymocyte nuclear protein 1 (thymocyte protein thy28) (EVE superfamily)

PHATRDRAFT_7562 - thymocyte nuclear protein 1 (thymocyte protein thy28) (EVE superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_7562
GO ID Go Term p-value q-value Cluster
GO:0006281 DNA repair 0.00359045 1 Phatr_bicluster_0064
GO:0006206 pyrimidine base metabolism 0.0108267 1 Phatr_bicluster_0064
GO:0005975 carbohydrate metabolism 0.0119731 1 Phatr_bicluster_0064
GO:0006777 Mo-molybdopterin cofactor biosynthesis 0.0162 1 Phatr_bicluster_0064
GO:0007155 cell adhesion 0.0347981 1 Phatr_bicluster_0064
GO:0006464 protein modification 0.158622 1 Phatr_bicluster_0064
GO:0006508 proteolysis and peptidolysis 0.465714 1 Phatr_bicluster_0064
GO:0006118 electron transport 0.473356 1 Phatr_bicluster_0064
GO:0008152 metabolism 0.564066 1 Phatr_bicluster_0064
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