Phatr_bicluster_0074 Residual: 0.46
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_0074 0.46 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_11116 short-chain dehydrogenase reductasesuperfamily protein (NADB_Rossmann superfamily)

PHATRDRAFT_11116 - short-chain dehydrogenase reductasesuperfamily protein (NADB_Rossmann superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11116
PHATRDRAFT_13383 vesicular fusion (AAA)

PHATRDRAFT_13383 - vesicular fusion (AAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13383
PHATRDRAFT_33540 mago nashi-like protein 2 (Mago_nashi superfamily)

PHATRDRAFT_33540 - mago nashi-like protein 2 (Mago_nashi superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33540
PHATRDRAFT_33580

PHATRDRAFT_33580 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33580
PHATRDRAFT_36528

PHATRDRAFT_36528 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36528
PHATRDRAFT_37993

PHATRDRAFT_37993 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37993
PHATRDRAFT_38057

PHATRDRAFT_38057 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38057
PHATRDRAFT_39088 two component regulator three y domain protein

PHATRDRAFT_39088 - two component regulator three y domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39088
PHATRDRAFT_39869

PHATRDRAFT_39869 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39869
PHATRDRAFT_40362

PHATRDRAFT_40362 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40362
PHATRDRAFT_42514 at-hsfa8 (arabidopsis thaliana heat shock transcription factor a8) dna binding transcription factor (HSF_DNA-bind superfamily)

PHATRDRAFT_42514 - at-hsfa8 (arabidopsis thaliana heat shock transcription factor a8) dna binding transcription factor (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42514
PHATRDRAFT_42767

PHATRDRAFT_42767 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42767
PHATRDRAFT_43347 udp-galactose transporter (UAA)

PHATRDRAFT_43347 - udp-galactose transporter (UAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43347
PHATRDRAFT_43972 coenzyme f420 hydrogenase family beta subunit family (FrhB_FdhB_C)

PHATRDRAFT_43972 - coenzyme f420 hydrogenase family beta subunit family (FrhB_FdhB_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43972
PHATRDRAFT_44118 hypothetical orf yml018cp

PHATRDRAFT_44118 - hypothetical orf yml018cp

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44118
PHATRDRAFT_44241 leucine carboxyl methyltransferase superfamily (LCM superfamily)

PHATRDRAFT_44241 - leucine carboxyl methyltransferase superfamily (LCM superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44241
PHATRDRAFT_44493

PHATRDRAFT_44493 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44493
PHATRDRAFT_45743

PHATRDRAFT_45743 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45743
PHATRDRAFT_46419 ubiquitin ligase complex f-box protein (AMN1 superfamily)

PHATRDRAFT_46419 - ubiquitin ligase complex f-box protein (AMN1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46419
PHATRDRAFT_46530 probable glycosyltransferase

PHATRDRAFT_46530 - probable glycosyltransferase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46530
PHATRDRAFT_46539 cd029_mouseuncharacterized protein c4orf29 homolog precursor (DUF2048 superfamily)

PHATRDRAFT_46539 - cd029_mouseuncharacterized protein c4orf29 homolog precursor (DUF2048 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46539
PHATRDRAFT_46954 (MULE)

PHATRDRAFT_46954 - (MULE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46954
PHATRDRAFT_47962 ubiquitin familyexpressed (UBL)

PHATRDRAFT_47962 - ubiquitin familyexpressed (UBL)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47962
PHATRDRAFT_49130 glycosylfamily 2 (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_49130 - glycosylfamily 2 (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49130
PHATRDRAFT_49693 glycerophosphoryl diester phosphodiesterase (SdiA-regulated superfamily)

PHATRDRAFT_49693 - glycerophosphoryl diester phosphodiesterase (SdiA-regulated superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49693
PHATRDRAFT_49839 tetratricopeptide tpr_2 repeat protein

PHATRDRAFT_49839 - tetratricopeptide tpr_2 repeat protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49839
PHATRDRAFT_49856 atp-binding-cassette protein (ABC_ATPase superfamily)

PHATRDRAFT_49856 - atp-binding-cassette protein (ABC_ATPase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49856
PHATRDRAFT_50037

PHATRDRAFT_50037 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50037
PHATRDRAFT_50168 (DUF3754 superfamily)

PHATRDRAFT_50168 - (DUF3754 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50168
PHATRDRAFT_50442 arf-gap protein (ArfGap)

PHATRDRAFT_50442 - arf-gap protein (ArfGap)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50442
PHATRDRAFT_8770 eh-domain containing protein (EHD)

PHATRDRAFT_8770 - eh-domain containing protein (EHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8770
GO ID Go Term p-value q-value Cluster
GO:0007530 sex determination 0.0019758 1 Phatr_bicluster_0074
GO:0050757 thymidylate synthase biosynthesis 0.00591714 1 Phatr_bicluster_0074
GO:0043087 regulation of GTPase activity 0.0215467 1 Phatr_bicluster_0074
GO:0008152 metabolism 0.109996 1 Phatr_bicluster_0074
GO:0006464 protein modification 0.118 1 Phatr_bicluster_0074
GO:0016567 protein ubiquitination 0.13382 1 Phatr_bicluster_0074
GO:0006355 regulation of transcription, DNA-dependent 0.359328 1 Phatr_bicluster_0074
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