Phatr_bicluster_0230 Residual: 0.25
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_0230 0.25 Phaeodactylum tricornutum
Displaying 1 - 27 of 27
PHATRDRAFT_11151 dihydrodipicolinate synthase (DHDPS)

PHATRDRAFT_11151 - dihydrodipicolinate synthase (DHDPS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11151
PHATRDRAFT_11740 orotate phosphoribosyltransferase (PRTases_typeI)

PHATRDRAFT_11740 - orotate phosphoribosyltransferase (PRTases_typeI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11740
PHATRDRAFT_15019 rrna methylase family protein (SpoU)

PHATRDRAFT_15019 - rrna methylase family protein (SpoU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15019
PHATRDRAFT_16281 mgc83338 protein (RRM_eIF3G_like)

PHATRDRAFT_16281 - mgc83338 protein (RRM_eIF3G_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16281
PHATRDRAFT_17779 nucleosome assembly protein (NAP)

PHATRDRAFT_17779 - nucleosome assembly protein (NAP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17779
PHATRDRAFT_20589 diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (diphth2_R)

PHATRDRAFT_20589 - diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (diphth2_R)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20589
PHATRDRAFT_24408 mgc154353 protein (RimI)

PHATRDRAFT_24408 - mgc154353 protein (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24408
PHATRDRAFT_25204 phosphoribosylaminoimidazole carboxylase (PLN02948)

PHATRDRAFT_25204 - phosphoribosylaminoimidazole carboxylase (PLN02948)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25204
PHATRDRAFT_31975 protein phosphatasecatalytic subunit (MPP_PP5_C)

PHATRDRAFT_31879 - protein phosphatasecatalytic subunit (MPP_PP5_C)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31879
PHATRDRAFT_33523 wd-40 repeat family protein (WD40 superfamily)

PHATRDRAFT_31975 - wd-40 repeat family protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31975
PHATRDRAFT_3578 plastid ribosomal protein l21 large ribosomal subunit (rplU)

PHATRDRAFT_33523 - plastid ribosomal protein l21 large ribosomal subunit (rplU)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33523
PHATRDRAFT_36743 pseudouridylate synthase (PseudoU_synth_PUS1_PUS2)

PHATRDRAFT_3578 - pseudouridylate synthase (PseudoU_synth_PUS1_PUS2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3578
PHATRDRAFT_38881 (Ribosomal_L7Ae)

PHATRDRAFT_36743 - (Ribosomal_L7Ae)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36743
PHATRDRAFT_40901

PHATRDRAFT_38881 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38881
PHATRDRAFT_42495 tryptophanyl-trna synthetase (TrpRS_core)

PHATRDRAFT_40901 - tryptophanyl-trna synthetase (TrpRS_core)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40901
PHATRDRAFT_43016 (Utp21 superfamily)

PHATRDRAFT_42495 - (Utp21 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42495
PHATRDRAFT_43135 valyl trna synthetase (PTZ00419)

PHATRDRAFT_43016 - valyl trna synthetase (PTZ00419)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43016
PHATRDRAFT_44446 rh26_orysj dead-box atp-dependent rna helicase 26 (DEXDc superfamily)

PHATRDRAFT_43135 - rh26_orysj dead-box atp-dependent rna helicase 26 (DEXDc superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43135
PHATRDRAFT_44794

PHATRDRAFT_44446 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44446
PHATRDRAFT_45520 fertility restorer

PHATRDRAFT_44794 - fertility restorer

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44794
PHATRDRAFT_45976 (PPR_2)

PHATRDRAFT_45520 - (PPR_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45520
PHATRDRAFT_46132

PHATRDRAFT_45976 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45976
PHATRDRAFT_48430 transportin 2 (importinkaryopherin beta 2b) (KAP95)

PHATRDRAFT_46132 - transportin 2 (importinkaryopherin beta 2b) (KAP95)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46132
PHATRDRAFT_51303 signal recognition particle 68 kda protein

PHATRDRAFT_48430 - signal recognition particle 68 kda protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48430
PHATRDRAFT_52094 (RRM_SF superfamily)

PHATRDRAFT_51303 - (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51303
PHATRDRAFT_8842 rna polymerase i subunit hrpa39 (RNAP_I_II_AC40)

PHATRDRAFT_52094 - rna polymerase i subunit hrpa39 (RNAP_I_II_AC40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52094

PHATRDRAFT_8842 - (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8842
GO ID Go Term p-value q-value Cluster
GO:0006436 tryptophanyl-tRNA aminoacylation 0.00641182 1 Phatr_bicluster_0230
GO:0006221 pyrimidine nucleotide biosynthesis 0.00641182 1 Phatr_bicluster_0230
GO:0006438 valyl-tRNA aminoacylation 0.00641182 1 Phatr_bicluster_0230
GO:0006418 tRNA aminoacylation for protein translation 0.0115276 1 Phatr_bicluster_0230
GO:0006189 'de novo' IMP biosynthesis 0.0159584 1 Phatr_bicluster_0230
GO:0042254 ribosome biogenesis and assembly 0.0191218 1 Phatr_bicluster_0230
GO:0009116 nucleoside metabolism 0.0285555 1 Phatr_bicluster_0230
GO:0006334 nucleosome assembly 0.0502429 1 Phatr_bicluster_0230
GO:0006470 protein amino acid dephosphorylation 0.0594 1 Phatr_bicluster_0230
GO:0008033 tRNA processing 0.0624342 1 Phatr_bicluster_0230
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