Phatr_bicluster_0046 Residual: 0.37
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_0046 0.37 Phaeodactylum tricornutum
Displaying 1 - 49 of 49
PHATRDRAFT_14915 ribosomal protein l1 (Ribosomal_L1)

PHATRDRAFT_14915 - ribosomal protein l1 (Ribosomal_L1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14915
PHATRDRAFT_17504 cell division protein (FtsH_fam)

PHATRDRAFT_17504 - cell division protein (FtsH_fam)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17504
PHATRDRAFT_19661 pspa im30 family protein (PspA)

PHATRDRAFT_19661 - pspa im30 family protein (PspA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19661
PHATRDRAFT_20504 trehalose-6-phosphate synthase (PLN02205)

PHATRDRAFT_20504 - trehalose-6-phosphate synthase (PLN02205)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20504
PHATRDRAFT_21873 peptide chain release factor 2 (prfB)

PHATRDRAFT_21873 - peptide chain release factor 2 (prfB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21873
PHATRDRAFT_22019 isovaleryl-coa dehydrogenase (PTZ00461)

PHATRDRAFT_22019 - isovaleryl-coa dehydrogenase (PTZ00461)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22019
PHATRDRAFT_27082 suppressor of ty (Spt4)

PHATRDRAFT_27082 - suppressor of ty (Spt4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27082
PHATRDRAFT_27659 50s ribosomal protein l17 (rplQ)

PHATRDRAFT_27659 - 50s ribosomal protein l17 (rplQ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27659
PHATRDRAFT_31367 nadh:flavin oxidoreductase nadh oxidase (DCR_FMN)

PHATRDRAFT_31367 - nadh:flavin oxidoreductase nadh oxidase (DCR_FMN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31367
PHATRDRAFT_34994

PHATRDRAFT_34994 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34994
PHATRDRAFT_37232 2-oxoglutaratee1 subunit

PHATRDRAFT_37232 - 2-oxoglutaratee1 subunit

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37232
PHATRDRAFT_37840

PHATRDRAFT_37840 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37840
PHATRDRAFT_37959 thf1_synp6protein thf1 (ThylakoidFormat superfamily)

PHATRDRAFT_37959 - thf1_synp6protein thf1 (ThylakoidFormat superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37959
PHATRDRAFT_39864 rna binding s1 domain protein (HHH_3)

PHATRDRAFT_39864 - rna binding s1 domain protein (HHH_3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39864
PHATRDRAFT_42995 enhancer of polycomb-like protein (EPL1 superfamily)

PHATRDRAFT_42995 - enhancer of polycomb-like protein (EPL1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42995
PHATRDRAFT_43205

PHATRDRAFT_43205 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43205
PHATRDRAFT_43730 polymerase (dna directed)epsilon 3 (p17 subunit) (H4 superfamily)

PHATRDRAFT_43730 - polymerase (dna directed)epsilon 3 (p17 subunit) (H4 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43730
PHATRDRAFT_43902 (HA)

PHATRDRAFT_43902 - (HA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43902
PHATRDRAFT_43921

PHATRDRAFT_43921 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43921
PHATRDRAFT_43955 adenylyl cyclase (CHD)

PHATRDRAFT_43955 - adenylyl cyclase (CHD)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43955
PHATRDRAFT_44015

PHATRDRAFT_44015 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44015
PHATRDRAFT_44691

PHATRDRAFT_44691 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44691
PHATRDRAFT_45064 probable carboxypeptidase (M32_Taq)

PHATRDRAFT_45064 - probable carboxypeptidase (M32_Taq)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45064
PHATRDRAFT_46474

PHATRDRAFT_46474 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46474
PHATRDRAFT_47249

PHATRDRAFT_47249 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47249
PHATRDRAFT_47297 nudix hydrolasemitochondrialexpressed (Nudix_Hydrolase superfamily)

PHATRDRAFT_47297 - nudix hydrolasemitochondrialexpressed (Nudix_Hydrolase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47297
PHATRDRAFT_47458 zgc:162979 protein (Es2 superfamily)

PHATRDRAFT_47458 - zgc:162979 protein (Es2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47458
PHATRDRAFT_47518 exported protein (Alginate_lyase)

PHATRDRAFT_47518 - exported protein (Alginate_lyase)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47518
PHATRDRAFT_47521

PHATRDRAFT_47521 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47521
PHATRDRAFT_47665

PHATRDRAFT_47665 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47665
PHATRDRAFT_47907

PHATRDRAFT_47907 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47907
PHATRDRAFT_48093

PHATRDRAFT_48093 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48093
PHATRDRAFT_48264 ribonuclease activity regulator protein (Methyltransf_6 superfamily)

PHATRDRAFT_48264 - ribonuclease activity regulator protein (Methyltransf_6 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48264
PHATRDRAFT_48300 beta-glucan synthesis-associated protein kre6 (Glyco_hydrolase_16 superfamily)

PHATRDRAFT_48300 - beta-glucan synthesis-associated protein kre6 (Glyco_hydrolase_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48300
PHATRDRAFT_48471 tetratricopeptide tpr_2 (TPR_12)

PHATRDRAFT_48471 - tetratricopeptide tpr_2 (TPR_12)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48471
PHATRDRAFT_48507

PHATRDRAFT_48507 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48507
PHATRDRAFT_48519 ph-response regulator protein pala rim20 (ALIX_LYPXL_bnd)

PHATRDRAFT_48519 - ph-response regulator protein pala rim20 (ALIX_LYPXL_bnd)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48519
PHATRDRAFT_48709

PHATRDRAFT_48709 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48709
PHATRDRAFT_49047 threonine dehydratase (PRK09224)

PHATRDRAFT_49047 - threonine dehydratase (PRK09224)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49047
PHATRDRAFT_49132

PHATRDRAFT_49132 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49132
PHATRDRAFT_49153 (TRX_family)

PHATRDRAFT_49153 - (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49153
PHATRDRAFT_49199

PHATRDRAFT_49199 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49199
PHATRDRAFT_49287

PHATRDRAFT_49287 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49287
PHATRDRAFT_49481 heterogeneous nuclear ribonucleoprotein a b (RRM)

PHATRDRAFT_49481 - heterogeneous nuclear ribonucleoprotein a b (RRM)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49481
PHATRDRAFT_49755

PHATRDRAFT_49755 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49755
PHATRDRAFT_50293 soul heme-binding protein (DUF2358 superfamily)

PHATRDRAFT_50293 - soul heme-binding protein (DUF2358 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50293
PHATRDRAFT_50373 (Methyltransf_32 superfamily)

PHATRDRAFT_50373 - (Methyltransf_32 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50373
PHATRDRAFT_50451

PHATRDRAFT_50451 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50451
PHATRDRAFT_52425 cdc14 cell division cycle 14 homolog a (DSPn superfamily)

PHATRDRAFT_52425 - cdc14 cell division cycle 14 homolog a (DSPn superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_52425
GO ID Go Term p-value q-value Cluster
GO:0009097 isoleucine biosynthesis 0.00395159 1 Phatr_bicluster_0046
GO:0005992 trehalose biosynthesis 0.00788854 1 Phatr_bicluster_0046
GO:0045941 positive regulation of transcription 0.0118109 1 Phatr_bicluster_0046
GO:0006415 translational termination 0.0273554 1 Phatr_bicluster_0046
GO:0030163 protein catabolism 0.0426705 1 Phatr_bicluster_0046
GO:0006508 proteolysis and peptidolysis 0.0548534 1 Phatr_bicluster_0046
GO:0006118 electron transport 0.057921 1 Phatr_bicluster_0046
GO:0006520 amino acid metabolism 0.0908976 1 Phatr_bicluster_0046
GO:0006412 protein biosynthesis 0.131107 1 Phatr_bicluster_0046
GO:0008152 metabolism 0.325688 1 Phatr_bicluster_0046
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