Phatr_bicluster_0215 Residual: 0.22
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_0215 0.22 Phaeodactylum tricornutum
Displaying 1 - 29 of 29
PHATRDRAFT_10782 rna helicase (DEADc)

PHATRDRAFT_10782 - rna helicase (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10782
PHATRDRAFT_12779 dna-directed rna polymerases i and iii 16 kda polypeptide (RNAP_I_III_AC19)

PHATRDRAFT_12779 - dna-directed rna polymerases i and iii 16 kda polypeptide (RNAP_I_III_AC19)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12779
PHATRDRAFT_13428 (WD40 superfamily)

PHATRDRAFT_13428 - (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13428
PHATRDRAFT_13820 bystin family protein (Bystin)

PHATRDRAFT_13820 - bystin family protein (Bystin)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13820
PHATRDRAFT_17523 ribonucleoside-diphosphatebeta subunit family protein (RNRR2)

PHATRDRAFT_17523 - ribonucleoside-diphosphatebeta subunit family protein (RNRR2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17523
PHATRDRAFT_17974 rnu3ip2 protein (WD40 superfamily)

PHATRDRAFT_17974 - rnu3ip2 protein (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_17974
PHATRDRAFT_18217 mitogen-activated protein kinase organizer 1 (WD40)

PHATRDRAFT_18217 - mitogen-activated protein kinase organizer 1 (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18217
PHATRDRAFT_25394 loc100036868 protein (nop2p)

PHATRDRAFT_25394 - loc100036868 protein (nop2p)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25394
PHATRDRAFT_32036 noc2l_arath nucleolar complex protein 2 homolog (protein noc2 homolog) (Noc2 superfamily)

PHATRDRAFT_32036 - noc2l_arath nucleolar complex protein 2 homolog (protein noc2 homolog) (Noc2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32036
PHATRDRAFT_35048 polybindingnuclear 1 (RRM_SF superfamily)

PHATRDRAFT_35048 - polybindingnuclear 1 (RRM_SF superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35048
PHATRDRAFT_35267 (RBFA superfamily)

PHATRDRAFT_35267 - (RBFA superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35267
PHATRDRAFT_35966 nop seven associated protein

PHATRDRAFT_35966 - nop seven associated protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35966
PHATRDRAFT_40101 corneal wound healing-related protein (Mak10 superfamily)

PHATRDRAFT_40101 - corneal wound healing-related protein (Mak10 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40101
PHATRDRAFT_42626

PHATRDRAFT_42626 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42626
PHATRDRAFT_43055

PHATRDRAFT_43055 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43055
PHATRDRAFT_43676

PHATRDRAFT_43676 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43676
PHATRDRAFT_43703 af332588_1cell growth-regulating nucleolar protein

PHATRDRAFT_43703 - af332588_1cell growth-regulating nucleolar protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43703
PHATRDRAFT_45441 mis3_schpo ribosomal rna assembly protein mis3 (COG1094)

PHATRDRAFT_45441 - mis3_schpo ribosomal rna assembly protein mis3 (COG1094)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45441
PHATRDRAFT_45727 mak5_emeni atp-dependent rna helicase mak5 (SrmB)

PHATRDRAFT_45727 - mak5_emeni atp-dependent rna helicase mak5 (SrmB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45727
PHATRDRAFT_45844 at1g04130 f20d22_10 (TPR)

PHATRDRAFT_45844 - at1g04130 f20d22_10 (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45844
PHATRDRAFT_46259 rna-dependent helicase (DEADc)

PHATRDRAFT_46259 - rna-dependent helicase (DEADc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46259
PHATRDRAFT_46848 (COG2520)

PHATRDRAFT_46848 - (COG2520)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46848
PHATRDRAFT_47198 receptor for activated c (WD40 superfamily)

PHATRDRAFT_47198 - receptor for activated c (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47198
PHATRDRAFT_51897 nucleolar protein 10 (WD40 superfamily)

PHATRDRAFT_51897 - nucleolar protein 10 (WD40 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51897
PHATRDRAFT_6258 af155362_1charged amino acid rich leucine zipper factor-1 (Sas10)

PHATRDRAFT_54038 - af155362_1charged amino acid rich leucine zipper factor-1 (Sas10)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54038
PHATRDRAFT_8777 af361826_1 at1g42440 f7f22_7 (DUF663)

PHATRDRAFT_6258 - af361826_1 at1g42440 f7f22_7 (DUF663)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_6258
PHATRDRAFT_9929 at3g22660 mwi23_3 (Ebp2 superfamily)

PHATRDRAFT_8777 - at3g22660 mwi23_3 (Ebp2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8777
PHATRDRAFT_9989 putatative 28 kda protein (COG1094)

PHATRDRAFT_9929 - putatative 28 kda protein (COG1094)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9929

PHATRDRAFT_9989 - dead (asp-glu-ala-asp) box polypeptide 55 (SrmB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9989
GO ID Go Term p-value q-value Cluster
GO:0009186 deoxyribonucleoside diphosphate metabolism 0.00370096 1 Phatr_bicluster_0215
GO:0006364 rRNA processing 0.00984487 1 Phatr_bicluster_0215
GO:0006350 transcription 0.0256773 1 Phatr_bicluster_0215
GO:0005975 carbohydrate metabolism 0.0754495 1 Phatr_bicluster_0215
GO:0006810 transport 0.21473 1 Phatr_bicluster_0215
Log in to post comments