Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3492

Protein phosphatase 2C-like (NCBI)

CircVis
Functional Annotations (10)
Function System
Serine/threonine protein phosphatase cog/ cog
protein serine/threonine phosphatase activity go/ molecular_function
calcium-dependent protein serine/threonine phosphatase activity go/ molecular_function
magnesium-dependent protein serine/threonine phosphatase activity go/ molecular_function
magnesium-dependent protein serine/threonine phosphatase complex go/ cellular_component
CTD phosphatase activity go/ molecular_function
calcium-dependent protein serine/threonine phosphatase regulator activity go/ molecular_function
myosin phosphatase activity go/ molecular_function
myosin phosphatase regulator activity go/ molecular_function
myosin phosphatase complex go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3492
(Mouseover regulator name to see its description)

RSP_3492 is regulated by 23 influences and regulates 0 modules.
Regulators for RSP_3492 (23)
Regulator Module Operator
RSP_0607 153 tf
RSP_0927 153 tf
RSP_1231 153 tf
RSP_1776 153 tf
RSP_2026 153 tf
RSP_3322 153 tf
RSP_3339 153 tf
RSP_3400 153 tf
RSP_3464 153 tf
RSP_3684 153 tf
RSP_0071 119 tf
RSP_0511 119 tf
RSP_0607 119 tf
RSP_0927 119 tf
RSP_1435 119 tf
RSP_1776 119 tf
RSP_2026 119 tf
RSP_2130 119 tf
RSP_2494 119 tf
RSP_3095 119 tf
RSP_3203 119 tf
RSP_3616 119 tf
RSP_3700 119 tf

Warning: RSP_3492 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7958 6.80e-08 AaAGGacAAGCcaAaAcCacTGaG
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7959 1.30e-05 ACcAattCGcccTcAaaATAGcCt
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8026 3.20e-08 t.aaaatGgaTGAAAcCaat
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8027 3.80e-03 CtTgcCCTTTctGcagGA
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Motif Help

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.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_3492

RSP_3492 is enriched for 10 functions in 3 categories.
Module neighborhood information for RSP_3492

RSP_3492 has total of 39 gene neighbors in modules 119, 153
Gene neighbors (39)
Gene Common Name Description Module membership
RSP_0834 xanB mannose-6-phosphate isomerase / mannose-1-phosphate guanylyltransferase (NCBI) 125, 153
RSP_0835 manB phosphomannomutase (NCBI) 153, 246
RSP_1324 flgH Flagellar L-ring protein (NCBI) 153, 359
RSP_1325 RSP_1325 putative flagellar basal-body P-ring formation protein FlgA (NCBI) 153, 359
RSP_1326 RSP_1326 putative flagellar basal body rod protein (NCBI) 153, 359
RSP_1327 RSP_1327 putative flagellar basal body rod protein (NCBI) 153, 359
RSP_1328 RSP_1328 flagellar biosynthetic protein FliQ (NCBI) 153, 359
RSP_1329 fliE putative flagellar hook-basal body complex protein (NCBI) 153, 359
RSP_1330 RSP_1330 putative flagellar basal-body rod protein FlgC (NCBI) 153, 359
RSP_1331 RSP_1331 hypothetical protein (NCBI) 153, 359
RSP_1981 RSP_1981 Deoxyribodipyrimidine photolyase (NCBI) 153, 282
RSP_2944 RSP_2944 hypothetical protein (NCBI) 77, 153
RSP_2995 RSP_2995 possible phage major capsid protein, gp36 (NCBI) 77, 153
RSP_3472 RSP_3472 hypothetical protein (NCBI) 79, 119
RSP_3474 RSP_3474 hypothetical protein (NCBI) 79, 119
RSP_3475 RSP_3475 Serine/Threonine protein kinase (NCBI) 79, 119
RSP_3476 RSP_3476 hypothetical protein (NCBI) 79, 119
RSP_3477 RSP_3477 hypothetical protein (NCBI) 79, 119
RSP_3478 RSP_3478 hypothetical protein (NCBI) 79, 119
RSP_3479 RSP_3479 hypothetical protein (NCBI) 79, 119
RSP_3480 RSP_3480 hypothetical protein (NCBI) 79, 119
RSP_3481 RSP_3481 hypothetical protein (NCBI) 79, 119
RSP_3482 RSP_3482 hypothetical protein (NCBI) 79, 119
RSP_3483 RSP_3483 hypothetical protein (NCBI) 79, 119
RSP_3484 RSP_3484 hypothetical protein (NCBI) 79, 119
RSP_3485 RSP_3485 hypothetical protein (NCBI) 79, 119
RSP_3486 RSP_3486 Possible outer membrane protein, OmpA family (NCBI) 79, 119
RSP_3487 RSP_3487 hypothetical protein (NCBI) 79, 119
RSP_3488 RSP_3488 hypothetical protein (NCBI) 79, 119
RSP_3489 RSP_3489 hypothetical protein (NCBI) 119, 153
RSP_3490 RSP_3490 hypothetical protein (NCBI) 119, 153
RSP_3491 RSP_3491 hypothetical protein (NCBI) 119, 153
RSP_3492 RSP_3492 Protein phosphatase 2C-like (NCBI) 119, 153
RSP_3494 RSP_3494 OmpA/MotB domain protein (NCBI) 119, 153
RSP_3575 gvpK putative gas vesicle synthesis protein (NCBI) 153, 325
RSP_3578 gvpF2 putative gas vesicle synthesis protein (NCBI) 153, 253
RSP_3582 gvpN ATPase (NCBI) 153, 253
RSP_3612 RSP_3612 hypothetical protein (NCBI) 153, 300
RSP_6070 RSP_6070 hypothetical protein (NCBI) 153, 205
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_3492
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend