Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_3692

Carbohydrate kinase, PfkB/Ribokinase (NCBI)

CircVis
Functional Annotations (4)
Function System
Sugar kinases, ribokinase family cog/ cog
ribokinase activity go/ molecular_function
D-ribose metabolic process go/ biological_process
Pentose phosphate pathway kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_3692
(Mouseover regulator name to see its description)

RSP_3692 is regulated by 20 influences and regulates 0 modules.
Regulators for RSP_3692 (20)
Regulator Module Operator
RSP_0768 94 tf
RSP_1077 94 tf
RSP_1231 94 tf
RSP_1518 94 tf
RSP_1867 94 tf
RSP_2922 94 tf
RSP_3464 94 tf
RSP_3694 94 tf
RSP_1077 189 tf
RSP_1220 189 tf
RSP_1607 189 tf
RSP_1660 189 tf
RSP_1776 189 tf
RSP_1867 189 tf
RSP_3001 189 tf
RSP_3064 189 tf
RSP_3179 189 tf
RSP_3418 189 tf
RSP_3464 189 tf
RSP_3684 189 tf

Warning: RSP_3692 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
7908 8.50e-09 TtCtC..ccat.A.GaCatGAccc
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7909 3.50e-04 tCgACCTctgGggcacCaccGtCg
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8098 2.00e-03 aAtgaCctTtcgGaA
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8099 2.60e+00 CAgaAAgAAaat
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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_3692

RSP_3692 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Sugar kinases, ribokinase family cog/ cog
ribokinase activity go/ molecular_function
D-ribose metabolic process go/ biological_process
Pentose phosphate pathway kegg/ kegg pathway
Module neighborhood information for RSP_3692

RSP_3692 has total of 44 gene neighbors in modules 94, 189
Gene neighbors (44)
Gene Common Name Description Module membership
RSP_0115 RSP_0115 Class I triheme cytochrome c (NCBI) 94, 313
RSP_0216 RSP_0216 hypothetical protein (NCBI) 189, 213
RSP_0226 RSP_0226 Naringenin-chalcone synthase (NCBI) 62, 189
RSP_0227 RSP_0227 hypothetical protein (NCBI) 88, 189
RSP_0512 RSP_0512 multisensor hybrid histidine kinase (NCBI) 94, 304
RSP_0566 RSP_0566 possible transporter, DMT superfamily (NCBI) 94, 357
RSP_1063 RSP_1063 Putative Cyclic-diGMP cyclase/phophodiesterase (NCBI) 19, 189
RSP_1143 RSP_1143 4Fe-4S ferredoxin, iron-sulfur cluster binding protein (NCBI) 94, 326
RSP_1378 RSP_1378 hypothetical protein (NCBI) 175, 189
RSP_1414 RSP_1414 hypothetical protein (NCBI) 54, 94
RSP_1432 RSP_1432 hypothetical protein (NCBI) 94, 157
RSP_1619 RSP_1619 hypothetical protein (NCBI) 189, 235
RSP_1631 RSP_1631 hypothetical protein (NCBI) 94, 347
RSP_1632 RSP_1632 hypothetical protein (NCBI) 94, 347
RSP_1633 RSP_1633 hypothetical protein (NCBI) 94, 347
RSP_1867 RSP_1867 transcriptional regulator, AsnC family (NCBI) 189, 356
RSP_1919 RSP_1919 hypothetical protein (NCBI) 94, 106
RSP_1964 RSP_1964 hypothetical protein (NCBI) 94, 147
RSP_2054 RSP_2054 hypothetical protein (NCBI) 31, 94
RSP_2057 RSP_2057 hypothetical protein (NCBI) 94, 347
RSP_2076 RSP_2076 hypothetical protein (NCBI) 189, 355
RSP_2280 RSP_2280 PAS sensor hybrid histidine kinase (NCBI) 94, 325
RSP_2281 RSP_2281 two-component trancriptional regulator, winged helix family (NCBI) 94, 265
RSP_2474 RSP_2474 hypothetical protein (NCBI) 189, 320
RSP_2477 RSP_2477 hypothetical protein (NCBI) 189, 193
RSP_2675 RSP_2675 hypothetical protein (NCBI) 73, 189
RSP_2991 RSP_2991 hypothetical protein (NCBI) 14, 189
RSP_2998 RSP_2998 Hypothetical Terminase large subunit (NCBI) 14, 189
RSP_2999 RSP_2999 hypothetical protein (NCBI) 14, 189
RSP_3001 RSP_3001 Possible Endonuclease (NCBI) 14, 189
RSP_3542 RSP_3542 hypothetical protein (NCBI) 73, 189
RSP_3632 RSP_3632 hypothetical protein (NCBI) 31, 94
RSP_3651 RSP_3651 putative membrane protein (NCBI) 189, 233
RSP_3692 RSP_3692 Carbohydrate kinase, PfkB/Ribokinase (NCBI) 94, 189
RSP_3693 RSP_3693 BtpA protein (NCBI) 94, 233
RSP_3694 RSP_3694 Putative transcription activator (NCBI) 94, 233
RSP_3765 RSP_3765 hypothetical protein (NCBI) 94, 347
RSP_3766 RSP_3766 hypothetical protein (NCBI) 94, 347
RSP_3773 RSP_3773 hypothetical protein (NCBI) 189, 380
RSP_3779 RSP_3779 hypothetical protein (NCBI) 94, 146
RSP_3812 RSP_3812 recombinase (NCBI) 103, 189
RSP_3813 parB ParB-like nuclease (NCBI) 189, 288
RSP_3814 RSP_3814 hypothetical protein (NCBI) 189, 304
RSP_3816 RSP_3816 hypothetical protein (NCBI) 19, 189
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_3692
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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