Organism : Synechococcus elongatus PCC 7942 | Module List :
Synpcc7942_1499

Ferredoxin (2Fe-2S)

CircVis
Functional Annotations (6)
Function System
Ferredoxin cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
2 iron, 2 sulfur cluster binding go/ molecular_function
Photosynthesis kegg/ kegg pathway
fdx_plant tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for Synpcc7942_1499
(Mouseover regulator name to see its description)

Warning: No Regulators were found for Synpcc7942_1499!

Warning: Synpcc7942_1499 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
1703 8.60e-02 gtTttgaatcccttcctcTCcGtT
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1704 2.20e+03 taTtcAgaaatTTtT
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1705 1.50e+04 GcAGCaCTgg.cTctActC
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1907 1.40e+01 aCTgTTTAGGTTG
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1908 6.50e+01 agcgTtgctATTtT
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1909 3.40e+03 aAacgaTAaGaaAtAggatT
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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 Synpcc7942_1499

Synpcc7942_1499 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ferredoxin cog/ cog
electron transport go/ biological_process
electron carrier activity go/ molecular_function
2 iron, 2 sulfur cluster binding go/ molecular_function
Photosynthesis kegg/ kegg pathway
fdx_plant tigr/ tigrfam
Module neighborhood information for Synpcc7942_1499

Synpcc7942_1499 has total of 47 gene neighbors in modules 61, 130
Gene neighbors (47)
Gene Common Name Description Module membership
Synpcc7942_0001 "DNA polymerase III, beta subunit (EC 2.7.7.7) (IMGterm)" 66, 130
Synpcc7942_0050 hypothetical protein 61, 122
Synpcc7942_0078 hypothetical protein 20, 61
Synpcc7942_0286 hypothetical protein 130, 184
Synpcc7942_0380 hypothetical protein 13, 130
Synpcc7942_0462 hypothetical protein 12, 130
Synpcc7942_0463 protein tyrosine phosphatase (IMGterm) 12, 130
Synpcc7942_0675 hypothetical protein 61, 118
Synpcc7942_0882 "Peptidase S16, lon-like (EC:3.4.21.53)" 66, 130
Synpcc7942_0915 3-dehydroquinate dehydratase (EC 4.2.1.10) (IMGterm) 3, 130
Synpcc7942_1135 cation transporter 7, 61
Synpcc7942_1152 rare lipoprotein A 66, 130
Synpcc7942_1265 hypothetical protein 41, 61
Synpcc7942_1453 "two component transcriptional regulator, winged helix family (IMGterm)" 130, 161
Synpcc7942_1499 Ferredoxin (2Fe-2S) 61, 130
Synpcc7942_1630 cytochrome c553 130, 161
Synpcc7942_1634 hypothetical protein 130, 182
Synpcc7942_1707 cell division protein Ftn6 hypothetical protein 61, 83
Synpcc7942_1741 murC UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (IMGterm) 130, 183
Synpcc7942_1744 hypothetical protein (EC:3.1.2.-) 4, 130
Synpcc7942_1761 hypothetical protein 66, 130
Synpcc7942_1813 "ATP-binding region, ATPase-like" 61, 145
Synpcc7942_1816 periplasmic sensor hybrid histidine kinase 61, 166
Synpcc7942_1817 response regulator receiver domain protein (CheY-like) 80, 130
Synpcc7942_1818 hypothetical protein 13, 61
Synpcc7942_1903 hypothetical protein 130, 139
Synpcc7942_1904 hemolysin secretion protein-like 130, 139
Synpcc7942_1906 hypothetical protein 130, 161
Synpcc7942_1919 "transcriptional regulator, XRE family (IMGterm)" 3, 61
Synpcc7942_1981 hypothetical protein 61, 130
Synpcc7942_2118 hypothetical protein 130, 183
Synpcc7942_2132 phosphoglucosamine mutase (EC 5.4.2.10) (IMGterm) 91, 130
Synpcc7942_2148 ATPase 61, 80
Synpcc7942_2149 ABC-2 type transport system permease protein 61, 80
Synpcc7942_2172 hypothetical protein 61, 86
Synpcc7942_2173 hypothetical protein 61, 86
Synpcc7942_2199 "DNA polymerase III, alpha subunit (EC 2.7.7.7) / intein (IMGterm)" 13, 61
Synpcc7942_2252 Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (IMGterm) 35, 61
Synpcc7942_2304 ppnK NAD(+) kinase (EC:2.7.1.23) 61, 139
Synpcc7942_2305 "two component transcriptional regulator, winged helix family (IMGterm)" 61, 139
Synpcc7942_2361 glutamate racemase (EC 5.1.1.3) (IMGterm) 44, 130
Synpcc7942_2392 hypothetical protein 57, 61
Synpcc7942_2427 "3-mercaptopyruvate sulfurtransferase (EC:2.8.1.1, EC:2.8.1.2)" 13, 61
Synpcc7942_2459 hypothetical protein 61, 139
Synpcc7942_2480 "Prolyl 4-hydroxylase, alpha subunit" 38, 61
Synpcc7942_2577 murQ Glucokinase regulatory-like protein (EC:4.2.-) 57, 61
Synpcc7942_2599 hypothetical protein 61, 88
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 Synpcc7942_1499
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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