Organism : Pseudomonas aeruginosa | Module List :
PA4687 hitA

ferric iron-binding periplasmic protein HitA (NCBI)

CircVis
Functional Annotations (5)
Function System
ABC-type Fe3+ transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4687
(Mouseover regulator name to see its description)

PA4687 is regulated by 48 influences and regulates 0 modules.
Regulators for PA4687 hitA (48)
Regulator Module Operator
PA0472 98 tf
PA0893 98 tf
PA0939 98 tf
PA1109 98 tf
PA1363 98 tf
PA2259 98 tf
PA2376 98 tf
PA2556 98 tf
PA2622 98 tf
PA3002 98 tf
PA3045 98 tf
PA3410 98 tf
PA3771 98 tf
PA3804 98 tf
PA3815 98 tf
PA4227 98 tf
PA4238 98 tf
PA4270 98 tf
PA5562 98 tf
PA0225 293 tf
PA0393 293 tf
PA0479 293 tf
PA0527 293 tf
PA0547 293 tf
PA0652 293 tf
PA0707 293 tf
PA0784 293 tf
PA0893 293 tf
PA1099 293 tf
PA1264 293 tf
PA1864 293 tf
PA2054 293 tf
PA2196 293 tf
PA2312 293 tf
PA2387 293 tf
PA2511 293 tf
PA2713 293 tf
PA2736 293 tf
PA2899 293 tf
PA3002 293 tf
PA3135 293 tf
PA3266 293 tf
PA3895 293 tf
PA3965 293 tf
PA4094 293 tf
PA4227 293 tf
PA4270 293 tf
PA4547 293 tf

Warning: PA4687 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
3028 4.00e-15 agAattaTTatCAtt
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3029 2.20e-13 tATTtACgtTCTTTaCaaTTctcc
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3414 2.60e-05 AaaaCcagACcaTctTaAAtAcAA
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3415 4.00e+00 AcTtTTCc
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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 PA4687

PA4687 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type Fe3+ transport system, periplasmic component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for PA4687

PA4687 has total of 44 gene neighbors in modules 98, 293
Gene neighbors (44)
Gene Common Name Description Module membership
PA0004 gyrB DNA gyrase subunit B (NCBI) 274, 293
PA0064 PA0064 hypothetical protein (NCBI) 293, 374
PA0065 PA0065 hypothetical protein (NCBI) 174, 293
PA0066 PA0066 hypothetical protein (NCBI) 165, 293
PA0067 prlC oligopeptidase A (NCBI) 293, 393
PA0068 PA0068 hypothetical protein (NCBI) 191, 293
PA0926 PA0926 hypothetical protein (NCBI) 98, 442
PA0927 ldhA D-lactate dehydrogenase (fermentative) (NCBI) 49, 98
PA0929 PA0929 two-component response regulator (NCBI) 98, 339
PA0930 PA0930 two-component sensor (NCBI) 98, 339
PA1086 flgK flagellar hook-associated protein (NCBI) 293, 347
PA1087 flgL flagellar hook-associated protein type 3 FlgL (NCBI) 293, 347
PA1088 PA1088 hypothetical protein (NCBI) 293, 347
PA1089 PA1089 hypothetical protein (NCBI) 293, 347
PA1090 PA1090 hypothetical protein (NCBI) 293, 347
PA1091 PA1091 hypothetical protein (NCBI) 293, 347
PA1494 PA1494 hypothetical protein (NCBI) 87, 293
PA3171 ubiG 3-demethylubiquinone-9 3-methyltransferase (NCBI) 198, 293
PA3268 PA3268 probable TonB-dependent receptor (NCBI) 98, 99
PA3299 fadD1 long-chain-fatty-acid--CoA ligase (NCBI) 293, 389
PA3488 PA3488 hypothetical protein (NCBI) 293, 473
PA3767 PA3767 hypothetical protein (NCBI) 98, 414
PA3768 PA3768 probable metallo-oxidoreductase (NCBI) 98, 414
PA3809 fdx2 ferredoxin (2Fe-2S) (NCBI) 98, 409
PA3810 hscA chaperone protein HscA (NCBI) 98, 409
PA3811 hscB co-chaperone HscB (NCBI) 98, 409
PA3812 iscA probable iron-binding protein IscA (NCBI) 98, 409
PA3813 iscU probable iron-binding protein IscU (NCBI) 98, 409
PA4370 icmP Insulin-cleaving metalloproteinase outer membrane protein precursor (NCBI) 98, 179
PA4371 PA4371 hypothetical protein (NCBI) 98, 511
PA4372 PA4372 hypothetical protein (NCBI) 98, 389
PA4373 PA4373 hypothetical protein (NCBI) 37, 98
PA4514 PA4514 probable outer membrane receptor for iron transport (NCBI) 98, 473
PA4515 PA4515 putative hydroxylase (NCBI) 98, 473
PA4516 PA4516 hypothetical protein (NCBI) 98, 473
PA4675 PA4675 probable TonB-dependent receptor (NCBI) 98, 99
PA4687 hitA ferric iron-binding periplasmic protein HitA (NCBI) 98, 293
PA4688 hitB iron (III)-transport system permease HitB (NCBI) 49, 293
PA5012 waaF heptosyltransferase II (NCBI) 98, 204
PA5161 rmlB dTDP-D-glucose 4,6-dehydratase (NCBI) 198, 293
PA5216 PA5216 probable permease of ABC iron transporter (NCBI) 98, 206
PA5217 PA5217 probable binding protein component of ABC iron transporter (NCBI) 98, 414
PA5413 ltaA low specificity l-threonine aldolase (NCBI) 293, 420
PA5531 tonB TonB protein (NCBI) 98, 414
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 PA4687
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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