Organism : Methanococcus maripaludis S2 | Module List :
MMP0386 HMmA

histone A

CircVis
Functional Annotations (6)
Function System
Histones H3 and H4 cog/ cog
intracellular go/ cellular_component
nucleus go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
transcription initiation factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0386
(Mouseover regulator name to see its description)

MMP0386 is regulated by 15 influences and regulates 7 modules.
Regulators for MMP0386 HMmA (15)
Regulator Module Operator
MMP0018
MMP0637
126 combiner
MMP0041
MMP1275
126 combiner
MMP0637
MMP1015
126 combiner
MMP0787 126 tf
MMP1015
MMP1275
126 combiner
MMP1275
MMP1347
126 combiner
MMP1275
MMP1376
126 combiner
MMP0031
MMP1704
38 combiner
MMP0041
MMP0568
38 combiner
MMP0480
MMP0568
38 combiner
MMP0568 38 tf
MMP0568
MMP1100
38 combiner
MMP0719
MMP1646
38 combiner
MMP1275 38 tf
MMP1499
MMP1646
38 combiner

Warning: MMP0386 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
737 3.90e+03 CCCTCcCc
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738 6.50e+03 ACCACC
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905 6.80e-01 Ag.A.ACaTcaAAtATATagaTAc
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906 1.60e+02 tAAtaTAcTAATaaAAAcCtA
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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 MMP0386

MMP0386 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Histones H3 and H4 cog/ cog
intracellular go/ cellular_component
nucleus go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
transcription initiation factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for MMP0386

MMP0386 has total of 61 gene neighbors in modules 38, 126
Gene neighbors (61)
Gene Common Name Description Module membership
MMP0219 ppaC putative manganese-dependent inorganic pyrophosphatase 35, 126
MMP0221 putP sodium/proline symporter 29, 38
MMP0233 hypothetical protein MMP0233 38, 115
MMP0243 hypothetical protein MMP0243 4, 25, 38
MMP0333 hypothetical protein MMP0333 4, 126
MMP0351 aspB-like1 DegT/DnrJ/EryC1/StrS aminotransferase 38, 80
MMP0352 putative oxidoreductase 38, 80, 162
MMP0383 slp S-layer protein 35, 126
MMP0386 HMmA histone A 38, 126
MMP0419 sodium:neurotransmitter symporter 24, 38
MMP0503 hypothetical protein MMP0503 4, 126
MMP0591 hypothetical protein MMP0591 35, 126
MMP0592 hypothetical protein MMP0592 35, 126
MMP0593 walker type ATPase 35, 126
MMP0655 hypothetical protein MMP0655 24, 38, 52
MMP0679 Na+/H+ antiporter-like protein 24, 38
MMP0689 xanthine/uracil permease family protein 38, 115
MMP0701 hypothetical protein MMP0701 38, 162
MMP0702 hypothetical protein MMP0702 24, 38, 162
MMP0736 PRC-barrel domain-containing protein 8, 19, 38
MMP0737 L-aspartate dehydrogenase 8, 38
MMP0795 hypothetical protein MMP0795 22, 126
MMP0839 hypothetical protein MMP0839 29, 38
MMP0840 TetR family transcriptional regulator 29, 38
MMP0910 hypothetical protein MMP0910 38, 86, 122
MMP0911 iron-sulfur flavoprotein 38, 80
MMP0934 hypothetical protein MMP0934 75, 126
MMP0935 hypothetical protein MMP0935 107, 126
MMP1094 ppsA phosphoenolpyruvate synthase 38, 80
MMP1103 hypothetical protein MMP1103 14, 38
MMP1130 hypothetical protein MMP1130 4, 38
MMP1191 mch N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase 35, 126
MMP1195 yneG putative cytoplasmic protein 25, 126
MMP1270 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator 24, 38
MMP1304 response regulator receiver protein 4, 126
MMP1305 hypothetical protein MMP1305 4, 126
MMP1471 hypothetical protein MMP1471 38, 115
MMP1518 sulfate/molybdate ABC-transporter ATPase subunit 35, 126
MMP1519 anion transport system permease 35, 126
MMP1520 hydrogenase accessory protein HypB 35, 126
MMP1541 hypothetical protein MMP1541 24, 38
MMP1560 mtrE tetrahydromethanopterin S-methyltransferase subunit E 35, 126
MMP1561 mtrD tetrahydromethanopterin S-methyltransferase subunit D 35, 126
MMP1562 mtrC tetrahydromethanopterin S-methyltransferase subunit C 35, 126
MMP1563 mtrB tetrahydromethanopterin S-methyltransferase subunit B 35, 126
MMP1564 mtrA tetrahydromethanopterin S-methyltransferase subunit A 35, 126
MMP1565 or900 tetrahydromethanopterin S-methyltransferase subunit A 35, 126
MMP1566 mtrG tetrahydromethanopterin S-methyltransferase subunit G 35, 126
MMP1567 mtrH tetrahydromethanopterin S-methyltransferase subunit H 35, 126
MMP1643 hypothetical protein MMP1643 35, 38
MMP1644 hypothetical protein MMP1644 35, 126
MMP1645 aspartate/glutamate/uridylate kinase 4, 126
MMP1714 roadblock/LC7 family protein 38, 162
MMP1715 small GTP-binding protein 38, 162
MMP1716 hmdII H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-like protein 38, 162
MMP1717 type 12 methyltransferase 35, 126
MMP1718 hypothetical protein MMP1718 35, 126
Unanno_17 None 8, 126
Unanno_3 None 107, 126
Unanno_45 None 9, 38
Unanno_51 None 4, 126
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 MMP0386
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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