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ExPlain Feature Transition - BIOBASE Biological Databases

1. search for over represented binding sites is selected the Match algorithm will use the positional weight matrices in the selected profile to search your sequences as well as a set of background sequences for binding sites which meet the cut off criteria and then reports those PWMs and sites which are over represented in your sequence set compared to the background sequence set This option is equivalent to running Analyze gt Binding sites search gt Match in ExPlain with a background set Note that when you select the FMatch option you will be asked to additionally provide information about the background set to be used 3 The profile group of positional weight matrices to be used As in ExPlain a number of prepared profiles are provided including the default Vertebrate Non Redundant profile along with a number of tissue specific profiles You can also create your own custom profiles from the collection of matrices within TRANSFAC or from your own uploaded matrices using the Profile creation tool accessed through the help section on the right hand side of the screen Last updated September 30 2015 Predict Transcription Factor Binding Sites hat tee Predicting TF binding sites trans a Teor Dinan aces or each seque i a poarta te ovipv is a 2 of mat os that fam analyzing ONA sequences ey gt a POSEN RT lt ated sequere sccomnpermed by a grat 3 Ei analya a gana or WE it neni Click the fs ad taatrix
2. i BKL Search and Tools W Functional analysis tools Step by step data analysis D miRNA Analysis ul Tissue specific Profiles D Cut off Values uj Composite Model Editor D Command Line Use LD Frequently Asked Questions O Create and compare matrices LJ Genome Trax Search Tool 3 SKL Data Management 3 BKL Analysis Scheduling 3 Consulted Databases i Be Citing the BKL Be Publications LD Disclaimer Creating composite models TRANSFAC s Model creation tool replaces the File gt Create new data gt Composite model option in ExPlain Composite model Construct ds equlatory model The tool for creating custom models is accessed through Match From any page within TRANSFAC click the tools menu and then the Predict TF binding sites link Last updated September 30 2015 BIOB SE BIOLOGICAL DATABASES search tools Gene regulation analysis tools gt BIOBASI cearch peach Step by step data analysis Create and compare matrices WHide search options Umit search to Predict TF binding sites Identify miRNA regulators Genes and proteins the Mat then and TRANSF the miRNA tool t mRNAs Pathways i Search genes and proteins by Name Identifier D BLASTp O Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species Y EEP RA a E ets of canes 6 haracti gt Upload a list of genes or proteins in Id
3. 30 2015 genomic coordinates in bed format The pull down menu that appears when this option is selected will specify what genome version is supported As of December 2014 the supported versions are human hg38 GRCh38 mouse mm10 GRCm38 and rat rn5 RGSC 5 0 Match and Composite model search TRANSFAC s Predict TF binding sites tool which includes the Match Composite model and FMatch analysis options replaces the Analyze gt Binding sites search gt Match and Analyze gt Binding sites search gt Search for new targets of TF combination functions in ExPlain Match Weight matrix based TFBS search Search for new targets of TF combination Identify genes regulated by composite model To access the Match tool from any page within TRANSFAC click the tools menu and then the Predict TF binding sites link BIOB SE BIGLOGICAL DATADASES search tools Gene regulation analysis tools Step by step data analysis Create and compare matrices VHide search options Umit search to Predict TF binding sites Identify miRNA regulators Genes and proteins SER ie h i qia i By SATE maRNAs Pathways Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species v pathways or ret gt Upload a list of genes or proteins in Identify shared networks Predict protein attribu
4. 4_01 mipoded trom iterate AP 4 G reference Boane gt r Last updated September 30 2015 When you have selected the desired matrix or matrices more than one matrix can be selected to represent a component click the Add to model button The recommended minFN cut off for the matrix or matrices is specified by default but can be over ridden by typing the desired cut off into the Cut off box Directionless orientation is specified by default but forward or reverse orientation can alternately be specified by selecting the desired option from the Orientation pull down menu Repeat this process for the second component At this point you can save the model keeping the remaining default parameters or by adapting them as desired 1 Order of components When the Use inverted order of components parameter is checked the default setting the order in which the components are identified within the submitted sequence will not be considered when determining a match For example if Matrix A is selected as component 1 and Matrix B is selected as component 2 the model will be returned in the results regardless of whether the order is A gt B or B gt A as long as the cut off criteria are met When the Use inverted order of components selection is turned off the order in which the components are identified will determine whether a match is made For example if Matrix A is selected as component 1 and Matrix B is selected
5. analysis gt Data gt Matrices gt Uploaded matrices folder of the my data menu UV Ate and will also be listed in the Profile creation tool accessed from the Match tool page which can be used to create a profile containing the matrix for use by Match Last updated September 30 2015 Alternatively you can create a matrix using a set of aligned or unaligned sequences For a description of how to create a matrix from a set of aligned sequences please see the Gene regulation analysis tools gt Create and compare matrices page of the TRANSFAC user manual BKL documentation LJ What s New _ Introduction to the BKL Known Limitations a BKL Reports s a Search and Tools Be Functional analysis tools uj Step by step data analysis D MIRNA Analysis it Predicting TF binding sites Genome Trax Search Tool D BKL Data Management d BKL Analysis Scheduling L Consulted Databases Citing the BKL Publications LD Disclaimer For a description of how to create a matrix from a set of unaligned sequences please see Finding novel motifs Seeder in this document Creating profiles TRANSFAC s Profile creation tool replaces the File gt Create new data gt PWM profile option in ExPlain PRF PWM profile Weight matrices profile for TFBS analyses The tool for creating custom profiles is accessed through Match From any page within TRANSFAC click the tools menu and then the Predic
6. the taskbar window open until the analysis completes the analysis results will automatically be loaded within the open window Last updated September 30 2015 Match Analysis Report Etura lo Blanch Analyt summary Match ety chore Total sequence henge ae Total number of eequerces e 20 Total number of geben 32 Fiori of aeecgertcee ath mite ED Pray of pie hd aver mee mimir of med pir eee 15 00 E Show parame ued Sequence SETHY Fat A 1 me Laat Mark Hl gn pepe Al Shearg DD af 10 ered ere a sa PRB ieee Pe Seypcnce details a gt cim gt C TGT rt Si alo m da d sh Ww miene 710 e St tam j st Mark al on page fie Bepeoet babii OS hereereg 28 H 28 arrr Mra Ftor cure Fait Er Dare PE Fir WEERALPRA Hr OL ERs sipha Gs 1 Oo LAMM VWESVENT LO Wert 112 LEOD 0 934 MPERA oe oi Fhir ae Pe G 94A 0 084 Cae gt Hibs on pgp 2 HN pr E a eT it 5 9 a0 timp do F ae M T TRECCE Tei T ape Pos a For a detailed description of the analysis report please see the BKL Search and Tools gt Predicting TF binding sites page of the TRANSFAC user manual Last updated September 30 2015 BKL documentation B What s New C Introduction to the BKL O Known Limitations SKL Reports BKL Search and Tools Functional analysis tools a uj Step by step data analysis LJ miRNA Analysis LE uj Tissue specific Profiles LJ Cut off Values A Pr
7. the yellow browse for file button to select a tab delimited or Excel file of gene names or identifiers apes or proteins in bulk and search for them browse for file Once you have selected the file use the prompts to specify whether your file contains a list of gene names or identifiers the species in the case of gene names or the identifier type in the case of identifiers and whether your file contains a header column and the first row should therefore be ignored Using the preview provided of the file contents you must specify which column contains the name or identifier to be used for matching specify this column as ID from the pull down menu and may optionally specify one column containing a numeric value such as fold change specify this column as Observation from the pull down menu All other columns must be set to Ignore Finally click the upload button to upload the contents of the file Last updated September 30 2015 T Upload a list of genes or proteins in bulk and search for them browse for file HUVEC GSE2639 txt Names Identifiers EEr Ar Ak LUZ 221131_at 1 05 205969_at 1 01 205435_s_at 1 01 207725_at 1 03 201000_at 1 01 You will receive a message noting which values could not be matched to an entry in the database and then the matched entries will be returned in the results section below Once the results are returned click the Save these results link
8. to save the list of genes for further analysis Genes and proteins 25 of 7856 total Ga Pi E Save ese resuts poor imece results 8 Pathfinder O Ontology Match FA FASTA EE Profiles tA a a 5 a Hame Speces Taxon Desonptron SEPTS Humar Septin amp interacts with PHUTLI and PNUTL2 may play a role in protein secretion localizes to secretory granules increased expression may be associated with several types of cancer C4 orf29 Hunan Member of the DUF2048 domain of unknown function family has low amilanty to nee 80290195000 which is involved in response to anora NMEy Human NME NM23 familly member 7 a putate nucleoside daphosphate kinase that Binding factors for gene l Search Hits on page 25 Search Term Observahon 709000_s_at 1 05 219980_at 0 96 219553 at 0 97 To save a subset of the genes use a combination of clicking column headers for sorting and the Filter link for filtering then select the desired subset to be saved using the check boxes next to each entry After saving the data set can be accessed from the my data menu Last updated September 30 2015 BIOB SE BIOLOGICAL CATARAS OS search tools my data FView more search options if you want to do a more s UPL Note that unlike ExPlain TRANSFAC supports uploading of mature miRNAs by name or identifier To upload a list of mature miRNAs such as hsa miR 155 5p as opposed to a list of MIRNA genes such as human MIR155 select th
9. you must specify which column contains the name or identifier to be used for matching specify this column as ID from the pull down menu and may optionally specify one column containing a numeric value such as fold change specify this column as Observation from the pull down menu All other columns must be set to Ignore HUVEC GSE2639 tet HUVEC GSE2639 I am uploading a list of a Genes i mi s Names Identifiers File contains column headers ves No Observation BIST a i ASGNT 1221131_at 1 05 205969_at 1 01 AKI 205435_sat 1 01 AANAT J207225_at 1 03 jaars 201000_at 1 01 When you start the Match analysis after filling in the required parameters the data set will be automatically uploaded and saved to your user account in the my data menu BIOB SE POLOGICAL DATABASES search tools my data 7 BIOBASE search FView more search options if you want to do a more Wi Last updated September 30 2015 Creating data subsets Whenever a list of Genes and proteins or miRNAs is displayed whether that list is the direct result of a search or is a previously saved data set that has been loaded from the my data menu individual entries can be selected using the checkboxes and then saved using the Save these results link BIOB SE Pe De FATA RANENI Search my data Fiter dialog Mo
10. BIOBQSE BIOLOGICAL DATABASES A QIAGEN Company QIAGEN ExPlain Transition Overview The current ExPlain tool will be phased out at the end of 2015 replaced with an enhanced version of TRANSFAC This document provides a mapping of the functions in ExPlain to the comparable functions in TRANSFAC to help you transition to the new interface While many of the functions of ExPlain have been integrated into TRANSFAC and enhanced further the set of tools that are primarily focused on basic statistical processing and conversion of raw data files have not been migrated due to low usage combined with the ready accessibility of high quality data pre processing tools made available by instrument providers and public resources For a more complete description of the features included in this document as well as a complete description of other features included in TRANSFAC please access the TRANSFAC user manual using the help menu accessible in the type right corner of the TRANSFAC interface BIOB SE heii iil search tools my data For any questions or to request that additional new features be considered for future implementation please contact us at support biobase international com Mapped features Loading gene and miRNA sets Creating data subsets Loading sequences and intervals Match and Composite model search Loading matrices Creating profiles Creating composite models Last updated September 30 2015 Finding novel m
11. Upload a list of genes or proteins Identify shared networks Predict protein attributes Ilse the Network analy tooi t maiyze se the BokKnowledge Tra rer t c 5 ef es y h th a s Til f lict ve f iv t Oe Q Genes and proteins search help connected nodes uncharacterized protein sequences View statistics for PROTEOME 2015 3 When the Match tool loads select the I am uploading a gene or miRNA set radio button select the Upload a new gene or miRNA set radio button and then click the yellow browse for file button to select a tab delimited or Excel file of gene names or identifiers BIOB s GE Welcome to TRANSFAC PROT Ee eee ee search tools my data Predict Transcription Factor Binding Sites what is this Enter gene set name I am uploading a list of Genes miRNAs containing Names Identifiers Which species Fiomo sapiens E Synonym handling Match synonyms if necessary File contains column headers Yes No Last updated September 30 2015 Once you have selected the file use the prompts to specify whether your file contains a list of genes or miRNAs whether it is a list of names or identifiers the species in the case of gene miRNA names or the identifier type in the case of identifiers and whether your file contains a header column and the first row should therefore be ignored Using the preview provided of the file contents
12. a kinase phosphorylating a target protein etc When Ignore directionality is turned off the set of considered relationships is extended to also include bidirectional relationships Examples of bidirectional relationships are protein protein binding interactions which result in bidirectional complex formation Ignoring directionality will generally produce larger networks and may merge smaller networks into larger networks When you are ready launch the analysis by clicking the perform network analyis button Your analysis will be forwarded to the taskbar If you keep the taskbar window open until the analysis completes the analysis results will automatically be loaded within the open window BIOB SE Welcome to TRANSFAC PROTEOME BIOLOGICAL DATABASES search tools my data Network Cluster Analysis Report what is this Return to network analysis Summary 32 human genes from file Expressed in lymph were converted to 31 proteins and analyzed for shared connections using the network cluster algorithm gt Show parameters used 2 networks were identified 7 input proteins were preliminarily part of an identified network but were removed due to the preferred network density specified To eg pa include these proteins in the networks you can re run the analysis with a lower preferred network density The proteins are c Ets 2 i 2Ralpha neuropilin2 show 13 input proteins have interaction partners but no connection to othe
13. as component 2 and Use inverted order of components is turned off only A gt B models will be returned in the results when the cut off criteria is met B gt A models will be ignored 2 Distance between components This parameter specifies the maximum distance in nucleotides that may exist between the two components in order for a pair of binding sites to be identified A negative starting distance specifies the number of nucleotides by which the two matrices may overlap A default distance of 5 to 30 is set which is appropriate for most analyses Once the model is saved it will appear in the my data menu as well as the model pull down menu of the Match tool when Composite model search by pairs of TFs is selected as the analysis method For a more detailed description of how to create a profile please see the Gene regulation analysis tools gt Predict TF binding sites gt Composite Model Editor page of the TRANSFAC user manual Last updated September 30 2015 E E BKL documentation 3 What s New C Introduction to the BKL a Known Umitations H E aK Reports H BKL Search and Tools Functional analysis tools uj Step by step data analysis J miRNA Analysis EE Predicting TF binding sites uj Tissue specific Profiles LJ Cut off Values A Profile Generation aj Command Line Use b Frequently Asked Questions 3 Create and compare matrices LJ Genome Trax Search Tool LD SKL Data Management D BKL Analysis Sc
14. cbon assay Comgied matrix anported from Ptetsture reference Matn Clasarfic aon SHLUH SANH MYB MYB neh Sequence aneCass 1 Giz GCAGsTGx_ _ AACeG_ hele a auc y a f Te Fest Prevous T 2 3 4 Went Last Once you have selected the matrix or matrices that you would like to include in your profile click the Select matrices button You will be given a preview of the set that you have selected Select matrices to include in the profile W Mark all Matrix W MyoD V MYOD_01 M00001 WI E47 V E47_01 M00002 7 v Myb V VMYB_01 M00003 W c Myb V CMYB_01 M00004 Quality high high high high FP frequency per 1kb nucleotides when false negative rate of 10 30 4 408 2 118 5 690 1 707 17 746 3 388 18 261 5 016 50 1 276 0 955 1 254 2 024 70 90 0 666 0 073 0 386 0 063 0 502 0 035 0 602 0 078 You can continue to add to or edit the set When you are satisfied with the set click the Proceed to cut off selection button On the next screen you will be asked to name your profile and to select the cut off values to be used Last updated September 30 2015 BIOB SE BIGLOGICAL DATABASES LA Ay mr i Plt search e to TRANSFAC Al As tools my data Select matrices and cut offs for your profile Please enter a name for your profile Select the following cut off for all matrices minFP Cl Unmark
15. e miRNAs radio button click the Upload a list of miRNAs in bulk link and then proceed as described above for uploading a list of genes BIOB SE a RES AAE ERE search tools my data BIOBASE search THide search options Limit search to me proteins O Transcription factors Vanants Matrices Diseases thways Drugs Search miRNA by Name Identifier Search which species Search all species ARNAS in bulk apd search for them oO miRNAs search help View statistics for PROTEOME 2014 4 TRANSFAC 2014 4 2 Match gene or miRNA set upload option To upload a list of genes or miRNAs and launch a Match analysis in one step from any location choose tools gt Predict TF binding sites Last updated September 30 2015 BIOB SE BIGLOGICAL DATABAEES search tools Gene regulaton analysis mt te ITORASF sea BIOBASE search Step by step data analysis Create and compare matrices VHide search options Linwt search to i Predict TF binding sites Identify miRNA regulators Genes and proteins sins Sted ies ia i i aa SSE mRNAs Pathways Search genes and proteins by Name Identifier BLasTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes 7 z hen wale aller naling and meta se the f t al analysis tool t Search all species v aiaa a SAE REA TE ain alt an car a jrated relatii nig haracts gt
16. e Date created 23 01 2015 Identifier V Defaultexa_31539 Score 1 780e 02 TGA TCA Nucleotide position frequency A G T Consensus 0 5500 0 1500 0 3000 0 0000 0 0000 0 0000 0 0000 1 0000 0 0000 0 0000 1 0000 0 0000 1 0000 0 0000 0 0000 0 0000 0 0000 0 5000 0 4500 0 0500 0 0000 0 0000 0 0000 1 0000 0 0500 0 9500 0 0000 0 0000 1 0000 0 0000 0 0000 0 0000 FA ga SB FP ai 4 P ave matrix and specif t of Note that this operation may take a few minutes When the process is complete this may take a few minutes due to the calculation of the cut off values you will be notified that the matrix has been saved to your library It will now be listed in the Gene regulation analysis gt Data gt Matrices gt Uploaded matrices folder of the my data menu my data and will also be listed in the Profile creation tool accessed from the Match tool page which can be used to create a profile containing the matrix for use by Match For a more detailed description of this tool please see the Gene regulation analysis tools gt Create and compare matrices page of the TRANSFAC user manual Last updated September 30 2015 B E skl documentation A What s New O Introduction to the BKL hi Known Limitations H BKL Reports a BKL Search and Tools uj Step by step data analysis LU miRNA Analysis it Predicting TF binding sites Genome Trax Search Tool 3 BKL Data Management A BKL Analysis Schedu
17. e supported 1 Gene level microarray and RNA seg data sets 2 ChlP seq data sets 3 Transcript level RNA seq data sets Access the workflows through the quick start section of the Home page Last updated September 30 2015 What s New MATCH tool Transcription factor binding site analysis Search DNA sequences for potential transcription factor binding sites How to gt MATCH Analysis videos gt Composite Model Analysis RR Genes Gene level microarray and RNA seq data sets This workflow accepts pre filtered up or down regulated genes as well as the complete list of genes analyzed in the experiment r 4 Sequences ChiP seq data sets This workflow accepts sequences _ FASTA EMBL Genbank or RAW format or genomic intervals in bed format which are used to extract the corresponding sequence gt Comparative Promoter Analysis gt Profile Creation gt Browse more videos Quick gt Getting started start with TRANSFAC ah Transcript level RNA seq data sets This workflow accepts pre filtered up or down regulated transcripts as well as the complete list of transcripts analyzed in the experiment Or by clicking the tools menu and then the Step by step data analysis link BIOB SE SOLO GICAL CATARASES search tools Gene regulation analysis tools 7 BIOBASE search Step by step data a
18. e information about how high versus low quality matrices are defined please see the BKL Search and Tools gt TF Binding Site Prediction gt Cut off Values page of the TRANSFAC user manual De selecting this option will allow the low quality matrices to be included in the analysis 3 Set cut offs Depending on the profile selected such as for the tissue specific profiles you may have the option to modify the cut off settings When this option is enabled you are able to select whether you want to use the minFP minFN or minSUM cut offs to use the cut offs from the profile which for prepared profiles are usually the minFN cut offs or to manually set your own cut offs 4 p value threshold As FMatch analyzes two sequence or gene sets in comparison a p value is calculated for over representation of sites for particular matrices in the analyzed set versus the background set FMatch compares the Match result of the two sets and optimizes the cut offs for each matrix used in the analysis to reach the best separation between the two sets Only those matrices for which the p value for over representation of the sites in the experimental set fits the p value threshold are reported By default the p value is set to 0 01 To make the p value more or less stringent type the new p value into the box When you are ready launch the analysis by clicking the start search button Your analysis will be forwarded to the taskbar If you keep
19. e selected using the pull down menu 2 Maximum connection distance between nodes This parameter specifies the maximum number of steps that may separate two nodes in the input list By default the parameter is set to 3 but you may select a distance from 1 to 5 Specifying a smaller maximum connection distance will generally produce more smaller networks while specifying a larger maximum connection distance will generally produce fewer larger networks In general as you increase the maximum connection distance smaller networks will become merged into larger networks 3 Preferred network density This parameter specifies the connectedness of a node to other nodes in the network By default the parameter is set to Medium but you may select densities of Very low Low Medium High and Very Last updated September 30 2015 high Specifying a lower preferred density favors the retention of nodes and will generally produce larger more branched networks Specifying a higher preferred density favors the removal of nodes whose connection to the network is more fragile and will generally produce smaller more dense networks 4 Ignore directionality This parameter specifies the type of relationships that are considered when building the networks By default Ignore directionality is turned off and only those relationships which are unidirectional are considered Examples of unidirectional relationships include a ligand activating its receptor
20. entify shared networks Predict protein attributes 7 the Network inalys too t analyze Use the Knowle je Tra j 2 Genes and proteins search help onnected nodes uncharacterized protein r View statistics for PROTEOME 2015 3 And then click the Create your own model link in the right hand side of the page or the Create new model link next to the model pull down menu that appears when Composite model search by pairs of TFs is selected as the analysis method BIOB SE POLOGA Parapatan search Predict Transcription Factor Binding Sites whet is this Predicting TF binding sites The Match gram uses or weg ea A seguente pote f AO site eD equerte ea e outpu Bisto y es tha hod sequerce a f e r grap ica e e fact and mat etale erature ed mformeton factor a efered d Sequence Learn more Matrices the complete TRANSPA nari brary ovecabie for use with Match but you may aiso hoose to Create or edd your cen motrices Profiles a selecton of commonly used profiles lector f matnces Ce avalado th amp armatvely y may Create your Ov an profile electing he rs e SF AC mo bra 55 well as ar y es tr DU have cote Vi Use defouk parameters Models a selection c avecable for Osta version 20144 Note that you can also access the Profile creation tool via the Create and compare matrices tool When the tool loads you can select the pair of components matrices that you would like to i
21. heduling LJ Consulted Databases a Citing the BKL Publications LJ Disclaimer Finding novel motifs Seeder The DECOD algorithm in TRANSFAC replaces the Seeder algorithm Analyze gt Binding sites search gt De novo motifs Seeder used for finding novel motifs in a set of sequences in ExPlain De novo motifs Seeder Identification of novel motifs by comparing with background sequences For more information about this algorithm please see the publication by Huggins et al 2011 Bioinformatics 27 2361 To identify a novel motif within a set of sequences use the Create and compare matrices tools which is accessed from any page within TRANSFAC by clicking the tools menu followed by clicking the Create and compare matrices link Last updated September 30 2015 BIOB SE BIOLOGICAL DATADASES search fools Gene regulation analysis tools ec BIOBASE search Saas Sati PS Step by step data analysis Create and compare matrices WHide search options Umit search to Predict TF binding sites Identify miRNA regulators Genes and proteins PLE TRS 3 i ay eras PT ies maRNAs Pathways Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species v nethwaye a PERE s pari f rated eu a gt Upload a list of genes or proteins Er a its Predict protein attributes
22. i ci aa iooi mRNAs Pathways Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species v a ete teint combos gt Upload a list of genes or proteins Identify shared networks Predict protein attributes er tool to Q Genes and proteins search help View statistics for PROTEOME 2015 3 When the tool loads you are given the option to analyze a previously uploaded list of genes or to upload a new list of genes Despite the different entry point the process for uploading a list of genes is the same as is described in Loading gene and miRNA sets Last updated September 30 2015 BIOB 5g Wecome to TRasrace shinai search tools my data Network Analysis what is this Select gene set Select gene set l Upload new gene set Use default parameters Ignore directionality erform network analysis Once you have selected the data set to be analyzed you can launch the analysis and it will be run with the default parameters which are set in the white section of the tool If you wish to make any changes to the parameters de select the Use default parameters and make the desired changes 1 Data version TRANSFAC supports the four most recent data versions By default the current version is selected but previous versions may b
23. lee tie s j a em the f Kr e T fep t Network analysis Tra Genes and proteins search help onnected nodes uncharacterized protein juences 3 View statistics for PROTEOME 2015 3 Once the tool loads select the Compile matrix from unaligned sequences option and fill in the requested fields in the yellow section including the set of sequences to be searched for the novel motif the set of background sequences to be used and the expected motif width a default setting of 8 is given Last updated September 30 2015 Create a new matrix whet th verlebrates W Use defauk parameters Soecty how many times the mot expected to appear within a sequence 1 U Ignore Mono and di nucleotide repeats At this point you can start the analysis keeping the remaining default parameters or by adapting them as desired in the white section 1 Specify the number of times the motif is expected to appear within a sequence default is set to 1 2 Ignore mono and di nucleotide repeats turned on by default Once the analysis completes a nucleotide position frequency table for the best scoring motif and consensus sequence logo preview will be created and you will be prompted to click the save matrix and specify cut off values button to finalize the upload Last updated September 30 2015 BIOBse SE erometo BIOLOGICAL DATABASES search tools my data Create matrices Matrix name Defaultexampl
24. ling a Consulted Databases 4 Citing the BKL H Publications ld Disclaimer Functional analysis The functional analysis tool in TRANSFAC replaces the Analyze gt Functional analysis gt Functional classification and Analyze gt Functional analysis gt Canonical pathways mapping functions of ExPlain ga Functional classification Classification into categories GO diseases tissues 1 Canonical pathways mapping Map to BKL pathways and signal chains The tool analyzes sets of genes and miRNAs for the presence of statistically over represented terms using a basic Fisher test analysis To access the functional analysis tool from any page within TRANSFAC click the tools menu and then the Identify shared attributes link Last updated September 30 2015 BIOB SE BIOLOGICAL DATABASES search toolis Gene regulaton analysis tools IOBASE sea 42 BIOBASE search Step by step data analysis Create and compare matrices YHide search options Limit search to Predict TF binding sites Identify miRNA regulators Genes and proteins hes aa a May ot an a SAREE miRNAs Pathways Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species d pathways or id customized nehwcris a ee red irated relate nij gt Upload a list of genes or proteins in Identify shared networks Predic
25. low quality matrices Matrix MyoD VSMYOD_01 MOOO01 E E47 VSE47_01 mMoooo2 v Myb VSVMYB_0O1 MOO003 W c Myb V CMYB_01 mooo04 Quality high high Core Matrix similarity and FP frequency at the selected cut offs FN10 minFN 0 701 0 800 4 408 0 740 0 765 5 690 0 670 0 734 17 746 0 705 0 733 18 261 FNSO 0 701 0 853 2 118 0 740 0 651 1 707 0 670 0 859 3 388 0 705 0 823 5 016 B save profile what is this FNSO 0 701 0 882 1 276 0 740 0 661 0 955 0 670 0 889 1 254 0 705 0 854 2 024 FN YO 0 701 0 908 0 666 0 740 0 919 0 386 0 670 0 909 0 502 0 705 0 904 0 602 FN9O 0 701 0 953 0 073 0 740 0 960 0 063 0 670 0 960 0 035 0 705 0 944 0 078 minFP minsUM 0 701 0 868 0 740 0 832 0 670 0 869 0 705 0 843 Core Matrix similarity tah When you are finished click the Save profile button The profile will now appear in the profile pull down menu of the Match tool For a more detailed description of how to create a profile please see the Gene regulation analysis tools gt Predict TF binding sites gt Profile Generation page of the TRANSFAC user manual Last updated September 30 2015 id BKL documentation D What s New D Introduction to the BKL D Known Limitations B BKL Reports
26. matory response Multiple Sclerosis Relapsing Remitting B lymphocytes bone marrow GO molecular function GO biological process GO cellular component a NI Disease T lymphocytes Organ or tissue thymocytes Cell Acquired Immunodeficiency Syndrome Taa lymph node Canonical pathway Leukemia Lymphocytic Chronic B Cell For a detailed description of the analysis report please see the Functional analysis tools gt Identify shared attributes page of the TRANSFAC user manual i Bic aie regulation analysis tools D Genome Trax Search Tool BK Data Management 3 BKL Analysis Scheduling 3 Consulted Databases E citing the BKL og Publications 3 Disclaimer Last updated September 30 2015 Network analysis The network analysis tool in TRANSFAC replaces the Analyze gt Network analysis gt Network clusters tool of ExPlain Network clusters Finding dusters of highly mutually connected molecules The tool analyzes sets of genes for networks enriched with members of your gene set To access the network analysis tool from any page within TRANSFAC click the tools menu and then the Identify shared networks link BIOB SE PICLOGICAL DATADASUS search tools Gene regulaton analysis tools Step by step data analysis Create and compare matrices VWHide search options Umit search to Predict TF binding sites Identify miRNA regulators Genes and proteins the Mate nriths
27. nalysis ireate and compare matrices View more search optons if you want t MATCH tool Transcription MMs RU T Identify miRNA regulators sequences fo e the Match algorithm and TRAN RNA analysis tool to ana Step by step data analysis i Genes Gene level nE a EE om cee oe accepts pre the complete vos View pathways and build networks Identify shared attributes equences ChIiP seq dat lt r j and metabo the Functona ar j tool t inalvre y E a eee pathways or build customized network A aia ee RIAS Te EROI in bed form Sia Ree eal characterist sequence ee Identify shared networks Predict protein attributes EB Transcripts Transcript le Use the Network analysis tool to analyze e the BioKnowledge Transfer tool to pre filtered u sets of genes for clusters of highly assign predictive functions to complete list Srm uncharacterized protein sequences For a detailed description of the workflow options please see the Gene regulation analysis tools gt Step by step data analysis page of the TRANSFAC user manual Last updated September 30 2015 Last updated September 30 2015
28. nclude in your model Last updated September 30 2015 BIOB SE ErFLESICEL BETA ead search tools my data Create a new composite model what is this Ej Use inverted order af components Specht the dancea between components 5 40 When you click the magnifying glass icon for a component a matrix selection window will open When the window opens you can browse the library of matrices by scrolling through the individual pages but you can more easily narrow the list by searching for specific matrices by name or by filtering the list to Exclude low quality matrices or to Show only user matrices matrices that you have uploaded BIOB SE Matrices Matrix accession Ending factor identifver Matrix category classification Sequence logo E m rah ve m gt Seawences MID Corr cued af MO0001 Myot VSMYOO_O1 roen incnacual genomic 685 mayor m i Asc i G Zc APN 11 sequences compaed MOoon E12 E2A E47 ITF 1 Toleza v3e47_01 wrt ienported Porn Metatute 47 G T referante Z G 24 sequences comptied Monod 3 eA YSvvYB_01 ere impored fom Merature yy G G reterarce m CANO c Ard daemi g M an eo gy ate at rf wences S isolormi Mydisoteem 40 sequences SELE MOO0D4 ie sackorndk Ciit VSCMYE_01 CASTing SAAS TDA Target omy MyS sscform C AyD F Getection assay ha apar r AtA detec soy S oom ay 2 5 sequences compilec matt MOO AP 4 SAP
29. ofile Generation LJ Composite Model Editor LD Command Line Use h Frequently Asked Questions D Create and compare matrices LD Genome Trax Search Tool LD SKL Data Management D SKL Analysis Scheduling LJ Consulted Databases ie Citing the BKL E Publications LJ D sclaimer DE Loading matrices TRANSFAC s Create and compare matrices tool replaces the File gt Create new data gt Weight matrix option in ExPlain m3 Weight matrix Make matrix from aligned sequences To load a custom matrix in TRANSFAC dat format or to create a matrix from a set of aligned or unaligned sequences use the Create and compare matrices tools which is accessed from any page within TRANSFAC by clicking the tools menu followed by clicking the Create and compare matrices link Last updated September 30 2015 BIOB SE BIOLOGICAL DATABASES search tools Gene regulaton analysis tools u ORASF cearch l BIOBASE searct Step by step data analysis Create and compare matrices VWHide search options Umit search to Predict TF binding sites identify miRNA reguiators Genes and proteins ohn aaa ren i p NA SRDE mRNAs Pathways Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species 7 pathways or build customized networks gt Upload a list of genes or proteins in Identify sha
30. otifs Seeder Functional analysis Network analysis Step by step analysis Wizard workflows Loading gene and miRNA sets The options described here replace the File gt Create new data gt Gene set and File gt Load data from file gt Gene set functions in ExPlain a v Gene set Enter paste accession numbers W Gene set Tab separated MS Excel There are two options for loading a list of genes into TRANSFAC for analysis by Match and other tools 1 Genes and proteins search From the TRANSFAC home page click the BIOBASE logo or choose search gt Start a new search click the View more search options link if it has not been previously clicked search tools my data EPPLOGILAL DATABASES Select the Genes and proteins radio button and then click the Upload a list of genes or proteins in bulk link Last updated September 30 2015 BIOB s SE Welcome to TRansrace PROTI BIOLOGICAL DATABASES search tools my data BIOBASE sea search FHid e search ophons limit search to Genes and proteins Transcription factors Variants MRNAS Matrices Diseases Pathways Drugs Search genes and proteins by 2 Name Identifier BLASTp TF binding site Search which species Search all species F Upload a list of genes or proteins in bulk afd search for them G Genes and proteins s arch help View statistics for PROTEOME 2014 4 TRANSFAC 2014 4 Click
31. r proteins in the input set and so could not be placed in a network To potentially include these proteins in the networks you can re run the analysis with a higher maximum connection distance between nodes The proteins are CCL21a FILizeta MASP1 show all gt Show results of the gene to protein conversion Networks identified e Save this report View selected network in Pathfinder Total network Input nodes Connecting nodes size count Input nodes in network count Connecting nodes in network mM 15 8 icami IFNgamma IL 10 IL 4 IL 5 7 IFNRII IL 10R IL 4R IL 5R Jak2 STAT1 VEGFR 3 VRP Tyk2 VEGFR 2 fr 3 3 CD26 cxcr4 SDF 1 0 First qq 2 gt Last Filter Hits on page 10 Last updated September 30 2015 For a detailed description of the analysis report please see the Functional analysis tools gt Identify shared networks page of the TRANSFAC user manual 3 ax documentation lad What s New Introduction to the BRL Li Known Limitations BKL Reports a i ext Search and Tools a BR View Pathways and build netwo Identify shared attributes Predict protein attributes t Gene regulation analysis tools Genome Trax Search Tool BKL Data Management BKL Analysis Scheduling Consulted Databases Citing the BKL Publications Disclaimer st Leo onwe Step by step analysis Wizard workflows The step by step analysis tool in TRANSFAC replaces the Wizard mode of ExPlain Three workflows ar
32. red networks Predict protein attributes the Network anal Poo to ana e the Fuokr ale Tra Fur ts of genes for jssters of fughiy 5 inp dictrve functions to Q Genes and proteins search help mnected nodes uncharacterized protein sequences View statistics for PROTEOME 2015 3 To upload a matrix in TRANSFAC dat format select the Upload matrix radio button click the browse for file button select the file to be uploaded and click the create matrix button BIOB s SE Bil ea alt search tools my data Create and compare matrices Create matrices Compare matrices against TF library Create a new matrix what is this A nucleotide position frequency table and consensus sequence logo preview will be created and you will be prompted to click the save matrix and specify cut off values button to finalize the upload Last updated September 30 2015 BIOB SE sisal search tools my data Create matrices Matrix name CREB_1105_03 Date created Identifier V 6CREB_1105_03 Nucleotide position frequency A C G T Consensus 1 3 20 T 0 1 21 G 24 1 A 0 25 C 2 23 G 2 1 22 T 11 13 1 M 16 1 2 A e matrix and specify cutoff value Note that this operation may take a few minutes When the process is complete this may take a few minutes due to the calculation of the cut off values you will be notified that the matrix has been saved to your library It will now be listed in the Gene regulation
33. rices tool When the tool loads you can browse the library of matrices by scrolling through the individual pages but you can more easily narrow the list by searching for specific matrices by name or by filtering the list to Exclude low quality matrices or to Show only user matrices matrices that you have uploaded Last updated September 30 2015 Create a new profile s Profiles are collections of pos onal weight matrices PWMs stich are used by Match to Match window bot thes tool may be used to creste custom profiles of your can search for predicted trarecripoon tector binding pies A selection of commonly used profiles are provided within the To create a cumem profile select the dered matnces from the Lobie proceed to at olf selecton and then name and save you profile Once saved your profile wil be made ava sbie for use withen he Match endow ARemetvely custom proftes may be created by performing a Matn search folowed ty forwarding the set of matrices to this tool and then following the steps outhred above Accession Matrix Matrix Identifier Number Quabty MOOO0 I tag VSMYOD0D_ OI M00002 hgh V E47_01 M00003 tegh VSVMYB_01 M0004 hoh V cMy6_01 MODODS hogh VSAP4_01 Showing I to 5 of 5 499 entnes E47 v Myd Matnik Category metrix compded from weSvidual gnome sites commaled matrix uenported trom bherature reference compted matx enported from Merature reference SELEX CAST no SAAR TDA Target dete
34. so that you can specify 1 whether you want Match to consider all available promoters for a gene or only the best supported promoter which is defined as the promoter with the most significant cluster of Ensembl transcription start sites and 2 what portion of the promoter sequence you want to consider Like in ExPlain TRANSFAC promoters are 11 000 bp in length spanning from 10 000 base pairs upstream of the TSS to 1 000 base pairs downstream of the TSS A typical range is 500 to 100 best supported promoter 2 The analysis method to be used Last updated September 30 2015 Match By default the analysis method will be set to Match search for TF binding sites When this method is selected the Match algorithm will use the positional weight matrices in the selected profile to search your sequences for binding sites which meet the cut off criteria This option is equivalent to running Analyze gt Binding sites search gt Match in ExPlain with no background set selected Composite model When Composite model search by pairs of TFs is selected the composite model algorithm which is based on the Match algorithm use models composed of pairs of matrices separated by a specified gap to search your sequences for co occurring binding sites This option is equivalent to running Analyze gt Binding sites search gt Search for new targets of TF combination in ExPlain FMatch When FMatch
35. t TF binding sites link Last updated September 30 2015 BIOB s SE BIOLOGICAL DATABASES search tools Gene regulaton analysis tools ITORAS F sez h BIOBASI aren Step by step data analysis Create and compare matrices WHide search options Umit search to Predict TF binding sites Identify miRNA regulators Genes and proteins the Mat thm and TRANSFA the miRNA a tan to rmRNAs Pathways E Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species 7 pathways or bui ustamized networks ets of genes or gt Upload a list of genes or proteins in Identify shared networks Predict protein attributes se ti we Mat Ts a ala al j j mpm gt Tere Fa i 2 Genes and proteins search help sequences View statistics for PROTEOME 2015 3 And then click the Create your own profile link in the right hand side of the page my data Ac ea erin Rrena A eaa E A PENN GESALA F y a previously uploaded sequence p Matrices the compicte TRANSFAC matrix library avadabdie for use wah Match but you may abs Profiles a sciection of commor icou gt On OF f e 1 of matricog ss made mM profig selecting from the matrices v FAC metrx library 53 well as any t you have created Note that you can also access the Profile creation tool via the Create and compare mat
36. t protein attributes the Network analysis tool to analyze e the BioKnow ra ert Q ets of genes for clusters of highly assign p Genes and proteins search help onnected nodes uncharacterized protein View statistics for PROTEOME 2015 3 When the tool loads you are given the option to analyze a previously uploaded list of genes or miRNAs or to upload a new list of genes or miRNAs Despite the different entry point the process for uploading a list of genes and miRNAs is the same as is described in Loading gene and miRNA sets BIOB SE BIOLOGICAL DATABASES search Once you have selected the data set to be analyzed click the perform functional analysis button Your analysis will be forwarded to the taskbar If you keep the taskbar window open until the analysis completes the analysis results will automatically be loaded within the open window Last updated September 30 2015 BIOB 4 SE BIOLOGICAL DATABASES search tools my data Functional Analysis Report what is this Return to functional analysis Summary 32 genes from file Expressed in lymph were analyzed using the Fisher Test for significantly enriched functional attributes using PROTEOME version 2014 4 Save this report Overview of terms log P value of term group 0 20 40 60 80 100 lymph endothelium endothelial cells blood vessels dendritic cells NK cells immune response HIV Infections tonsil lymphoid cells chemotaxis inflam
37. tes Network analysis tool t e the Knowledae Transfer tool to Genes and proteins search help nnected nodes View statistics for PROTEOME 2015 3 There are three types of input that are required in the yellow section of the Match tool Last updated September 30 2015 Match search for TF binding sites vertebrate_non_redundant_minFP 7 1 The data set to be analyzed The tool provides the option to analyze DNA sequences or to analyze a gene or miRNA set When I am analyzing DNA sequences is selected you are given the option to run Match against an example sequence against a previously uploaded sequence or set of sequences or to upload a new sequence or set of sequences Uploading sequences either as raw sequences i e FASTA Genbank or as genomic intervals is described in Loading sequences and intervals When I am analyzing a gene or miRNA set is selected you are given the option to run Match against an example gene against a previously uploaded list of genes or miRNAs or to upload a new list of genes or miRNAs Despite the different entry point the process for uploading a list of genes and miRNAs is the same as is described in Loading gene and miRNA sets When you choose the option to analyze a gene or miRNA set Match will extract the promoter sequence s associated with the gene s or miRNA s from the underlying database and use those sequences for its analysis You are provided with 2 additional parameters
38. unid 26 shee ee ee at gig e gt p sy BTR eee kL amp Exempla pone m PS n tni 4 g new ger aD of use wan M posd 2 hen net hoots reath or e RAPAE N N ve te gene s nat Matrices tiv A F af Profiles a osie Ji Use default parameters Similarly when using the Composite model option a number of prepared models are provided or you can create your own models using the Model creation tool also accessed through the help section on the right hand side of the screen Once the required inputs have been specified you can launch the analysis and it will be run with the default parameters which are set in the white section of the Match tool Use default parameters Data version J Use only high quality matrices Set cut offs Minimize false positives I _startsearch If you wish to make any changes to the parameters de select the Use default parameters and make the desired changes The parameter options differ based on the analysis method selected but collectively cover the following 1 Data version TRANSFAC supports the four most recent data versions By default the current version is selected but previous versions may be selected using the pull down menu 2 Use only high quality matrices Last updated September 30 2015 By default this option is used to exclude matrices which generate particularly high numbers of false positives from Match and FMatch analyses For mor
39. ysis toots Create and compare matrices LOBASE sear aT hy i Step by step data analysis WHide search options Umit search to Predict TF binding sites Identify miRNA regulators Genes and proteins mRNAs Pathways Search genes and proteins by Name Identifier BLASTp Functional analysis tools Search which species View pathways and build networks Identify shared attributes Search all species v a 6 ed on curated relatii Predict protein attributes lt tha g Ar yl e a Tra 4 gt Upload a list of genes or proteins er bd Identify shared networks of highly 1 protein sequences 2 Genes and proteins search help nected nodes View statistics for PROTEOME 2015 3 Within the Match tool select the I am analyzing DNA sequences radio button and the Upload a new sequence radio button Then select whether you wish to upload DNA sequences directly or to submit Genomic intervals for automatic sequence retrieval tools my data HIGLASICEL HATARAT z search Predict Transcription Factor Binding Sites what is this SEQUEntes ene OF MRA ices up to 1 000 000 nucleotides in EMBL Genbank or RAW oe is ELOLA L reset form Any sequence or set of sequences up to 1 000 000 nucleotides in length can be uploaded in FASTA EMBL Genbank or RAW format For human mouse and rat species you can alternatively upload a list of Last updated September
40. zila Firefox eji Expressed in lymph 25 of 32 total i ipio peral Besbhati miinalla grh ego buik hee idby dogiem hE Expat these results w Pathfine Filter search resulls Hits en page 25 Hame Seon Cesophan NRE Human Nuclear recept Pmbryogenesis and apophosis dow ms MRA is decreased in arndane tris i h VEGFC Human Vascular endot signaling mediates bone resorption amd parng horectal carcinomas and wanous other cancers cri tt idk irm ar PRomdings iir mahi Baand T1 aero in rharmeabavio hamannade diene ond maim sanracdatad im Alternatively the Filter link can be used to open a filter dialog box that allows you to actively filter the data set by any of the available columns and then save the filtered data set Loading sequences and intervals The options described here replace the File gt Create new data gt Sequences File gt Load data from file gt Sequence and File gt Load data from file gt Intervals BED file functions in ExPlain Za Sequences FASTA or EMBL format gt Sequence Paste nucdeotide sequence Intervals BED file Genome intervals Raw sequences as well as intervals for extracting sequences are loaded through the Match tool From any page within TRANSFAC click the tools menu and then the Predict TF binding sites link Last updated September 30 2015 BIOB SE BIOLOGICAL DATABASES search tools Gene regulaton anal

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