ANGIOGENES: A knowledge database for angiogenesis

Institute of Cardiovascular Regeneration, Goethe University Frankfurt
  1. Quick Search
  2. Advanced Search
  3. Supported Conditions
  4. Finding Homologs
  5. Browsing
  6. Downloads

1. Quick Search

It is advised to use ANGIOGENES advanced search. However, in many cases, simplified search offers a useful and simple graphical method to search and to compare data. Upon submission, quick search will return Venn diagrams displaying the numbers of all transcripts (left) and lncRNA (right) expressed, enriched or specific for certain cell line and tissue under normal condition or with treatment.
  1. Select condition 1 (Required) - Specifies the primary condition for the search, which is shown as the blue circles of the Venn diagrams on the left.
  2. Select expression 1 (Required) - Determines the type of expression shown by the Venn diagrams.
  3. Select condition 2 (Optional) - Allows for comparing a secondary condition to the primary target, which is shown as orange circles on the right of Venn diagrams.
  4. Select expression 2 (Optional) - Determines the type of expression shown by the Venn diagrams.
  5. Select condition 3 (Optional) - Allows for comparing a tertiary condition to the primary and secondary target, which is shown as green circles on the bottom of Venn diagrams.
  6. Select expression 3 (Optional) - Determines the type of expression shown by the Venn diagrams.
  7. Search - Clinking this button will submit the query.
To preform a quick search, the top selection boxes for a experiment and expression type must contain a tupel of species, cell-line, tissue and condition and an expression value. The second and third row of tissues and expression types is optional, however, both must be set for the form to be valid. Note: the 'Search' button will be disabled if the form is not valid.

Advanced Search

The advance search allows users greater control of search results within ANGIOGENES through the use of query tags and boolean operators

For example, the query "BIOTYPE:lincRNA" will return only sequences with the biotype lincRNA. A full listing of all query tags can be found in the table below.

Boolean operators allow users to combine query tags for even more expressive searches. This may seem overly complex at first, however, these methods allow users to make arbitrarily complex searches, limited only by their imagination and the RAM memory of the server. A detailed overview of logical conjunction can be found here.

However, there are only a few operators one needs to know for ANGIOGENES.

Operator Illustration Explanation
and The "and" operation returns only elements common to both sets.
or The "or" operator returns only elements common to either or both sets.
not The "not" operator returns only elements not in the second set.

A finaly note, if a query contains a space, then quotation marks should be added around the full string.
This is a cheat-sheet for the advanced search. A more comprehensive explanation can be found on the help page .

The advance search was designed in response to the high expression specificity of lncRNAs. We hope users will recognize its utility as queries are are only limited by ones imagination and the RAM memory of the server.
Expression Example (Links run searchs) Description
No tag. MALAT1 When no tag is specified the query is treated as an accession or gene name. Wildcards are supported.
SPECIFIC:(condition) SPECIFIC:"HAoEC--Heart--Normal" Returns sequences specific (i.e. not expressed elsewhere.) to the specified condition. See "Supported Conditions" on the Help page for a list of searchable values.
ENRICHED:(condition) ENRICHED:"HAoEC--Heart--Normal" Returns sequences with higher than average expression in the given condition. See "Supported Conditions" on the Help page for a list of searchable values.
EXPRESSED:(condition) EXPRESSED:"HAoEC--Heart--Normal" Returns transcripts expressed in the given condition. See "Supported Conditions" on the Help page for a list of searchable values.
HOMOLOGS:(Gene Accession) HOMOLOGS:ENSG00000003436 Returns homologs of searched genes. For a BLAST/BLAT search see Finding Homologs
POS:(tax_id):(chromosome):(start)-(end) POS:9606:1:914880-969309 Returns regions, genes, or transcripts falling withing the given position.
BIOTYPE:(biotype) BIOTYPE:lincRNA Returns regions, genes, or transcripts which contain a transcript annotated as the given biotype.
REGIONTYPE:(CGP|UCNEbase|VISTA) REGIONTYPE:UCNEbase Returns regions which contain the given region type. If searching for genes or transcripts, genes and transcripts contained within the given region type will be returned. For detail, please refer to C-It-Loci database: http://c-it-loci.uni-frankfurt.de
TAXID:(7955|9606|10090) TAXID:7955 Returns regions, genes, or transcripts associated with the given taxonomy. Taxonomy IDs (TAXID) are: 7955 (zebrafish), 9606 (human), and 10090 (mouse).
GO:(GO term accession) GO:0005515 Returns regions, genes, or transcripts which contain an annotation of the given Gene Ontology (GO) term.
Boolean Operators
and TAXID:7955 and BIOTYPE:lincRNA Returns accessions existing between two query sets.
or BIOTYPE:lincRNA or BIOTYPE:antisense Returns accessions existing in either of two query sets.
not POS:9606:1:814880-3069309 and not POS:9606:1:1714880-2169309 Returns accessions not in the query.
() BIOTYPE:lincRNA and (TAXID:9606 or TAXID:10090) Increases the precedence of a query.
* gata* Specifies where to use wildcards in query. Note: wildcards are only supported for tagless searches.
More Examples
Behavior Query Explination
Return all lncRNAs BIOTYPE:lincRNA or
BIOTYPE:processed_transcript or
BIOTYPE:3prime_overlapping_ncrna or
BIOTYPE:antisense or
BIOTYPE:non_coding or
BIOTYPE:retained_intron or
BIOTYPE:sense_intronic or
BIOTYPE:sense_overlapping 		Using the "or" operator, link all sub-types of lncRNA. See Ensembl's documentation for a description of each biotype.
Return lincRNAs falling within Conserved Gene Pairs (CGPs) BIOTYPE:lincRNA and REGIONTYPE:CGP One lncRNA characteristic is a lack of sequence conservation. Therefore, by using conserved gene pairs or other highly conserved regions, one can quickly find syntetic regions to hunt for related lncRNAs.

Supported Conditions

TAXID Supported Condition
10090 C166--Yolk sac--EPAS1 KD
10090 C166--Yolk sac--Normal
10090 Tie2plus EC--Cerebral cortex--Normal
10090 Tie2plus EC--kidney--Normal
10090 mES--Embryoid body--Gata1&2KO
10090 mES--Embryoid body--Normal
10090 mES--Embryoid body--SclKO
9606 BECs--Skin--Normal
9606 BECs--Skin--Under laminar flow
9606 HAoEC--Heart--Normal
9606 HAoEC--Heart--SAHA treatment
9606 HAoEC--Heart--TSA treatment
9606 HHSEC--Liver--Normal
9606 HMVEC-D--Skin--Normal
9606 HUVEC--Umbilical vein--EPAS1 KD
9606 HUVEC--Umbilical vein--Normal
9606 HUVEC--Umbilical vein--VEGF treatment 12h
9606 HUVEC--Umbilical vein--VEGF treatment 1h
9606 HUVEC--Umbilical vein--VEGF treatment 4h
9606 HUVEC--Umbilical vein--Virilizer
9606 HUVEC--Umbilical vein--WTAP
9606 HUVEC--Umbilical vein--cell polyAminus
9606 HUVEC--Umbilical vein--cell polyAplus
9606 HUVEC--Umbilical vein--cytosol polyAminus
9606 HUVEC--Umbilical vein--cytosol polyAplus
9606 HUVEC--Umbilical vein--nucleus polyAminus
9606 HUVEC--Umbilical vein--nucleus polyAplus
9606 HUVEC--Umbilical vein--siScr
7955 LECs--Lymphatic--FACS isolation of Kaede photconverted red ECs
7955 Unknown1--Pharyngeal arch--Normal GFPplus
7955 Unknown2--Pharyngeal arch--Normal GFPminus

Browsing

The large size of ANGIOGENES necessitates breaking queries into manageable sizes. This is accomplished via the browsing view. The browsing view breaks queries into pages of a given number of rows and allows navigation between pages via the “Previous” and “Next” buttons. Navigation to a desire page is also possible by setting the page number field to the desired page.


  1. The number of rows to show per page.
  2. Displays the number of the current page. When changed, this will redirect to the new page number
  3. Move to the previous page.
  4. Move to the next page.

Finding Homologs

As ANGIOGENES uses the same annotations as Ensembl, a number of services provided by Ensembl can be transfered to ANGIOGENES. For example a homology search using Ensembl's BLAST or BLAT.

To preform a BLAST/BLAT search simply go to Ensembl's BLAST Search page. Below is a image highliting improtant sections of the BLAST form.



Once a a job has been submitted the queue screen will show the jobs status.



When the job finishes the results are displayed in table format.



From here there are three ways a user can find data in ANGIOGENES:
  1. Using gene names
  2. Using the position
  3. Using Ensembl accessions (Find these by following the links on the Blast Results page.)

Record Pages

Record pages contain detailed information about a data type contained within ANGIOGENES. This can include annotation data, genomic coordinates, expression data, homologs, and GO terms depending on the data type.
Genome Browser
Each record page will contain at least one genome view. ANGIOGENES uses the Biodalliance genome browser. For details about this browser, please refer to http://www.biodalliance.org/
Visualization of Transcript Expressions
There are two ways to view expression data: a graphical view and a text view. Users can toggle between the two views using the provided buttons. The text view is a simple table comparing various transcript expressions versus conditions with numerical values representing the average FPKM values followed by the standard deviations with ± symbol. The graphical view scales the FPKM values using the equation y = 100.0 - (log(x)+12)*((3*x)/(x+1)+1), where y is the lightness value in the HSLA color.

Downloads

Downloads of the average gene expression values and all expression values with metadata are available. These are meant for use with list of accessions downloaded from search interface.

For example values can be extracted on linux machines using grep.
Ex:
grep -f downloaded_accesssions.txt angiogenes_gene_exps.tsv







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