Results: 3

1.
Figure 3.

Figure 3. From: AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.

Screenshot from AGRIS depicting features of ReIN. For each Locus ID or gene name available in the AtRegNet database, ReIN displays all interactions involving the searched gene. Detailed descriptions of features are available in REIN tutorial page (http://arabidopsis.med.ohio-state.edu/REIN/ReINtutorial.html).

Alper Yilmaz, et al. Nucleic Acids Res. 2011 January;39(Database issue):D1118-D1122.
2.
Figure 1.

Figure 1. From: AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.

AtTFDB query result table. Either TF family browsing or search query results indicate Locus ID, synonyms, links, sequences and AtRegNet related data. The updated AtTFDB provides improved integration with AtRegNet. Confirmed direct target counts are indicated with ‘C’, and unconfirmed one are indicated with ‘U’.

Alper Yilmaz, et al. Nucleic Acids Res. 2011 January;39(Database issue):D1118-D1122.
3.
Figure 2.

Figure 2. From: AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.

Results of querying word frequencies. Occurrence, scoring and positional distribution of a given word is calculated for various genomic segments. (A) A query is initiated by entering a word 5–15 letters (e.g. CTAACCA) in length into the search box. (B) The user is notified if the queried word matches a known CRE available in AtcisDB. (C) Total occurrences include possible multiple occurrences within a single sequence. For instance, CTAACCA is found a total of 138 times in 5′-UTR region sequences, and 135 genes contain this word in their 5′-UTR regions. Expected occurrences are calculated by a Hidden Markov Model, as described in ref. 14. The unique sequence occurrences column is hyperlinked to a list of genes that contain the word in the corresponding segments. (D) Flot (http://code.google.com/p/flot/), a Javascript plotting library, was used for visualization of positional distribution of a word within different sets. Only Proximal and Distal Promoters segments are shown here. Charts are interactive and are capable of zooming into a desired region.

Alper Yilmaz, et al. Nucleic Acids Res. 2011 January;39(Database issue):D1118-D1122.

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