(recopilated by Veronica Dávalos)

CELL LINES INFORMATION

1. Colorectal cancer cell lines analysis summary:  http://www.cephb.fr/gaccc/

 Microsatellite analysis in colorectal cancer cell linesMismatch repair gene defects in colorectal cancer cell linesMutations in coding repeats in colorectal cancer cell linesMutations of oncogenes and tumor suppressor genes in colorectal cancer cell lines 

2.  The ATCC Cell Biology Collection. http://www.lgcpromochematcc.com/common/catalog/cellBiology/cellBiologyIndex.cfm 

The ATCC Cell Biology Collection is the most comprehensive and diverse of its kind in the world, consisting of over 3,600 cell lines from over 80 different species. It holds over 950 cancer cell lines and over 1,000 hybridomas for production of monoclonal antibodies, as well as a variety of special collections. 

3. ECACC European Collection of cell cultures.http://www.ecacc.org.uk/ 

ECACC, a world leader in the supply of Authenticated Cell Lines. 

4. Mutations in cell lines.  http://www.sanger.ac.uk/genetics/CGP/CellLines/ 

Our target is to sequence all known cancer genes in all of the cell lines. However, we release data before we achieve this goal. Therefore the present results should be considered as work in progress.

SEQUENCES

1. Sequences. http://genome.ucsc.edu 

We encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Blat quickly maps your sequence to the genome. The Table Browser provides convenient access to the underlying database. VisiGene lets you browse through a large collection of in situ mouse and frog images to examine expression patterns. Genome Graphs allows you to upload and display genome-wide data sets.  

2. Manipulate and Display a DNA Sequence. http://www.vivo.colostate.edu/molkit/manip/index.html 

Input a DNA (or RNA) sequence and obtain its inverse, complement or inverse complement.   7.  

3. Sequence Comparison & Homology-Identity Analyses http://restools.sdsc.edu/biotools/biotools1.html 

A lot of tools for sequence analysis.

  8.  Translate a DNA Sequence into a Protein. http://www.expasy.ch/tools/dna.html 

Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.

 9. Predictions. http://restools.sdsc.edu/biotools/biotools16.html 

Poly-A Site Prediction, Exon (ORF) Prediction, , Splice Site Prediction TATA Signaling, Promoter & Trans-Factor Bind Site Prediction, tRNA Gene Prediction.

EPIGENETICS

1. Information and protocols about epigenetic.

1. SOFTWARE FOR EPIGENETIC

•              for finding the region of interest:
• CpG island Searcher (D.Takai) screens DNA sequences for CpG islands and generates a graphical output.
• for prediction of methylation probability:
• Methylator attempts to predict whether CpG in a DNA sequence are likely to be methylated or not.
• for primer design and verification:
• MethPrimer (Long-Cheng Li) is a on-line tool for designing bisulfite-conversion-based Methylation PCR Primers. It can design primers for Methylation-Specific PCR (MSP) and Bisulfite-Sequencing PCR or Bisulfite-Restriction PCR. The input sequence is DNA sequence in any format. The program returns results in both text and graphic view.

VECTORS AND RESTRICTION MAPS

1. Vectors information.

On-line DNA sequence tool to find large, non-overlapping, open reading frames and sites for all restriction enzymes-from New England BioLabs.

1. WEB cutter

GENES

1. Gene data. Analysis of large set of genes simultaneously.  http://source.stanford.edu

SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.

The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches.

DATABASES

1. Crosslink of useful data bases.

Harvester crawls and crosslinks the following bioinformatic sites:

BLAST - CDART - CDD - ensEMBL - Entrez - GenomeBrowser - gfp-cDNA - Google-Scholar - gopubmed - H-Inv - HomoloGene - Hwiki-Forum - iHOP - IPI - MapView - Mitocheck - OMIM - PolyMeta - PSORT II - SMART - SOSUI - SOURCE - STRING - Unigene - UniprotKB

PROTOCOLS

1. Useful protocols.

General Techniques Collections, PCR Protocols & Techniques.

SCIENTIFIC TERMS

1. Dictionary of Cancer Terms