GeneX

In the table below are some of the tools, databases and other resources that we have reviewed over the last few months. If you know of others that merit inclusion in this group, we would be happy to oblige. Please send us a note and give us at least a top-level URL for the resource. If you think that this list misrepresents the capabilities of an entry (ie, if an entry has been updated recently) or if you can think of additional information that would be valuable to include, we'd be grateful for the input.

Abbreviations are expanded at the bottom of the page.

Databases with Application to Gene ExpressionDemo

SW Name (Org)

Sequence Analysis

Gene Expr Analysis

Database function

Interface

Free Database Access?

SW Free?

Public Data Deposit?

Output

Type*

Online Docs

Schema

Pubs

Other URLs

GeneX (NCGR)

L

clust,perm SOM,PCA, stats,prof plots,viz, eisen

DB (PostgreSQL, Sybase)

HTML XWin Java

Yes

Yes

Yes w/ registration

Data formatted for J-Express, xcluster, xgobi, or in GeneXML and soon MAML

O

No

Yes

IBM Systems J 40(2),'01

GeneX Listservs

maxd (Manchester)

No

2D plots, clust, filt,via MaxdView

DB (PostgreSQL, MySQL, Oracle8i

Java

No?

Yes

No?

ASCII

A

EBI's Schema

No?

Data Loading Tool

Stanford MicroArray DB (Stanford)

?

?

DB

HTML

No

For Acad nonprofits

No

HTML ascii

A

Yes

Yes

Yes

No

AMAD (UCSF, microarrays.org)

No

Yes* via Cluster TreeView

Perl flatfile DB

HTML javascript

No

Yes

No

ASCII

A

Yes

Flatfile

No

Screenshots FAQ

MicroArray Project (NHGRI)

BLAST

ImAn, clustering

DB

Java HTML

Demo1 Demo2

Yes*

No

Java screens

G

Yes

Yes

Yes

NHGRI ArrayDB v 2.2.03 (NHGRI)

Not Apparent fr Descr

Described, but not available(?)

DB Sybase Oracle

HTML

Demo

Yes w/ Registration>

No

ASCII, image, binary data

G

Few

Yes

Yes

Change Log

cDNA DB (NHGRI)

DB of CloneID, Unigene Sets

No

DB

FileMakerPro

No

Data Free

No

FMPro

G

Yes

No

No

ExpressDB v2.00 (Harvard)

No

No

DB

HTML Javascript

Yes

No

No*

HTML Tables

A

Yes

Logical Model Physical Model Table Defs

Yes

Yes

EPODB (U Penn)

L

No

DB

HTML Java

Yes

No

No*

HTML Tables

A

Yes

Yes

Yes

Controlled Vocabulary

RNA Abundance DB (U Penn)

?

?

DB

HTML

Yes

?

No*

HTML

A

Yes

No

No

Controlled Vocabulary, Slides

GenomXtools (VisualGenomics)

Yes*

clust, plots, map

Int

win32

No

No

No

win32 ascii

$

No

No

No

No

ArrayExpress (EBI)

?

?

DB

?

Yes

?

Yes

GEML ascii HTML

G

No

Yes

No

Meeting Data mining

Gene Expression Omnibus (NCBI)

L

No

DB

email HTML Tables

Yes

No

Yes

GEO-XML

G

Yes

Yes

No

DB Tables

GeneChip Analysis Suite (Affymetrix)

L

ImAn, clust, stats

A - GATC

win32

No

No

No

win32 GATC

$

No

GATC (PDF)

No

Data Flow

GeneChip LIMS (Affymetrix)

No

No

DB

win32

No

No

No

win32 GATC

$

No

GATC (PDF)

No

Data Flow

GeneChip Data Mining Tool (Affymetrix)

L

clust, stats, plots, viz

A - GATC

win32

No

No

No

win32 ascii

$

No

GATC (PDF)

No

Data Flow

Array Explorer (Spotfire)

No

clust, stats, PCA, eisen, plots, viz

A - GATC

win32

No

No

No

win32 ascii

$

Yes

NA

No

No

Genesight (BioDiscovery)

No

ImAn, clust, PCA, stats, plots, viz

Int

win32

No

No

No

win32 ascii

$

No

No

Promo/Tech Report

Related products

CloneTracker (BioDiscovery)

No

Sybase-based LIMS DB

DB

Win32

No

No

No

win32 ascii

$

No

No

No

Related products

GeneSpring (Silicon Genetics)

L

clust, PCA, stats, plots, viz, map

A

Java

Yes

No

Yes*

Java ascii

$

Full

No

No

Resolver (Rosetta)

L

ImAn, clust, PCA, stats, plots, viz, map

Int

Java

No

No

No

Java ascii

$

No

No

No

Response to OMG GE RFI

LifeArray (Incyte)

Yes

clust, PCA, stats, plots

A - GATC, others

Java

No

No

No

Java ascii

$

No

No

No

No

SSBM (Informax)

Yes

L

Int

Java

No

No

No

Java ascii

$

No

No

No

No

Expressionist (GeneData)

Yes*

clust, PCA, stats, MDS, plots, viz

A

Java

N

N

N

Various

$

No

No

No

No

GXD (Jackson Labs)

No

No

DB

HTML

Yes

No

Soon

HTML ascii

O

Yes

No

Yes

Mouse Anatomical Dictionary

GeneExpress (Gene Logic)

L

clust, PCA, stats, plots, viz

Int

Java

No

No

No

varies

$

No

No

No

No

ChipDB (Whitehead)

No

?

DB

HTML

Yes

No

No

HTML ascii

A

No

No

No

GENECLUSTER

Other resources

• General Gene Expression Resources
  • Joel Bader's CSHL GE Analysis abstract
  • Patrik D'haeseleer's work on Gene Expression Networks
  • Cluster/TreeView Manual
  • SpotFire's Webcasts on Gene Expression
  • The Perl Data Language - Number crunching capabilities for Perl
• Listservs
  • Plant Arrays ListServ
• Other Collections of Gene Expression Resources
  • Leming Shi's DNA Microarray site
  • Indiana U's Genomics Links
• Statistics Resources
  • David Lanes's Online Stats Books and Tutorials
  • Texasoft's Online Statistics Tutorials
  • Free Chapters of Intuitive Biostatistics
  • GraphPad Online Resources
  Other weird stuff of interest
  • Jellyfish, a free Java sequence analysis app
  • Rob Tibshirani's SAM (Significance Analysis for Microarrays).

Abbreviations:

• Sequence, Gene Expr Analysis, Primary Function
  • ArCon = Array construction, planning, layout tool
  • clust = clustering via a number of algorithms
  • SOM = Self Organizing Maps
  • perm = Permutation Testing
  • prof = profile filtering
  • eisen = Eisen-type maps and dendrograms
  • GE = Gene Expression
  • GP = General Purpose
  • ImAn = Image Analysis
  • L = Limited
  • map = chromosome maps or localization
  • MDS = Multi-Dimensional Scaling
  • NA = Not Applicable
  • norm = Normalization of data
  • PCA = Principle Component Analysis
  • plots = 2D plotting capability
  • stats = statistical tools
  • viz = 3D (or higher) visualization
  • Yes* = Available via another module in the suite.
  • ? = Unknown
• Database Function
  • DB = is substantially a Database
  • Int = comes with an integrated Database
  • A = can access other databases
  • GATC = a particular type of Database schema designed by Affymetrix and Molecular Dynamics for storing gene expression data.
• Interface
  • HTML = Hypertext Markup language, the lingua franca of the Web
  • Java = an interpreted language that supposedly allows "write-once, run anywhere",
  • Javascript = unrelated to Java, typically used to add lightweight, browser-based intelligence to interfaces
  • win32 = the native Microsoft Windows interface
  • tcl/tk = tcl is another interpreted language that allows it to run on many platforms; tk is the GUI interface that allows point+click utility
  • XWin = the X11 Windowing system, typically runs on Linux, Unix workstations altho there is Xserver software available for MS Windows and Macs. Allows one screen to show output from multiple networked machines simultaneously.
  • CLI = Command Line Interface, the oldest, but still powerful way of interacting with computers, as in DOS, terminal windows and shell commands.
• SW Free?
  • Yes* - Most of the software is free, but it uses commercial software in its implementation which is NOT free.
  • A - Free to Academic & non-profits, Costs commercial entities.
• Public Data Deposit
  • yes* = The database supports public data upload, but only via vendor-specific tools
  • no* = Much of the data is public but the public cannot directly submit their data to the database.
• Type
  • A = Academic research project
  • G = Government organization.
  • $ = Commercial project; for gene expression especially, these products tend to be extremely expensive.
  • O = Non-profit Organization