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Melbourne Brain Genome Project

MBGP Data

Displaying our data.

This page is designed to display two types of data:

  • transcriptome data generated by the Melbourne Brain Genome Project
  • the SAGE data generated both by the Melbourne Brain Genome Project and by external groups
The transcriptome data represents an extension of the known gene data set by using all sources of transcribed data. The transcriptome has been added as a feature to the UCSC Draft Genome browser for visualisation. For a more detailed explanation of this procedure, please see the recent article in Nature or the detailed guidelines at UCSC.

Public SAGE data : NCBI GEO

Here all publically available SAGE data from the NCBI GEO database is displayed. This is all short SAGE data. The information to the left of the track, in purple, consists of the following information: geneid_searchmethod_clusternumber_uniqueongenome_totalpublicSAGEcount
where
  • geneid refers to the best (i.e. highest quality) id that could be assigned to the cluster that the SAGE tag was matched to.
  • searchmethod indicates whether the 10/17 bases were found following the 3' most (graph_last) or second 3' most (graph_last) NlaIII site
  • clusternumber indicates the number assigned to the cluster of sequences.
  • uniqueongenome indicates whether or not the sequence was found uniquely on the genome - l for a long SAGE tag found uniquely on the genome that the public SAGE tag matches to, s for a short SAGE tag found uniquely on the genome that the public SAGE tag matches to, b for both.
  • totalpublicSAGEcount indicates the abundance of this tag within all NCBI GEO SAGE data



GEO ID Description of dataset
GDS102 Identification of candidate genes involved in the regulation of forelimb/hindlimb identity and development.
GDS103 Characterization of the transcriptomes of P19 embryonic carcinoma cells in an undifferentiated, pluripotent state and after induction to differentiate into cardiomyocytes.
GDS338 Analysis of gene expression in somatic cells of fetal and adult testis. Differentially regulated genes provide insight into mechanisms regulating testis function both during development and in the adult animal.
GDS370 Analysis of cerebellum of postnatal day 10 lurcher (Lc +/-) mouse, compared to wild type littermate. Lurcher mice are characterized by massive losses of cerebellar granule cells and Purkinje cells.
GDS379 Examination of dendritic cells derived from CBA/Ca bone marrow. Cells treated with IL-10, lipopolysaccharide (LPS), IL-10 and LPS or vitamin D3.
GDS380 Examination of dendritic cells derived from CBA/Ca embryonic stem cell line ESF 116, and lipopolysaccharide (LPS) response.
GDS381 The Cancer Genome Anatomy Project SAGE library collection. The goal of CGAP is to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment.
GDS382 Comparison of CD4+CD25+ and CD4+CD25- splenic T cells from naive CBA/Ca, purified by MACS. Resting and CD3-activated populations compared. Regulatory T cell activity with a view to transplantation tolerance examined.
GDS383 Comparison of murine CD4+ Th1, Th2 and Tr1/Treg clones with identical TCR specificity for the male transplantation antigen H-Y.
GDS392 Analysis of early chondrogenesis in the murine chondrogenic cell line ATDC5 induced by bone morphogenetic protein 4 (BMP4).
GDS485 Examination of molecular mechanisms underlying pathophysiological processes associated with angiotensin (AngII) dependent hypertension. Mice administered AngII continuously for 7 days and kidney tissue examined.
GDS497 Liver expression profile of mild hyperlipidemic apolipoprotein E3-Leiden (E3L) transgenic mice compared with wild type C57BL/6JIco (B6) mice to identify genes determining lipoprotein homeostasis and atherosclerosis.
GDS537 Generation of gene expression profile of normal postnatal cornea. C57/Bl6 postnatal (PN) day 9 and 6 week old adult total corneas examined. Provides insight into corneal epithelial cell stratification, development, and function.


Last updated: 10th June 2004
Datasets available 14
Total no. of tags 91,139
Unique tags: 42,059
Unique tags with a match 21,771


Guide to UCSC Custom track : score information
Gene type Score
Ref genes 1000
Known gene 857
mgc genes 714
riken Clones 571
mRNA data 429
EST data 286
genomic 143
  • To view public SAGE data, where one tag matches one gene, please click here

  • To view public SAGE data, where one tag may match to many positions within the genome, please click here
For further information on the NCBI data, please visit the GEO site.
Public data : Mouse atlas project

Unique Long SAGE tags with match 79,756
Unique Long SAGE tags with no match 456,130

  • To view mouse atlas long SAGE data, where one tag matches one gene, please click here
  • To view mouse atlas long SAGE data, where one tag may match to many positions within the genome, please click here
  • To view all of the mouse atlas short SAGE data, (including short tags derived from long SAGE tags), where one tag matches one gene, please click here



Comments:-
  • Please note that these files take a few minutes to open as the area displayed is so large (an entire chromosome).
  • The transcriptome data is displayed as the consensus sequence. Displaying all of the sequences used in a cluster would result in a very large display, and this data is redunandant as it is currently displayed by UCSC.
  • It is not possible to display individually every single tag, e.g.
    LibA AAAAAAAAAC position
    LibC AAAAAAAAAC position
    as this is far too much data for UCSC to cope with
  • I have used "ESTgraph" as the name of the program we used to generate the clusters.
  • I have called every block an "exon".
  • I haven't included chr*_random - how much use are these files?
  • I have hidden all tracks bar our own, so that the user can decide what they would like to view (but this can be changed).
  • Tracks can be different colors. n the first example below chr1 is green, chr2 is *very* blue, chr3 is a better blue, for the complete range of colours please see the RGB Color Calculator
Advantages:-
  • Displays the entire chromosome - users can either zoom in or specify a region of interest
Disadvantages:-
  • Currently clusters are only identified by their cluster id

Option 1a : following how everyone else has done it (.BED format).
Please pick a chromosome:-

chromosomes 10 & 11 chromosome 1 chromosome 2 chromosome 3 chromosome 4 chromosome 5 chromosome 6 chromosome 7 chromosome 8 chromosome 9 chromosome 10 chromosome 11 chromosome 12 chromosome 13 chromosome 14 chromosome 15 chromosome 16 chromosome 17 chromosome 18 chromosome 19 chromosome X chromosome Y

Option 1b : following how everyone else has done it (.GFF)
Please pick a chromosome:-

chromosome 1 chromosome 2 chromosome 3 chromosome 4 chromosome 5 chromosome 6 chromosome 7 chromosome 8 chromosome 9 chromosome 10 chromosome 11 chromosome 12 chromosome 13 chromosome 14 chromosome 15 chromosome 16 chromosome 17 chromosome 18 chromosome 19 chromosome X chromosome Y

Option 2 : our tags (experimental) (.GFF)
Please pick a chromosome:-

chromosome 1 chromosome 2 chromosome 3 chromosome 4 chromosome 5 chromosome 6 chromosome 7 chromosome 8 chromosome 9 chromosome 10 chromosome 11 chromosome 12 chromosome 13 chromosome 14 chromosome 15 chromosome 16 chromosome 17 chromosome 18 chromosome 19 chromosome X chromosome Y

Comments:-
  • Each tag is displayed individually.
  • Only tags that appear in any of libraries are included (an 'experimental' SAGE tag track as opposed to 'virtual').
  • 10 bases are displayed for each tag (could lengthen this to 14, including the CATG might help to identify the tag as a SAGE tag?).
  • The file format has an option, "group" whereby "All lines with the same group are linked together into a single item". I have currently given each line a unique id for this, as I wanted to display each 10 bp tag individually, however this could be changed?

Last modified on the 9th June 2004.
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