LncRNA ReleaseNotes: Difference between revisions

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==September 8, 2011==
==September 16, 2011==
===Wrong phage genome ID===
===lncRNA Annotation===
Phage genome VIMSS IDs don't work (MicrobesOnline IDs), for instance, http://proportal.mit.edu/protein/70464/0/, and select VIMSS.
<B>Description</B>


However,the ones for the cyanobacterial genes work.
The initial analysis to identify differentially regulated lncRNAs during cardiomyocyte differentiation using the sequencing files designated in the above. Move forward in further analyzing these data. 


Solution:
<B>Datasets</B>


The VIMSS IDs for proteins are defined in data_dna table, in which many proteins do not have VIMSS ID defined and need to be updated from MicrobesOnline website.
The lncRNA annotation file which has been sorted from all lncRNAs contained in ENSEMBL and from the Guttman et al. Nature paper.
 
===Broken link for data download===
The link to Supplementary Data fails: http://proportal.mit.edu/expression/18/, for instance, http://proportal.mit.edu/download/pubmed_17016519/.
 
Solution:
 
The supplementary data is available on the Proportal Download page http://proportal.mit.edu/download/, where links for downloading are pointed to a different location, for instance, the link for Nitrogen Availability Gene Expression Project is http://chisholmlab.mit.edu/kat/download/pubmed_17016519/.
 
Make the following change on templates/gene_express_project.html from,
 
        Download: <a href="/download/pubmed_{{pub.pubmed.pubmed_id}}/">Supplementary Data</a> <br />
to,
 
        Download: <a href="http://chisholmlab.mit.edu/kat/download/pubmed_{{pub.pubmed.pubmed_id}}/">Supplementary Data</a> <br />
 
'''The supplementary data should be made available directly from Proportal website in next release.'''


==August 29, 2011==
==August 29, 2011==

Revision as of 13:05, 14 September 2011

September 16, 2011

lncRNA Annotation

Description

The initial analysis to identify differentially regulated lncRNAs during cardiomyocyte differentiation using the sequencing files designated in the above. Move forward in further analyzing these data.

Datasets

The lncRNA annotation file which has been sorted from all lncRNAs contained in ENSEMBL and from the Guttman et al. Nature paper.

August 29, 2011

EB differentiation time course

Progress

A report was delivered on Aug. 29, 2011. The missing experimental dataset at D4 will be conducted and included in the next round of analysis.

August 16, 2011

EB differentiation time course

Description

Analyze the RNA-Seq data generated for the lncRNA (lnc011) knockdown (kd) and control ESC lines (0d) that were differentiated into EBs (6d and 9d).

Goals

The goal is to display the differentially expressed genes in a figure and to further analyze the genes that are mis-regulated as a function of the kd relative to the control (scrambled). Heat map or more informative presentation of the data is expected.

To learn more about how lnc (lnc11) may control cell fate specification by "plotting" the expression of the mis-regulated genes (in the GO categories) along the cardiomyocyte differentiation pathway using the RNA-Seq data for the various time points (namely D0, D4, D5.3, and D10).

Datasets

Tables attached including fold change relative to control.

The file (all.ComparisonExpn.txt) contains counts and FPKM that was generated with the sequencing files.

The big spreadsheet is with all the tests for differential expression. There are some semi-redundant columns for counts and fpkms. If there are no reads for d0 and d4, there won't be any counts or a stat test, but if there are reads for d5.3, then day0 and day4 will be shown as 0 and a stat test will be conducted.

Methods

Ideally generate a GO-type figure and gene network figure possibly by selecting the genes included in over-represented GO categories. The preliminary GO analysis via GOStat (attached) using a 1.5x cut-off for "down-regulated genes" shows enrichment for categories that have roles in heart function including muscle contraction, sarcomere function, heart development, blood circulation, etc.

Progress

The report was delivered on Aug. 29, 2011. The missing experimental dataset at D4 will be conducted and included in the next round of analysis.

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