lncRNA function

ncRNAs:

• housekeeping ncNRAs (e.g. ribosomal, transfer, snRNAs, snoRNAs)
• regulatory ncRNAs (e.g. miRNAs, piRNAs, siRNAs and lncRNAs)
• other regulatory ncRNAs (e.g. promoter-associated RNAs (PARs) and enhancer RNAs (eRNAs))

LncRNAs may have different roles:

• gene activators (signaling),
• repressors (decoy),
• cis and trans gene expression regulators (guides) and
• chromatin modificators (scaffolds) without the need to be mutually exclusive.

lncRNA types:

• sense/antisense
• bidirectional
• intronic
• intergenic

Learning to use biomaRt

http://davetang.org/muse/2012/04/27/learning-to-use-biomart/

hierarchically cluster in R?

Once you have your data cleaned (i.e. removed the first column), this really just requires three lines of code:

Clean data (assign row names from first column, then remove first column):

dat <- mtfx.in
rownames(dat) <- dat[, 1]
dat <- dat[, -1]

Cluster and reorder:

row.order <- hclust(dist(dat))$order
col.order <- hclust(dist(t(dat)))$order

dat[row.order, col.order]

Results:

     col5 col4 col1 col3 col2 col6
row6    0    0    0    0    3    3
row5    0    0    0    0    3    3
row1    0    0    0    0    3    3
row3    0    0    0    0    3    3
row2    6    6    6    6    6    6
row4    6    6    6    6    6    6

map bed file to gene(another bed)

sort-bed hsa.bed > hsa.bed.2

sort-bed miRNA/GSM1097888_CD34_smallRNA-seq.bed > miRNA/GSM1097888_CD34_smallRNA-seq.bed.2

bedmap --skip-unmapped --echo --echo-map --count --sum hsa.bed.2 miRNA/GSM1097888_CD34_smallRNA-seq.bed.2 > b.bed.2

or

bedmap --skip-unmapped --echo --max hsa.bed.2 GSM973662/miRNA.bed.2 > a.bed.2