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For all users, CPSS can analyze the small RNA deep sequencing datain different architecture: single and paired.

By using CPSS, small RNA NGS data can be analyzed systematically in one platform after a single submission of data by integration of annotation and functional analysis of novel and/or differentially expressed miRNAs. CPSS generates an analysis report including: 1) annotation analysis, which provides a comprehensive analysis for small RNA transcriptome, such as the length distribution and genome mapping of the sequencing reads, small RNA annotation, prediction of novel miRNAs, identification of differentially expressed miRNAs, piRNAs and other small RNAs between samples, and detection of miRNA SNPs and isoforms; 2) functional analysis, which provides the functional analysis of miRNAs, e.g. predicting miRNA target genes by multi-tools, enriching Gene Ontology terms (GO), performing signalling pathways, and protein-protein interaction (PPI) analysis for the predicted genes.

1. The expression profile of know miRNAs of the single sample A (B). Users could sort this list according to RNA name and the counts of small RNAs.

Total read counts: all total number of tags annotated in same miRNA locus.
Most abundant: the unique tag which was expressed mostly compared to other tags annotated in same miRNA locus.
Absolute count: all total number of tags.
Relative count: normalized based on the total number of all the clean reads mapped onto genome in each sample (Normalized counts=Reads per Million).
Ref sequence: The sequence of the miRNAs from miRBase.
Tag sequence: the sequence of unique tag which was expressed mostly compared to other tags annotated in same miRNA locus.




2. The expression profile of piRNAs of the single sample A (B). Users could sort this list according to RNA name and the counts of small RNAs.

Total read counts: all total number of tags annotated in same piRNA locus.
Most abundant: the unique tag which was expressed mostly compared to other tags annotated in same piRNA locus.
Absolute count: all total number of tags.
Relative count: normalized based on the total number of all the clean reads mapped onto genome in each sample (Normalized counts=Reads per Million).
Ref sequence: The sequence of the piRNAs from piRNA database.
Tag sequence: the sequence of unique tag which was expressed mostly compared to other tags annotated in same piRNA locus.




3. The expression profile of rRNAs of the single sample A (B). Users could sort this list according to RNA name and the counts of small RNAs.

Total read counts: all total number of tags annotated in same rRNA locus.
Most abundant: the unique tag which was expressed mostly compared to other tags annotated in same rRNA locus.
Absolute count: all total number of tags.
Relative count: normalized based on the total number of all the clean reads mapped onto genome in each sample (Normalized counts=Reads per Million).
Ref sequence: The sequence of the rRNAs from Rfam.
Tag sequence: the sequence of unique tag which was expressed mostly compared to other tags annotated in same rRNA locus.




4. The expression profile of snRNAs of the single sample A (B). Users could sort this list according to RNA name and the counts of small RNAs. And the Ref sequence are compressed to save the space of the web page.

Total read counts: all total number of tags annotated in same snRNA locus.
Most abundant: the unique tag which was expressed mostly compared to other tags annotated in same snRNA locus.
Absolute count: all total number of tags.
Relative count: normalized based on the total number of all the clean reads mapped onto genome in each sample (Normalized counts=Reads per Million).
Ref sequence: The sequence of the snRNAs from Rfam.
Tag sequence: the sequence of unique tag which was expressed mostly compared to other tags annotated in same snRNA locus.




5. The expression profile of snoRNAs of the single sample A (B). Users could sort this list according to RNA name and the counts of small RNAs. And the Ref sequence are compressed to save the space of the web page.

Total read counts: all total number of tags annotated in same snoRNA locus.
Most abundant: the unique tag which was expressed mostly compared to other tags annotated in same snoRNA locus.
Absolute count: all total number of tags.
Relative count: normalized based on the total number of all the clean reads mapped onto genome in each sample (Normalized counts=Reads per Million).
Ref sequence: The sequence of the snoRNAs from Rfam.
Tag sequence: the sequence of unique tag which was expressed mostly compared to other tags annotated in same snoRNA locus.




6. The expression profile of novel miRNAs of the single sample A (B). Users could sort this list according to MFE and the counts of small RNAs. And the secondary structure of these potential novel miRNAs are predicted. Click on the picture to view larger version.

Location: chromosomal localization of predicted novel miRNA precursor.
Length: nucleotide number of predicted novel miRNA precursor.
MFE: The minimal free energy for mireap.
Seq: the sequence of predicted novel miRNA precursor.
Mature-5P: the predicted novel miRNA from 5' of the precursor.
Mature-3P: the predicted novel miRNA from 3' of the precursor.
Count: all total number of the predicted novel miRNAs.




7. Detailed annotation of known miRNA isoforms expressed in sample A (B),including miRNA ID and isoform of mature sequence.

The original mature miRNA sequences are labeled by red and listed at the first line in web page.




8. Statistical results of the different kinds of isoforms in the sample A (B). In CPSS, the different kinds of isoforms could be detected including 1) trimming or additions of nucleotides at 3' end of the reference miRNA sequence, 2) trimming or additions of nucleotides at 5' end of the reference miRNA sequence, and 3) trimming or additions of nucleotides at both 3' and 5' end of the reference miRNA sequence.

Added: additions of nucleotides at the end of the miRNA sequence.
Trim: trimming of nucleotides at the end of the miRNA sequence.




9. Detailed annotation of known miRNA SNP expressed in the sample A (B),including miRNA ID, SNPs of mature sequence, and mutant position.Users could realize if these "miRNA SNP candidates" have been reported or annotated by mapping to dbSNP.

The original mature miRNA sequences are labeled by red and listed at the first line in web page.




10. Differentially expressed miRNAs (Based on most abundant unique tag) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.




11. Differentially expressed miRNAs (Based on total read counts) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.






12. Differentially expressed piRNAs (Based on most abundant unique tag) in the paired samples. All the terms in this list could be sorted by users.

Expression: Normalized expression of the piRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this piRNA in sample A was higher than that in sample B.
"-" The expression level of this piRNA in sample B was higher than that in sample A.
Sig: Significance mark.




13. Differentially expressed piRNAs (Based on total read counts) in the paired samples. All the terms in this list could be sorted by users.

Expression: Normalized expression of the piRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this piRNA in sample A was higher than that in sample B.
"-" The expression level of this piRNA in sample B was higher than that in sample A.
Sig: Significance mark.






14. Differentially expressed rRNAs (Based on most abundant unique tag) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.




15. Differentially expressed rRNAs (Based on total read counts) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.






16. Differentially expressed snRNAs (Based on most abundant unique tag) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.




17. Differentially expressed snRNAs (Based on total read counts) in the paired samples. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.




18. Differentially expressed snoRNAs (Based on most abundant unique tag) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.




19. Differentially expressed snoRNAs (Based on total read counts) in the paired sample. All the terms in this list could be sorted by users.

Expression: Normalized expression of the miRNA.
Total: Total counts of genome mapped reads of the sample.
Trend: "+" The expression level of this miRNA in sample A was higher than that in sample B.
"-" The expression level of this miRNA in sample B was higher than that in sample A.
Sig: Significance mark.




20. Predicated targets of differentially expressed miRNAs (Based on most abundant unique tag) of the paired samples. Users could sort this list according to the name of miRNAs and target genes.



21. Predicated targets of differentially expressed miRNAs (Based on total read counts) of the paired samples. Users could sort this list according to the name of miRNAs and target genes.



22. Go analysis for predict targets of differentially expressed miRNAs (Based on most abundant unique tag) of the paired samples. Users could sort this list according to GO term, gene name, enrichment fold, and P value.

N: total number of genes annotated by GO in whole genome.
n: total number of genes annotated by a specific GO term in whole genome.
M: total number of genes annotated by GO in predicted miRNA targets.
m: total number of genes annotated by a specific GO term in predicted miRNA targets.




23. Go analysis for predict targets of differentially expressed miRNAs (Based on total read counts) in the single sample. Users could sort this list according to GO term, gene name, enrichment fold, and P value.

N: total number of genes annotated by GO in whole genome.
n: total number of genes annotated by a specific GO term in whole genome.
M: total number of genes annotated by GO in predicted miRNA targets.
m: total number of genes annotated by a specific GO term in predicted miRNA targets.




24. Pathway analysis of differentially expressed miRNAs' targets (Based on most abundant unique tag) of the paired samples. Users could sort this list according to pathway name, enrichment fold, and P value. Click on the name of KEGG pathway to view the picture of pathway.

N: total number of genes annotated by GO in whole genome.
n: total number of genes annotated by a specific GO term in whole genome.
M: total number of genes annotated by GO in predicted miRNA targets.
m: total number of genes annotated by a specific GO term in predicted miRNA targets.




25. Pathway analysis of differentially expressed miRNAs' targets (Based on total read counts) in the single sample. Users could sort this list according to pathway name, enrichment fold, and P value. Click on the name of KEGG pathway to view the picture of pathway.

N: total number of genes annotated by GO in whole genome.
n: total number of genes annotated by a specific GO term in whole genome.
M: total number of genes annotated by GO in predicted miRNA targets.
m: total number of genes annotated by a specific GO term in predicted miRNA targets.




26. Protein-protein interaction (PPI) analysis for predict targets of differentially expressed miRNAs (Based on most abundant unique tag) of the paired samples. All the term in these list could be sorted.

Neighborhood: computed from the inter-gene nucleotide count.
Fusion: derived from fused proteins in other species.
Cooccurence: derived from similar absence/presence patterns of genes.
Coexpression: derived from similar pattern of mRNA expression measured by DNA arrays and similar technologies.
Experimental: derived from experimental data, such as, affinity chromatography.
Database: derived from curated data of various databases.
Text mining: derived from the co-occurrence of gene/protein names in abstracts.




27.Protein-protein interaction (PPI) analysis for predict targets of differentially expressed miRNAs (Based on total read counts) of the paired samples. All the term in these list could be sorted.

Neighborhood: computed from the inter-gene nucleotide count.
Fusion: derived from fused proteins in other species.
Cooccurence: derived from similar absence/presence patterns of genes.
Coexpression: derived from similar pattern of mRNA expression measured by DNA arrays and similar technologies.
Experimental: derived from experimental data, such as, affinity chromatography.
Database: derived from curated data of various databases.
Text mining: derived from the co-occurrence of gene/protein names in abstracts.