Welcome to CPSS

Released: Feb/22/2012 version 1.1

CPSS (Computational Platform for analysis of Small RNA deep Sequencing data) is a web server which provides a comprehensively and systemically integrated pipeline for analyzing small RNA deep sequencing data.

  • Reads length distribution
  • Genome mapping of the sequencing reads
  • RNA quantification
  • Novel microRNA prediction
  • MicroRNA target prediction
  • GO analysis for the predicted target genes
  • Pathway analysis for genes in the enriched GO terms
  • Protein-Protein interaction analysis for genes in the enriched GO terms

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Samples upload.

  

    Sample data from Mus musculus.  More test data.

    Sample data from Mus musculus.  More test data.

Species selection.



Parameters for mapping tools.

Parameters for SOAP.

      M:  0: exact match; 2: 1 mismatch; 3: all; 4: best hits.
      v:   Maximum number of mismatches
      r:   Report repeat hits 0:none 1:random one.

Parameters for BlastN.
      E:   Blast e-value

Filter for miRNA isoform.

Absolute reads count >:

Contributes to the total number (%) :

Use Z-score cut-off :

Parameters for novel miRNA prediction.

miReap miRDeep

Parameters for singnification test of difference.

Parameters for miRNA.

      P value:
      Fold change:

Parameters for piRNA.

      P value:
      Fold change:

Parameters for Rfam.

      P value:
      Fold change:

Parameters for miRNA target prediction.

Select main tools for target prediction

miRanda RNAhybrid

Parameters for miRNA target prediction tools.
  miRanda
      Energy:   Minimal free energy (MFE)
      Score:
  RNAhybrid
      Energy:   Minimal free energy (MFE)
      P value:

Select additional tools for miRNA for target prediction.

MicroCosm microT_v3.0 MirTarget2
miRNAMap TargetScan TargetSpy

Select integration method for main tool targets and additional tools target.

Union Intersection

Parameters for GO and Pathway.

Parameters for GO analysis of novel miRNA's target.
      P value:   The threshold for hypergeometric test
      Enrichment fold:

Parameters for Pathway analysis of novel miRNA's target.
      P value:   The threshold for hypergeometric test
      Enrichment fold:

Parameter for protein-protein interaction.

      Score: