Table 1.
Top 20 enriched functions for seRNA proximal genes in each state during iPS cell differentiation to neurons. The differentiation process went from cell state k = 0 to k = 2. The q-value was adjusted using Benjamini and Hochberg corrections with ConsensusPathDB. Note that the RNA biosynthetic process or metabolic process related GO terms are marked with @, signal transduction and cellular process related terms with #, development-related terms with ◎, and cellular response related terms with $
| GO terms (k = 0) | q-value | GO terms (k = 1) | q-value | GO terms (k = 2) | q-value |
|---|---|---|---|---|---|
| # regulation of cellular process | 1.3E-12 | @ regulation of metabolic process | 5.4E-10 | ◎ cellular developmental process | 2.0E-07 |
| @ regulation of RNA metabolic process | 3.8E-11 | # regulation of cellular process | 7.3E-10 | # regulation of cellular process | 2.0E-07 |
| @ transcription, DNA-templated | 3.8E-11 | @ negative regulation of cellular metabolic process | 3.2E-09 | cellular response to chemical stimulus | 5.4E-07 |
| @ regulation of nucleobase-containing compound metabolic process | 4.4E-11 | @ regulation of cellular metabolic process | 4.4E-09 | ◎ multicellular organismal development | 5.4E-07 |
| @ RNA biosynthetic process | 1.2E-10 | @ negative regulation of metabolic process | 7.7E-09 | ◎ cell differentiation | 7.4E-07 |
| @ regulation of gene expression | 1.3E-10 | @ regulation of macromolecule metabolic process | 7.7E-09 | negative regulation of biological process | 5.1E-06 |
| negative regulation of biological process | 2.4E-10 | @ regulation of primary metabolic process | 1.5E-08 | ◎ system development | 9.4E-06 |
| @ regulation of metabolic process | 2.4E-10 | # negative regulation of cellular process | 1.5E-08 | ◎ cellular response to organic substance | 1.3E-05 |
| @ regulation of macromolecule biosynthetic process | 4.9E-10 | negative regulation of biological process | 1.7E-08 | regulation of signaling | 1.4E-05 |
| $ cellular response to chemical stimulus | 5.6E-10 | $ cellular response to chemical stimulus | 1.7E-08 | macromolecular complex subunit organization | 2.1E-05 |
| @ regulation of nitrogen compound metabolic process | 6.3E-10 | @ negative regulation of macromolecule metabolic process | 1.7E-08 | ◎ muscle structure development | 5.3E-05 |
| @ regulation of cellular metabolic process | 6.3E-10 | ◎ multicellular organismal development | 3.0E-08 | # negative regulation of cellular process | 7.2E-05 |
| @ regulation of primary metabolic process | 8.1E-10 | positive regulation of biological process | 6.0E-08 | positive regulation of biological process | 7.7E-05 |
| ◎ cell differentiation | 8.1E-10 | ◎ system development | 1.3E-07 | $ response to organic substance | 7.9E-05 |
| @ regulation of biosynthetic process | 8.1E-10 | $ cellular response to organic substance | 2.0E-07 | @ regulation of metabolic process | 7.9E-05 |
| # positive regulation of cellular process | 8.1E-10 | ◎ tissue development | 2.4E-07 | @ regulation of RNA metabolic process | 9.4E-05 |
| # negative regulation of metabolic process | 8.1E-10 | @ regulation of cellular component biogenesis | 4.6E-07 | @ transcription, DNA-templated | 9.4E-05 |
| @ regulation of macromolecule metabolic process | 8.2E-10 | @ regulation of gene expression | 5.0E-07 | @ regulation of nucleobase-containing compound metabolic process | 9.4E-05 |
| positive regulation of biological process | 8.8E-10 | ◎ cellular developmental process | 7.9E-07 | @ regulation of macromolecule biosynthetic process | 9.4E-05 |
| ◎ cellular developmental process | 8.8E-10 | # positive regulation of cellular process | 1.0E-06 | regulation of gene expression | 1.0E-04 |