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Real Time PCR

  • These were calculated from the delta Ct between deflagellated and non-deflagellated RNA.
  • The results were corrected for induction of a G protein beta subunit.
  • The results are averages of three independent isolates of RNA.
  • To get fold induction:
    • Postive numbers: Fold Induction = (2^(corrected delta Ct))-1
    • Negative numbers: Fold Induction = -(2^(absolute value of corrected delta Ct))-1)

Quick Search

  • Searches these fields for matches to your query
  • v2_name --- the C_ name that JGI assigned each model
  • v2_homology.v2_id --- the 6 digit number given by JGI to each model
  • v2_homology.description --- the NCBI description associated with the BLAST matches to each of the models
  • v2_homology.accession --- the NCBI accession number of the BLAST matches to each of the models
  • v2_homology.organism --- the NCBI organism field associated with the BLAST matches
  • model_desc.description) --- Pazour's annotation of each of the models
  • Note that this can bring back a lot of garbage because of the search to the NCBI description. If you are looking for something like kinases, it is better to search the interpro data on the Advanced Search page.

BLAST view

  • pE is the -LOG of the BLAST E value with 0 set arbitraily to 300 and no match set to -2
  • Humans (Hs) ciliated
  • Thalassiosira pseudonana (Tp) ciliated but cilia lack central pairs, radial spokes, inner dynein arms and retrograde IFT
  • Arabidoposis (At) lack cilia
  • Cyanidioschyzon merolae (Cm) lack cilia
  • Dictyostelium (Dd) lack cilia
  • Saccharomyces (Sc) lack cilia

Expression Data

  • RT-PCR is our data, displayed as fold induction and calculated as described above
  • WFM 30 Min, WFM 45 Min, and WFM 120 Min, are array data from Stolc et al., PNAS 102:3703-3707, displayed as % induction
  • SKD RT-PCR is real time PCR data from Li et al., Cell 117:541-552, displayed as fold induction

Mapping Data Forward to JGI version 4 

The original information that drives this database was generated by Mascot searches of the JGI version 2 assembly and it is these matches that drives the organization of the data displayed here. With the refinement of the assemblies and the release of newer versions, there is a need to connect the version 2 data to these newer assemblies.

The best way to do this would be to rescan our spectra against the JGIv4 assembly and reassemble this database from the new data. Unfortunately, this is more work than I am willing to do. So I have implemented a less perfect, but hopefully still useful forward mapping strategy. To do this, the best proteins dataset from JGIv4 was scanned with the unique peptide set from CrFPv2. All JGIv4 models that contained at least one CrFPv2 peptide was selected for further analysis.

The proteins from CrFPv2 were then blasted against the selected JGIv4 models with a cutoff of 1e-50 and the best matches are displayed on the information pages with the best match listed first. Those models that did not have a match were reblasted with a cutoff of 1e-20 and the output manually examined to include only with regions of 100% match.

Examination of the output suggests that it is pretty good, but it can contain errors and so one should examine
the peptide tracks at JGI to ensure that the correct model has been chosen.