Additional file 1 of Genome-wide identification, evolutionary and functional analyses of KFB family members in potato
Bibliographic record
Abstract
Additional file 1 Table S1. The information of profile HMMs of F-box and Kelch domains in Pfam database. Table S2. The sequences and positions information of F-box domains in 44 StKFB members. Table S3. The sequences and positions information of Kelch motifs in 44 StKFB members. Table S4. The 20 conserved motifs in StKFB proteins identified by MEME software and motifs annotation analysis by InterProScan. Table S5. The orthologous KFB genes identified by comparison between potato and other plants. Table S6. Expression profiles of 44 StKFB genes in different potato tissues, in potato plants with different treatments and in tubers with different colors. The FPKM values of 44 StKFB genes in different potato tissues and in potato plants with different treatments were extracted from RNA-Seq Gene Expression Data: DM_RH_RNA-Seq_FPKM_expression_matrix_for_DM_v4.03_13dec2013_desc.xlsx, the excel file of FPKM values of all the representative transcripts across 40 DM and 16 RH libraries ( http://spuddb.uga.edu/pgsc_download.shtml ); the FPKM values in tubers with different colors was extracted from RNA-seq data in our lab deposited in the NCBI Sequence Read Archive under the Bioproject accession PRJNA729884. Table S7. Quality of transcriptome sequencing of potato tuber with three colors. Raw reads: Number of reads in raw data; Clean reads: Number of reads filtered from raw data; Raw bases: The number of bases in the raw data; Clean bases: The number of bases filtered from the raw data; Error rate: Error rate of data sequencing; Q20: Percentage of bases with a Phred value greater than 20; Q30: Percentage of bases with a Phred value greater than 30; GC content: The percentage of G and C in clean reads. Table S8. Sequence alignment results of reads mapped to the reference genome (DM v4.03/v4.04). Total reads: the number of clean reads used for mapping analysis; Total mapped: the number of reads that could be mapped to the reference genome; Multiple mapped: the number of reads mapped to multiple locations in the reference genome; Uniquely mapped: the number of reads mapped to single location in the reference genome; Read-1 and Read-2: the number of reads mapped to the reference genome in Read 1 and Read 2, respectively; Reads mapped to ‘+’ and Reads mapped to ‘-’: the number of reads mapped to the positive and negative strands of the reference genome, respectively; Non-splice reads: the number of reads with the entire segment mapped to exons; Splice reads: the number of segmented reads mapped on two different exons; Reads mapped in proper pairs:the number of reads paired mapped to the reference genome; Proper-paired reads map to different chrom: the number of paired reads mapped to different chromosomes in the reference genome. Table S9. All primers used in qRT-PCR. Table S10. The annotation of 44 StKFBs and their corresponding orthologous genes in Arabidopsis thaliana. The potato StKFB protein sequences were aligned with those of Arabidopsis thaliana using Blastp.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.984 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".