| ID | Name |
|---|---|
| 7-7 | 野生型 |
| 7-111 | 突变体 |
7-7-R
7-7-T
7-111-R
7-111-T
| Iterm | 7-111-R | 7-7-R | 7-111-T | 7-7-T |
|---|---|---|---|---|
| Total | 33421015 | 17057680 | 36125969 | 37219183 |
| rRNA | 9679013 (28.96%) | 3451860 (20.24%) | 2389272 (6.61%) | 376013 (1.01%) |
| non rRNA | 23742002 (71.04%) | 13605820 (79.76%) | 33736697 (93.39%) | 36843170 (98.99%) |
7-7-R
7-7-T
7-111-R
7-111-T
| Iterm | 7-111-R | 7-7-R | 7-111-T | 7-7-T |
|---|---|---|---|---|
| unique mapped reads of RNA | 10548663 | 4743168 | 5635056 | 5271249 |
| unique mapped reads of DNA | 5064442 | 456997 | 3928551 | 6091270 |
| unique mapped reads of Intron | 207337 | 73397 | 450475 | 527807 |
| unique mapped ambiguous reads of RNA | 191480 | 287350 | 364688 | 418920 |
File list
- lbx_results.txt
- lbx.merge.counter
- lbxfc_results.txt
- lbxFC.pdf
- lbxrs_results.txt
- lbxRs.pdf
- lbxvolcano.pdf
| File name | Note |
|---|---|
| lbx_results.txt | The results of fist pipline are named with suffix ” v1”, which are generated by comparing mRNA and RPF log2 fold changes: The element log2FC_TE_v1 represents the log2 fold change of TE; The pvalue_v1 represent statistical significance. The sencond pipline are named with suffix ” v2”, which are derived by comparing log2 ratios between two conditions: log2FC_TE_v2, and pvalue_v2 are log2 ratio of TE, and pvalues. Finally, the more conserved results (with larger-Pvalue) was select as the final assessment of differential translation, which are named with suffix ” final”. The pvalue.adjust is the estimated false discovery rate corresponding to the pvalue_final. |
| lbx.merge.counter | Each condition reads count. |
| lbxFC.pdf | Figure 1: Scatter plot of log2 fold changes |
| lbxfc_results.txt | Figure 1: result records. |
| lbxRs.pdf | Figure 2: Scatter plot of log2 RPF-to-mRNA ratios |
| lbxrs_results.txt | Figure 2: result records. |
| lbxvolcano.pdf | It can also be useful to evaluate the fold changes cutoff and p values thresholds by looking at the volcano plot. |
- blue: for genes whoes mRNA_log2FC larger than log2FC.cutoff (transcriptional level).
- red: for genes whoes RPF_log2FC larger than log2FC.cutoff (translational level).
- green: for genes changing homodirectionally at both level.
- yellow: for genes changing antidirectionally at two levels.
- Figure 1: Scatter plot of log2 fold changes
Those genes in which the difference of mRNA_log2FC and RPF_log2FC did not exceed more than log2FC.cutoff are excluded. The points will be color-coded with the pvalue_final obtained with xtail (more significant p values having darker color). By default the log2FC.cutoff is 1.
-
blue: for genes whoes log2R larger in first condition than second condition.
-
red: for genes whoes log2R larger in second condition than the first condition.
-
green: for genes whoes log2R changing homodirectionally in two condition.
-
yellow: for genes whoes log2R changing antidirectionally in two conditon.
- Figure 2: Scatter plot of log2 RPF-to-mRNA ratios
Those genes in which the difference of log2R in two conditions did not exceed more than log2R.cutoff are excluded. The points will be color-coded with the pvalue_final obtained with xtail (more significant p values having darker color). By default the log2R.cutoff is 1.
File list
| File name | Note |
|---|---|
| RiboCode_ORFs_result.txt | contains the information of predicted ORFs in each transcript. |
| RiboCode_ORFs_result_collapsed.txt | combines the ORFs with the same stop codon in different transcript isoforms: the one harboring the most upstream in-frame ATG is chosen. |
Some column names of the result file:
| Column | mean |
|---|---|
| - ORF_ID | The identifier of ORFs that predicated. |
| - ORF_type | The type of ORF is annotated according the relative location to associated CDS. The following ORF categories are reported: |
| "annotated" (overlapping annotated CDS, have the same stop with annotated CDS) | |
| "uORF" (in upstream of annotated CDS, not overlapping annotated CDS) | |
| "dORF" (in downstream of annotated CDS, not overlapping annotated CDS) | |
| "Overlap_uORF" (in upstream of annotated CDS, overlapping annotated CDS) | |
| "Overlap_dORF" (in downstream of annotated CDS, overlapping annotated CDS" | |
| "Internal" (in internal of annotated CDS, but in a different frame relative annotated CDS) | |
| "novel" (in non-coding genes or non-coding transcripts of coding genes). | |
| - ORF_tstart, ORF_tstop | the beginning and end of ORF in RNA transcript (1-based coordinate) |
| - ORF_gstart, ORF_gstop | the beginning and end of ORF in genome (1-based coordinate) |
| - pval_frame0_vs_frame1 | significance levels of P-site densities of frame0 greater than of frame1 |
| - pval_frame0_vs_frame2 | significance levels of P-site densities of frame0 greater than of frame2 |
| - pval_combined | integrated P-value |
| #read_length | proportion(per total mapped reads) | predicted_psite | f0_sum | f1_sum | f2_sum | f0_percent | pvalue1 | pvalue2 | pvalue_combined |
|---|---|---|---|---|---|---|---|---|---|
| # 30 | 23.45% | 12 | 54979 | 5055 | 8040 | 80.76% | 0.00014652626009624466 | 0.0004229273113302267 | 4.3151740824280333e-07 |
| # 29 | 5.06% | 12 | 11074 | 3784 | 1779 | 66.56% | 0.0002995597005840259 | 0.0003563133512190236 | 7.173383508666136e-07 |
| #read_length | proportion(per total mapped reads) | predicted_psite | f0_sum | f1_sum | f2_sum | f0_percent | pvalue1 | pvalue2 | pvalue_combined |
| # 28 | 22.95% | 12 | 51889 | 6952 | 1806 | 85.56% | 0.00014652626009624466 | 0.00014652626009624466 | 1.516508550767744e-07 |
| # 29 | 43.83% | 12 | 78951 | 3609 | 8621 | 86.59% | 0.00014652626009624466 | 0.00014652626009624466 | 1.516508550767744e-07 |
预期是111的stalling增加，您看看是否有这个现象
Htt
3-nt periodicity plot generated by RiboMiner
-
7-7
-
111
Length distribution of read length.
Exon means reads mapped to transcriptome (exon).intergenic region means reads mapped to intergenic region of genes. And intron means reads mapped to intron
- 7-7
Intergenic
Intron
Exon
- 111
Intergenic
Intron
Exon
Reads mapped to different reading frames.
- 7-7
- 111
A general reads distribution along transcripts.
B. Distribution of polarity scores.
polarity 分布如果都在0附近说明对这个转录本来说reads分布相对于转录本中心来说分布比较均匀，如果左偏，或者右偏说明有很多的转录本上的reads分布不均匀，在转录本5'端多了或者少了
C. Ribosome density profiles along CDS regions.
left: read density on the position away from start codon. right: read density on the position away from stop codon.
D. Ribosome density profiles along UTR regions.
这种图y值=（每个位置上的RPM）/(n codon之后的density均值）
left: read density on the position away from start codon. right: read density on the position away from stop codon.
7_111翻译起始有点慢 start codon多很多，考虑翻译起始受抑制吧
Figure 3: Ribosome density among different amino acids and codons.
A. Relative ribosome density on different amino acids for 7-7 sample.
B. Relative ribosome density on different codons for 7-7 sample.
C. Relative ribosome density on different amino acids for 7-7 sample.
D. Relative ribosome density on different codons for 7-7 sample.
E. The change ratio of ribosome density between 7-7 sample and 7-111 sample among different amino acids.
Notes: all these analysis are based on total transcripts.
| Name | Transcript | Translation | Number |
|---|---|---|---|
| transcript_down_translation_up: | transcript 7-111 high 7-7 transcirpt low, | translation 7-111 low 7-7 high | 320 |
| transcript_only_down: | transcript 7-111 high 7-7 transcirpt low, | translation not change | 1027 |
| transcript_only_up: | transcript 7-111 low 7-7 transcirpt high, | translation not change | 316 |
| transcript_translation_down: | transcript 7-111 high 7-7 transcirpt low, | translation 7-111 high 7-7 low | 284 |
| transcript_translation_up: | transcript 7-111 low 7-7 transcirpt high, | translation 7-111 low 7-7 high | 85 |
| transcript_up_translation_down: | transcript 7-111 low 7-7 transcirpt high, | translation 7-111 high 7-7 low | 124 |
| translation_only_down: | transcript not change, | translation 7-111 high 7-7 low | 64 |
| translation_only_up: | transcript not change, | translation 7-111 low 7-7 high | 68 |
transcript_down_translation_up
transcript_up_translation_down
Ribosome density among triplete-AA motifs.
在 QQQ motif 附近存一个很高的峰可能是stalling 现象。 这个很高很高的的峰，可能是这个突变体引起的，或者是由于某个单个位置density高引起的噪音。 需要生物学重复。
A. Relative ribosome density on poly-proline acid.
transcript_down_translation_up
transcript_up_translation_down
B. Relative ribosome density.
transcript_down_translation_up
transcript_up_translation_down
tAI是表示tRNA gene copy numbers对翻译影响的，值越大说明翻译相对越快，CAI是评估codon usage对翻译速率影响的，值越大，说明转录本中optimal codon越读，翻译越快
c7-tAIPlot_homo_average_start_codon.pdf
c7-tAIPlot_homo_average_stop_codon.pdf
c7-tAIPlot_opposite_average_start_codon.pdf
c7-tAIPlot_opposite_average_stop_codon.pdf
c7-tAIPlot_transcrpt_average_start_codon.pdf
c7-tAIPlot_transcrpt_average_stop_codon.pdf
c7-tAIPlot_translation_average_start_codon.pdf
c7-tAIPlot_translation_average_stop_codon.pdf
c9-cAIPlot_homo_average_start_codon.pdf
c9-cAIPlot_homo_average_stop_codon.pdf
c9-cAIPlot_opposite_average_start_codon.pdf
c9-cAIPlot_opposite_average_stop_codon.pdf
c9-cAIPlot_transcrpt_average_start_codon.pdf
c9-cAIPlot_transcrpt_average_stop_codon.pdf
c9-cAIPlot_translation_average_start_codon.pdf
c9-cAIPlot_translation_average_stop_codon.pdf
d3_hydropathy_homo_average_start_codon.pdf
d3_hydropathy_homo_average_stop_codon.pdf
d3_hydropathy_opposite_average_start_codon.pdf
d3_hydropathy_opposite_average_stop_codon.pdf
d3_hydropathy_transcript_average_start_codon.pdf
d3_hydropathy_transcript_average_stop_codon.pdf
d3_hydropathy_translation_average_start_codon.pdf
d3_hydropathy_translation_average_stop_codon.pdf
d4_charge_homo_average_start_codon.pdf
d4_charge_homo_average_stop_codon.pdf
d4_charge_opposite_average_start_codon.pdf
d4_charge_opposite_average_stop_codon.pdf
d4_charge_transcript_average_start_codon.pdf
d4_charge_transcript_average_stop_codon.pdf
d4_charge_translation_average_start_codon.pdf
d4_charge_translation_average_stop_codon.pdf
总结下问题: 1. tAI, cAI在start峰的意义
在start codon上的可以忽略不看，因为start codon上的值是相对固定的都是AUG上计算出来的值，没什么意义
2. global tAI，cAI纵坐标不一样，是什么意义
tAI是表示tRNA gene copy numbers对翻译影响的，值越大说明翻译相对越快，CAI是评估codon usage对翻译速率影响的，值越大，说明转录本中optimal codon越读，翻译越快
3. polarity score分布峰宽增加有什么意义?
polarity 分布如果都在0附近说明对这个转录本来说reads分布相对于转录本中心来说分布比较均匀，如果左偏，或者右偏说明有很多的转录本上的reads分布不均匀，在转录本5'端多了或者少了
4. 是否可以初步分析下QQQ是否有stalling现象。非常感谢！