Within-species exploratory view · GSE43013

Sugar glider native expression

Petaurus breviceps

Sample QC, log-transformed PCA, and the most variable source-native feature IDs from Per-sample GEO-supplied FPKM files.

View PCA → Open Igf1 gene profile → Source samples → LACA content → Open GEO ↗
Samples
4
Native features
20,380
Expression unit
GEO-supplied FPKM
4 samples in this species view
20,380 source-native feature IDs
GSE43013 GEO-supplied FPKM
2 Table S1 tissues represented
Exploratory ordination

PCA of log1p native expression

SVD PCA after feature-wise centering after log1p(GEO-supplied FPKM). Axes apply only to this species and dataset.

Sugar glider GSE43013 PCA Scatter plot of 4 samples. Each point is keyboard focusable and labelled by accession and tissue. pbr.kd.1 · Kidney · PC1 -98.96 · PC2 17.41 pbr.kd.2 · Kidney · PC1 -99.02 · PC2 -17.50 pbr.br.1 · Brain · PC1 97.77 · PC2 7.51 pbr.br.2 · Brain · PC1 100.21 · PC2 -7.43
Observed ranges: PC1 -99.02 to 100.21; PC2 -17.50 to 17.41.

Tissue legend

  • Brain2
  • Kidney2
Transform
log1p(GEO-supplied FPKM)
Feature policy
Intersection of native feature IDs across samples within each species.
Normalization
The source reports Cufflinks FPKM; LACA applies log1p only for within-species PCA/QC.
Sample-level quality context

Detected features and expression totals

These are descriptive summaries of the supplied GEO-supplied FPKM values—not read-depth QC metrics and not thresholds for sample exclusion.

Sample Tissue Detected native features Total GEO-supplied FPKM Median positive value
pbr.kd.1 ↗ GSM1055071 Kidney 13,731 9.546e+6 16.7698
pbr.kd.2 ↗ GSM1055072 Kidney 13,594 8.655e+6 17.0012
pbr.br.1 ↗ GSM1055116 Brain 14,329 7.002e+6 26.0996
pbr.br.2 ↗ GSM1055117 Brain 14,195 6.777e+6 26.7571
Source-native feature ranking

Top variable native feature IDs

Ranked by variance after log1p transformation within this exact view. IDs are reported verbatim from the source matrix and must not be treated as cross-species orthologs.

  1. 01
    tRNA-Trp
    log1p variance
    35.1975
    mean native value
    14,510.8
    detected samples
    2/4
  2. 02
    tRNA-Gly
    log1p variance
    34.9525
    mean native value
    14,000.4
    detected samples
    2/4
  3. 03
    tRNA-Ser-2
    log1p variance
    32.7346
    mean native value
    23,307.5
    detected samples
    1/4
  4. 04
    tRNA-Leu-2
    log1p variance
    27.2600
    mean native value
    27,217.3
    detected samples
    3/4
  5. 05
    tRNA-Val
    log1p variance
    26.2824
    mean native value
    22,614.1
    detected samples
    3/4
  6. 06
    tRNA-Lys
    log1p variance
    24.9681
    mean native value
    5,471.3
    detected samples
    1/4
  7. 07
    tRNA-Asp
    log1p variance
    23.2662
    mean native value
    3,868.6
    detected samples
    1/4
  8. 08
    PBRG00000000232
    log1p variance
    20.3647
    mean native value
    1,848.8
    detected samples
    3/4
  9. 09
    tRNA-Gln
    log1p variance
    19.0232
    mean native value
    1,535.6
    detected samples
    1/4
  10. 10
    PBRG00000002419
    log1p variance
    17.6288
    mean native value
    911.4570
    detected samples
    3/4
  11. 11
    PBRG00000002515
    log1p variance
    16.3426
    mean native value
    891.7575
    detected samples
    4/4
  12. 12
    PBRG00000013271
    log1p variance
    15.4254
    mean native value
    622.0450
    detected samples
    4/4
  13. 13
    PBRG00000002304
    log1p variance
    15.1672
    mean native value
    864.3765
    detected samples
    4/4
  14. 14
    PBRG00000013374
    log1p variance
    14.3266
    mean native value
    488.9193
    detected samples
    4/4
  15. 15
    PBRG00000002887
    log1p variance
    14.0475
    mean native value
    329.3833
    detected samples
    2/4
  16. 16
    PBRG00000000105
    log1p variance
    13.9684
    mean native value
    493.9342
    detected samples
    4/4
  17. 17
    PBRG00000002290
    log1p variance
    13.9439
    mean native value
    545.1291
    detected samples
    4/4
  18. 18
    PBRG00000002403
    log1p variance
    13.4666
    mean native value
    394.1402
    detected samples
    4/4
  19. 19
    PBRG00000000147
    log1p variance
    13.2692
    mean native value
    540.1259
    detected samples
    4/4
  20. 20
    PBRG00000000955
    log1p variance
    13.2078
    mean native value
    459.6121
    detected samples
    4/4
  21. 21
    PBRG00000002181
    log1p variance
    13.1494
    mean native value
    578.6195
    detected samples
    4/4
  22. 22
    PBRG00000002508
    log1p variance
    13.1422
    mean native value
    297.8942
    detected samples
    3/4
  23. 23
    PBRG00000011475
    log1p variance
    13.0978
    mean native value
    2,195.7
    detected samples
    4/4
  24. 24
    PBRG00000002406
    log1p variance
    13.0645
    mean native value
    1,487.0
    detected samples
    4/4
  25. 25
    PBRG00000007629
    log1p variance
    13.0578
    mean native value
    1,404.9
    detected samples
    4/4
Reproducible boundary

What this page computes—and what it does not

Input

Per-sample GEO-supplied FPKM files

The source reports Cufflinks FPKM; LACA applies log1p only for within-species PCA/QC.

Within-species computation

QC · PCA · variable features

Intersection of native feature IDs across samples within each species.

Not computed

No cross-species expression test

No matrix merge, differential-expression result, lifespan regression, or causal claim is presented here.

Source integrity

GSE43013_RAW.tar

SHA-256 550e7fd866249caa7d43d85beef62dd19f4d139cc41dae0b2d0a012ccb9e3bf1

Back to source records → All 41 mammals →