Within-species exploratory view · GSE43013

Asian badger native expression

Meles meles

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 → Open GEO ↗
Samples
6
Native features
16,975
Expression unit
GEO-supplied FPKM
6 samples in this species view
16,975 source-native feature IDs
GSE43013 GEO-supplied FPKM
3 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.

Asian badger GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. mle.lv.1 · Liver · PC1 105.78 · PC2 62.63 mle.lv.2 · Liver · PC1 103.97 · PC2 62.95 mle.kd.1 · Kidney · PC1 38.80 · PC2 -86.51 mle.kd.2 · Kidney · PC1 35.07 · PC2 -86.77 mle.br.1 · Brain · PC1 -142.95 · PC2 25.75 mle.br.2 · Brain · PC1 -140.67 · PC2 21.95
Observed ranges: PC1 -142.95 to 105.78; PC2 -86.77 to 62.95.

Tissue legend

  • Brain2
  • Kidney2
  • Liver2
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
mle.lv.1 ↗ GSM1055013 Liver 15,455 1.007e+7 7.4697
mle.lv.2 ↗ GSM1055014 Liver 15,338 1.072e+7 7.8004
mle.kd.1 ↗ GSM1055061 Kidney 15,934 4.601e+7 12.2313
mle.kd.2 ↗ GSM1055062 Kidney 16,224 3.509e+7 12.9023
mle.br.1 ↗ GSM1055106 Brain 16,534 926,120.4 20.2083
mle.br.2 ↗ GSM1055107 Brain 16,444 1.050e+6 17.9430
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-Pro
    log1p variance
    70.7315
    mean native value
    1.099e+7
    detected samples
    4/6
  2. 02
    tRNA-Glu
    log1p variance
    55.9191
    mean native value
    1.311e+6
    detected samples
    4/6
  3. 03
    tRNA-Tyr
    log1p variance
    49.3751
    mean native value
    577,104.5
    detected samples
    4/6
  4. 04
    tRNA-Met
    log1p variance
    48.2735
    mean native value
    595,688.3
    detected samples
    4/6
  5. 05
    tRNA-Ala
    log1p variance
    47.9902
    mean native value
    494,528.3
    detected samples
    4/6
  6. 06
    tRNA-Cys
    log1p variance
    47.5200
    mean native value
    438,008.3
    detected samples
    4/6
  7. 07
    tRNA-Thr
    log1p variance
    47.1965
    mean native value
    459,757.3
    detected samples
    4/6
  8. 08
    tRNA-Leu-1
    log1p variance
    46.3962
    mean native value
    422,788.0
    detected samples
    4/6
  9. 09
    tRNA-His
    log1p variance
    43.3515
    mean native value
    263,115.0
    detected samples
    4/6
  10. 10
    tRNA-Asn
    log1p variance
    40.5196
    mean native value
    170,425.0
    detected samples
    4/6
  11. 11
    tRNA-Arg
    log1p variance
    39.2530
    mean native value
    139,022.0
    detected samples
    4/6
  12. 12
    tRNA-Lys
    log1p variance
    37.7728
    mean native value
    106,419.3
    detected samples
    4/6
  13. 13
    tRNA-Ser-2
    log1p variance
    35.9742
    mean native value
    76,497.8
    detected samples
    4/6
  14. 14
    tRNA-Ile
    log1p variance
    33.3164
    mean native value
    50,284.8
    detected samples
    4/6
  15. 15
    MLEG00000000825
    log1p variance
    32.5751
    mean native value
    25,732.4
    detected samples
    6/6
  16. 16
    tRNA-Gly
    log1p variance
    30.1998
    mean native value
    32,133.6
    detected samples
    4/6
  17. 17
    tRNA-Asp
    log1p variance
    30.0754
    mean native value
    29,539.0
    detected samples
    4/6
  18. 18
    tRNA-Leu-2
    log1p variance
    29.6457
    mean native value
    27,269.1
    detected samples
    4/6
  19. 19
    tRNA-Ser-1
    log1p variance
    25.5453
    mean native value
    5,228.9
    detected samples
    3/6
  20. 20
    6741586
    log1p variance
    24.4021
    mean native value
    9,990.8
    detected samples
    4/6
  21. 21
    MLEG00000018423
    log1p variance
    21.3844
    mean native value
    9,887.8
    detected samples
    4/6
  22. 22
    MLEG00000000833
    log1p variance
    21.1559
    mean native value
    6,118.9
    detected samples
    5/6
  23. 23
    MLEG00000017384
    log1p variance
    20.9625
    mean native value
    8,523.9
    detected samples
    5/6
  24. 24
    6741607
    log1p variance
    20.6562
    mean native value
    4,820.4
    detected samples
    5/6
  25. 25
    MLEG00000018430
    log1p variance
    19.4802
    mean native value
    2,187.3
    detected samples
    4/6
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 →