Within-species exploratory view · GSE43013

Golden hamster native expression

Mesocricetus auratus

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
9
Native features
16,363
Expression unit
GEO-supplied FPKM
9 samples in this species view
16,363 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.

Golden hamster GSE43013 PCA Scatter plot of 9 samples. Each point is keyboard focusable and labelled by accession and tissue. mau.lv.1 · Liver · PC1 105.64 · PC2 -63.29 mau.lv.2 · Liver · PC1 103.76 · PC2 -61.96 mau.lv.3 · Liver · PC1 107.59 · PC2 -64.36 mau.kd.1 · Kidney · PC1 31.48 · PC2 89.35 mau.kd.2 · Kidney · PC1 31.11 · PC2 92.99 mau.kd.3 · Kidney · PC1 33.80 · PC2 89.39 mau.br.1 · Brain · PC1 -137.87 · PC2 -27.91 mau.br.2 · Brain · PC1 -136.64 · PC2 -28.80 mau.br.3 · Brain · PC1 -138.86 · PC2 -25.42
Observed ranges: PC1 -138.86 to 107.59; PC2 -64.36 to 92.99.

Tissue legend

  • Brain3
  • Kidney3
  • Liver3
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
mau.lv.1 ↗ GSM1055007 Liver 14,485 1.363e+6 8.0805
mau.lv.2 ↗ GSM1055008 Liver 14,262 1.045e+6 8.4472
mau.lv.3 ↗ GSM1055009 Liver 14,439 1.437e+6 7.4761
mau.kd.1 ↗ GSM1055057 Kidney 15,434 2.813e+6 13.3752
mau.kd.2 ↗ GSM1055058 Kidney 15,345 2.219e+6 13.3537
mau.kd.3 ↗ GSM1055059 Kidney 15,126 1.240e+6 12.2449
mau.br.1 ↗ GSM1055101 Brain 15,785 1.022e+6 16.5728
mau.br.2 ↗ GSM1055102 Brain 15,711 1.064e+6 16.0659
mau.br.3 ↗ GSM1055103 Brain 15,846 2.810e+6 17.6709
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-Ser-1
    log1p variance
    50.6215
    mean native value
    462,694.4
    detected samples
    5/9
  2. 02
    tRNA-Pro
    log1p variance
    31.4227
    mean native value
    23,917.8
    detected samples
    5/9
  3. 03
    tRNA-Arg
    log1p variance
    30.1443
    mean native value
    18,369.3
    detected samples
    4/9
  4. 04
    tRNA-Glu
    log1p variance
    29.8759
    mean native value
    25,445.2
    detected samples
    5/9
  5. 05
    tRNA-Leu-1
    log1p variance
    26.7059
    mean native value
    12,679.3
    detected samples
    4/9
  6. 06
    tRNA-Tyr
    log1p variance
    25.9092
    mean native value
    8,036.5
    detected samples
    4/9
  7. 07
    tRNA-Asn
    log1p variance
    24.2536
    mean native value
    7,530.9
    detected samples
    3/9
  8. 08
    MAUG00000000492
    log1p variance
    23.7457
    mean native value
    30,138.6
    detected samples
    9/9
  9. 09
    tRNA-Ala
    log1p variance
    23.1507
    mean native value
    5,507.6
    detected samples
    3/9
  10. 10
    tRNA-Lys
    log1p variance
    19.2170
    mean native value
    4,817.1
    detected samples
    2/9
  11. 11
    tRNA-Leu-2
    log1p variance
    18.7627
    mean native value
    4,169.2
    detected samples
    2/9
  12. 12
    MAUG00000020596
    log1p variance
    18.7181
    mean native value
    3,187.5
    detected samples
    8/9
  13. 13
    tRNA-Cys
    log1p variance
    18.6943
    mean native value
    4,562.1
    detected samples
    2/9
  14. 14
    tRNA-Asp
    log1p variance
    17.5194
    mean native value
    3,086.5
    detected samples
    2/9
  15. 15
    tRNA-Gly
    log1p variance
    17.1190
    mean native value
    2,769.5
    detected samples
    2/9
  16. 16
    tRNA-His
    log1p variance
    16.4981
    mean native value
    2,224.7
    detected samples
    2/9
  17. 17
    MAUG00000020625
    log1p variance
    16.2700
    mean native value
    2,238.9
    detected samples
    8/9
  18. 18
    MAUG00000002523
    log1p variance
    16.1405
    mean native value
    2,258.6
    detected samples
    9/9
  19. 19
    MAUG00000003740
    log1p variance
    15.9791
    mean native value
    2,212.1
    detected samples
    9/9
  20. 20
    MAUG00000018951
    log1p variance
    15.3831
    mean native value
    2,507.2
    detected samples
    8/9
  21. 21
    MAUG00000016694
    log1p variance
    15.3351
    mean native value
    4,437.7
    detected samples
    9/9
  22. 22
    MAUG00000009245
    log1p variance
    15.2294
    mean native value
    3,886.4
    detected samples
    9/9
  23. 23
    MAUG00000000033
    log1p variance
    15.1068
    mean native value
    2,793.5
    detected samples
    9/9
  24. 24
    MAUG00000020590
    log1p variance
    15.0599
    mean native value
    1,748.4
    detected samples
    9/9
  25. 25
    MAUG00000001883
    log1p variance
    15.0056
    mean native value
    3,881.3
    detected samples
    8/9
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

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