Within-species exploratory view · GSE43013

House shrew native expression

Suncus murinus

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
3
Native features
8,761
Expression unit
GEO-supplied FPKM
3 samples in this species view
8,761 source-native feature IDs
GSE43013 GEO-supplied FPKM
1 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.

House shrew GSE43013 PCA Scatter plot of 3 samples. Each point is keyboard focusable and labelled by accession and tissue. smu.lv.1 · Liver · PC1 -3.15 · PC2 9.02 smu.lv.2 · Liver · PC1 10.03 · PC2 -1.99 smu.lv.3 · Liver · PC1 -6.88 · PC2 -7.03
Observed ranges: PC1 -6.88 to 10.03; PC2 -7.03 to 9.02.

Tissue legend

  • 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
smu.lv.1 ↗ GSM1055028 Liver 8,761 1.063e+6 25.6504
smu.lv.2 ↗ GSM1055029 Liver 8,761 1.084e+6 25.2001
smu.lv.3 ↗ GSM1055030 Liver 8,761 1.054e+6 24.5794
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
    SMUG00000009536
    log1p variance
    2.1756
    mean native value
    11.6309
    detected samples
    3/3
  2. 02
    SMUG00000009198
    log1p variance
    2.1434
    mean native value
    11.6096
    detected samples
    3/3
  3. 03
    SMUG00000009401
    log1p variance
    2.0492
    mean native value
    32.0251
    detected samples
    3/3
  4. 04
    SMUG00000003728
    log1p variance
    1.7984
    mean native value
    16.9158
    detected samples
    3/3
  5. 05
    SMUG00000009303
    log1p variance
    0.7865
    mean native value
    13.0613
    detected samples
    3/3
  6. 06
    SMUG00000003632
    log1p variance
    0.7593
    mean native value
    13.6120
    detected samples
    3/3
  7. 07
    SMUG00000002981
    log1p variance
    0.7294
    mean native value
    13.8914
    detected samples
    3/3
  8. 08
    SMUG00000003458
    log1p variance
    0.7169
    mean native value
    149.6633
    detected samples
    3/3
  9. 09
    SMUG00000006598
    log1p variance
    0.6820
    mean native value
    20.7236
    detected samples
    3/3
  10. 10
    SMUG00000005909
    log1p variance
    0.6470
    mean native value
    311.5363
    detected samples
    3/3
  11. 11
    SMUG00000003123
    log1p variance
    0.5434
    mean native value
    41.8070
    detected samples
    3/3
  12. 12
    SMUG00000004561
    log1p variance
    0.5338
    mean native value
    13.6225
    detected samples
    3/3
  13. 13
    SMUG00000003124
    log1p variance
    0.4878
    mean native value
    57.5804
    detected samples
    3/3
  14. 14
    SMUG00000009177
    log1p variance
    0.4746
    mean native value
    11.3203
    detected samples
    3/3
  15. 15
    SMUG00000004183
    log1p variance
    0.3970
    mean native value
    10.1244
    detected samples
    3/3
  16. 16
    SMUG00000006035
    log1p variance
    0.3712
    mean native value
    28.7902
    detected samples
    3/3
  17. 17
    SMUG00000009682
    log1p variance
    0.3484
    mean native value
    15.5421
    detected samples
    3/3
  18. 18
    SMUG00000005427
    log1p variance
    0.3054
    mean native value
    13.2143
    detected samples
    3/3
  19. 19
    SMUG00000008964
    log1p variance
    0.2908
    mean native value
    6.0285
    detected samples
    3/3
  20. 20
    SMUG00000002436
    log1p variance
    0.2729
    mean native value
    29.1965
    detected samples
    3/3
  21. 21
    SMUG00000004118
    log1p variance
    0.2729
    mean native value
    12.0814
    detected samples
    3/3
  22. 22
    SMUG00000005330
    log1p variance
    0.2680
    mean native value
    22.8336
    detected samples
    3/3
  23. 23
    SMUG00000007789
    log1p variance
    0.2668
    mean native value
    136.5628
    detected samples
    3/3
  24. 24
    SMUG00000004599
    log1p variance
    0.2639
    mean native value
    18.9154
    detected samples
    3/3
  25. 25
    SMUG00000004905
    log1p variance
    0.2624
    mean native value
    15.3342
    detected samples
    3/3
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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