Within-species exploratory view · GSE43013

Siberian chipmunk native expression

Tamias sibiricus

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
20,345
Expression unit
GEO-supplied FPKM
4 samples in this species view
20,345 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.

Siberian chipmunk GSE43013 PCA Scatter plot of 4 samples. Each point is keyboard focusable and labelled by accession and tissue. tsi.kd.1 · Kidney · PC1 104.46 · PC2 -19.51 tsi.kd.2 · Kidney · PC1 102.61 · PC2 19.73 tsi.br.1 · Brain · PC1 -102.75 · PC2 -5.98 tsi.br.2 · Brain · PC1 -104.32 · PC2 5.76
Observed ranges: PC1 -104.32 to 104.46; PC2 -19.51 to 19.73.

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
tsi.kd.1 ↗ GSM1055080 Kidney 14,669 1.091e+6 24.8318
tsi.kd.2 ↗ GSM1055081 Kidney 14,772 1.085e+6 24.7991
tsi.br.1 ↗ GSM1055125 Brain 14,672 993,058.9 27.3358
tsi.br.2 ↗ GSM1055126 Brain 16,322 982,996.3 23.7536
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
    TSIG00000016093
    log1p variance
    21.2017
    mean native value
    10,353.5
    detected samples
    4/4
  2. 02
    TSIG00000008370
    log1p variance
    19.2839
    mean native value
    2,051.5
    detected samples
    4/4
  3. 03
    TSIG00000008238
    log1p variance
    18.7846
    mean native value
    1,933.3
    detected samples
    4/4
  4. 04
    TSIG00000017275
    log1p variance
    18.6027
    mean native value
    2,086.3
    detected samples
    4/4
  5. 05
    TSIG00000015210
    log1p variance
    18.1606
    mean native value
    802.5625
    detected samples
    2/4
  6. 06
    TSIG00000008290
    log1p variance
    18.0601
    mean native value
    1,904.4
    detected samples
    4/4
  7. 07
    TSIG00000008242
    log1p variance
    17.7747
    mean native value
    1,758.8
    detected samples
    4/4
  8. 08
    TSIG00000016131
    log1p variance
    17.1024
    mean native value
    1,451.9
    detected samples
    4/4
  9. 09
    TSIG00000008267
    log1p variance
    16.5907
    mean native value
    1,533.2
    detected samples
    4/4
  10. 10
    TSIG00000002760
    log1p variance
    16.5828
    mean native value
    857.9783
    detected samples
    4/4
  11. 11
    TSIG00000006174
    log1p variance
    16.1912
    mean native value
    538.2675
    detected samples
    2/4
  12. 12
    TSIG00000005913
    log1p variance
    16.0331
    mean native value
    832.9412
    detected samples
    4/4
  13. 13
    TSIG00000008233
    log1p variance
    15.9548
    mean native value
    797.9328
    detected samples
    4/4
  14. 14
    TSIG00000007281
    log1p variance
    15.9290
    mean native value
    3,565.5
    detected samples
    4/4
  15. 15
    TSIG00000006218
    log1p variance
    15.4521
    mean native value
    693.6331
    detected samples
    3/4
  16. 16
    TSIG00000008453
    log1p variance
    15.3292
    mean native value
    1,071.8
    detected samples
    4/4
  17. 17
    TSIG00000005872
    log1p variance
    15.2464
    mean native value
    734.2834
    detected samples
    4/4
  18. 18
    TSIG00000008302
    log1p variance
    15.0165
    mean native value
    1,908.8
    detected samples
    4/4
  19. 19
    TSIG00000007698
    log1p variance
    14.8132
    mean native value
    677.1602
    detected samples
    4/4
  20. 20
    TSIG00000005944
    log1p variance
    14.7288
    mean native value
    1,098.2
    detected samples
    4/4
  21. 21
    TSIG00000000292
    log1p variance
    14.3578
    mean native value
    513.1964
    detected samples
    3/4
  22. 22
    TSIG00000005966
    log1p variance
    13.6673
    mean native value
    818.4018
    detected samples
    3/4
  23. 23
    TSIG00000008269
    log1p variance
    13.6540
    mean native value
    687.7443
    detected samples
    4/4
  24. 24
    TSIG00000014407
    log1p variance
    13.5028
    mean native value
    563.2017
    detected samples
    4/4
  25. 25
    TSIG00000008261
    log1p variance
    13.4012
    mean native value
    283.3080
    detected samples
    2/4
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

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