Within-species exploratory view · GSE43013

Domestic goat native expression

Capra hircus

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
6
Native features
24,066
Expression unit
GEO-supplied FPKM
6 samples in this species view
24,066 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.

Domestic goat GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. chi.lv.1 · Liver · PC1 -108.47 · PC2 -8.48 chi.lv.2 · Liver · PC1 -102.98 · PC2 11.62 chi.kd.1 · Kidney · PC1 45.36 · PC2 -44.97 chi.kd.2 · Kidney · PC1 55.36 · PC2 13.94 chi.br.1 · Brain · PC1 55.36 · PC2 13.94 chi.br.2 · Brain · PC1 55.36 · PC2 13.94
Observed ranges: PC1 -108.47 to 55.36; PC2 -44.97 to 13.94.

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
chi.lv.1 ↗ GSM1054994 Liver 15,778 642,803.2 4.1118
chi.lv.2 ↗ GSM1054995 Liver 15,928 660,849.3 4.7662
chi.kd.1 ↗ GSM1055044 Kidney 17,885 2.662e+6 6.9743
chi.kd.2 ↗ GSM1055045 Kidney 18,499 7.576e+6 6.1815
chi.br.1 ↗ GSM1055089 Brain 18,499 7.576e+6 6.1815
chi.br.2 ↗ GSM1055090 Brain 18,499 7.576e+6 6.1815
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
    57.8057
    mean native value
    1.855e+6
    detected samples
    4/6
  2. 02
    tRNA-Ser-1
    log1p variance
    56.6746
    mean native value
    1.541e+6
    detected samples
    4/6
  3. 03
    tRNA-Glu
    log1p variance
    39.9195
    mean native value
    137,265.3
    detected samples
    4/6
  4. 04
    tRNA-Tyr
    log1p variance
    31.7934
    mean native value
    41,376.0
    detected samples
    4/6
  5. 05
    tRNA-Ala
    log1p variance
    30.2269
    mean native value
    30,801.9
    detected samples
    4/6
  6. 06
    tRNA-Ser-2
    log1p variance
    28.6745
    mean native value
    8,807.7
    detected samples
    3/6
  7. 07
    tRNA-Cys
    log1p variance
    27.6934
    mean native value
    18,326.9
    detected samples
    4/6
  8. 08
    tRNA-Arg
    log1p variance
    27.5979
    mean native value
    17,460.4
    detected samples
    4/6
  9. 09
    tRNA-Gly
    log1p variance
    26.9258
    mean native value
    16,363.5
    detected samples
    4/6
  10. 10
    tRNA-Lys
    log1p variance
    25.7682
    mean native value
    12,406.7
    detected samples
    4/6
  11. 11
    tRNA-Asn
    log1p variance
    25.3874
    mean native value
    13,760.2
    detected samples
    4/6
  12. 12
    100860821
    log1p variance
    25.1820
    mean native value
    10,063.9
    detected samples
    6/6
  13. 13
    102184301
    log1p variance
    23.4859
    mean native value
    8,412.7
    detected samples
    4/6
  14. 14
    tRNA-Trp
    log1p variance
    23.0662
    mean native value
    3,213.9
    detected samples
    3/6
  15. 15
    102171351
    log1p variance
    20.2209
    mean native value
    2,048.2
    detected samples
    2/6
  16. 16
    102184929
    log1p variance
    19.4126
    mean native value
    6,717.0
    detected samples
    6/6
  17. 17
    102184647
    log1p variance
    18.8526
    mean native value
    2,826.9
    detected samples
    6/6
  18. 18
    102174166
    log1p variance
    18.8308
    mean native value
    2,323.0
    detected samples
    6/6
  19. 19
    102176354
    log1p variance
    18.7685
    mean native value
    7,058.8
    detected samples
    6/6
  20. 20
    tRNA-Leu-2
    log1p variance
    18.6090
    mean native value
    2,858.4
    detected samples
    4/6
  21. 21
    102174926
    log1p variance
    18.3740
    mean native value
    1,663.9
    detected samples
    6/6
  22. 22
    102168699
    log1p variance
    18.2527
    mean native value
    1,897.2
    detected samples
    5/6
  23. 23
    102179029
    log1p variance
    17.2673
    mean native value
    1,570.8
    detected samples
    6/6
  24. 24
    100861216
    log1p variance
    16.7440
    mean native value
    950.3199
    detected samples
    3/6
  25. 25
    102186111
    log1p variance
    16.2973
    mean native value
    899.3885
    detected samples
    5/6
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

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