Within-species exploratory view · GSE43013

Guinea pig native expression

Cavia porcellus

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
25,028
Expression unit
GEO-supplied FPKM
9 samples in this species view
25,028 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.

Guinea pig GSE43013 PCA Scatter plot of 9 samples. Each point is keyboard focusable and labelled by accession and tissue. cpo.lv.1 · Liver · PC1 93.34 · PC2 60.69 cpo.lv.2 · Liver · PC1 96.19 · PC2 57.58 cpo.lv.3 · Liver · PC1 95.69 · PC2 58.13 cpo.kd.1 · Kidney · PC1 29.22 · PC2 -84.91 cpo.kd.2 · Kidney · PC1 39.09 · PC2 -74.43 cpo.kd.3 · Kidney · PC1 31.30 · PC2 -84.90 cpo.br.1 · Brain · PC1 -125.78 · PC2 18.30 cpo.br.2 · Brain · PC1 -127.72 · PC2 25.65 cpo.br.3 · Brain · PC1 -131.33 · PC2 23.91
Observed ranges: PC1 -131.33 to 96.19; PC2 -84.91 to 60.69.

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
cpo.lv.1 ↗ GSM1054996 Liver 14,939 9.324e+6 7.5013
cpo.lv.2 ↗ GSM1054997 Liver 14,905 1.435e+7 7.0727
cpo.lv.3 ↗ GSM1054998 Liver 14,662 1.278e+7 6.8569
cpo.kd.1 ↗ GSM1055046 Kidney 15,465 7.041e+6 11.7871
cpo.kd.2 ↗ GSM1055047 Kidney 15,008 7.267e+6 11.9558
cpo.kd.3 ↗ GSM1055048 Kidney 14,917 6.778e+6 13.0335
cpo.br.1 ↗ GSM1055091 Brain 16,165 9.935e+6 14.9950
cpo.br.2 ↗ GSM1055092 Brain 16,151 9.638e+6 14.5705
cpo.br.3 ↗ GSM1055093 Brain 16,123 8.644e+6 15.8324
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
    ENSCPOG00000020370
    log1p variance
    39.5542
    mean native value
    100,157.2
    detected samples
    3/9
  2. 02
    ENSCPOG00000014373
    log1p variance
    34.1966
    mean native value
    520,600.4
    detected samples
    9/9
  3. 03
    ENSCPOG00000017398
    log1p variance
    26.6496
    mean native value
    9,256.7
    detected samples
    4/9
  4. 04
    ENSCPOG00000024851
    log1p variance
    26.0968
    mean native value
    84,502.3
    detected samples
    9/9
  5. 05
    ENSCPOG00000017412
    log1p variance
    23.2809
    mean native value
    12,622.7
    detected samples
    6/9
  6. 06
    ENSCPOG00000017428
    log1p variance
    22.4592
    mean native value
    9,228.2
    detected samples
    6/9
  7. 07
    ENSCPOG00000017410
    log1p variance
    22.2330
    mean native value
    4,088.7
    detected samples
    4/9
  8. 08
    ENSCPOG00000017400
    log1p variance
    21.8831
    mean native value
    4,625.4
    detected samples
    3/9
  9. 09
    ENSCPOG00000028367
    log1p variance
    21.7083
    mean native value
    3,870.4
    detected samples
    4/9
  10. 10
    ENSCPOG00000026035
    log1p variance
    21.2769
    mean native value
    3,397.7
    detected samples
    3/9
  11. 11
    ENSCPOG00000017408
    log1p variance
    21.1323
    mean native value
    3,954.7
    detected samples
    5/9
  12. 12
    ENSCPOG00000027702
    log1p variance
    20.8937
    mean native value
    13,775.5
    detected samples
    6/9
  13. 13
    ENSCPOG00000020925
    log1p variance
    20.3920
    mean native value
    3,715.7
    detected samples
    5/9
  14. 14
    ENSCPOG00000028141
    log1p variance
    20.1317
    mean native value
    6,677.4
    detected samples
    6/9
  15. 15
    ENSCPOG00000015111
    log1p variance
    18.9918
    mean native value
    3,159.9
    detected samples
    8/9
  16. 16
    ENSCPOG00000017411
    log1p variance
    18.2967
    mean native value
    16,341.9
    detected samples
    7/9
  17. 17
    ENSCPOG00000019680
    log1p variance
    18.2054
    mean native value
    1,585.3
    detected samples
    4/9
  18. 18
    ENSCPOG00000016482
    log1p variance
    17.4977
    mean native value
    1,743.4
    detected samples
    5/9
  19. 19
    ENSCPOG00000015936
    log1p variance
    17.3116
    mean native value
    1,548.9
    detected samples
    5/9
  20. 20
    ENSCPOG00000019960
    log1p variance
    17.0773
    mean native value
    1,797.8
    detected samples
    5/9
  21. 21
    ENSCPOG00000028005
    log1p variance
    16.5160
    mean native value
    1,308.5
    detected samples
    4/9
  22. 22
    ENSCPOG00000027814
    log1p variance
    16.4412
    mean native value
    1,071.8
    detected samples
    4/9
  23. 23
    ENSCPOG00000028976
    log1p variance
    16.1114
    mean native value
    1,376.1
    detected samples
    5/9
  24. 24
    ENSCPOG00000008709
    log1p variance
    16.1091
    mean native value
    1,868.0
    detected samples
    5/9
  25. 25
    ENSCPOG00000017988
    log1p variance
    15.8426
    mean native value
    972.2689
    detected samples
    3/9
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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