Within-species exploratory view · GSE43013

Old World rabbit native expression

Oryctolagus cuniculus

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
23,394
Expression unit
GEO-supplied FPKM
6 samples in this species view
23,394 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.

Old World rabbit GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. ocu.lv.1 · Liver · PC1 115.18 · PC2 -46.82 ocu.lv.2 · Liver · PC1 116.91 · PC2 -44.42 ocu.kd.1 · Kidney · PC1 -2.39 · PC2 91.88 ocu.kd.2 · Kidney · PC1 1.64 · PC2 90.52 ocu.br.1 · Brain · PC1 -122.71 · PC2 -53.49 ocu.br.2 · Brain · PC1 -108.63 · PC2 -37.68
Observed ranges: PC1 -122.71 to 116.91; PC2 -53.49 to 91.88.

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
ocu.lv.1 ↗ GSM1055021 Liver 14,556 2.076e+6 5.9681
ocu.lv.2 ↗ GSM1055022 Liver 14,311 3.010e+6 5.8143
ocu.kd.1 ↗ GSM1055069 Kidney 15,443 3.279e+6 15.6421
ocu.kd.2 ↗ GSM1055070 Kidney 15,402 4.860e+6 14.7257
ocu.br.1 ↗ GSM1055114 Brain 16,331 2.871e+6 16.9818
ocu.br.2 ↗ GSM1055115 Brain 16,666 3.387e+6 17.0914
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
    ENSOCUG00000016287
    log1p variance
    32.9144
    mean native value
    41,461.4
    detected samples
    5/6
  2. 02
    ENSOCUG00000023390
    log1p variance
    31.7577
    mean native value
    15,236.9
    detected samples
    3/6
  3. 03
    ENSOCUG00000006106
    log1p variance
    29.8335
    mean native value
    17,302.4
    detected samples
    6/6
  4. 04
    ENSOCUG00000020154
    log1p variance
    28.4328
    mean native value
    10,290.8
    detected samples
    2/6
  5. 05
    ENSOCUG00000021823
    log1p variance
    24.6286
    mean native value
    5,751.5
    detected samples
    3/6
  6. 06
    ENSOCUG00000010359
    log1p variance
    24.3177
    mean native value
    7,607.4
    detected samples
    3/6
  7. 07
    ENSOCUG00000027785
    log1p variance
    22.8248
    mean native value
    3,496.5
    detected samples
    2/6
  8. 08
    ENSOCUG00000020000
    log1p variance
    21.0501
    mean native value
    2,426.2
    detected samples
    3/6
  9. 09
    ENSOCUG00000007986
    log1p variance
    19.7564
    mean native value
    1,960.5
    detected samples
    5/6
  10. 10
    ENSOCUG00000019604
    log1p variance
    19.5433
    mean native value
    1,830.6
    detected samples
    2/6
  11. 11
    ENSOCUG00000017348
    log1p variance
    19.3071
    mean native value
    4,158.4
    detected samples
    5/6
  12. 12
    ENSOCUG00000019507
    log1p variance
    19.1581
    mean native value
    1,550.0
    detected samples
    3/6
  13. 13
    ENSOCUG00000011247
    log1p variance
    19.0186
    mean native value
    2,673.4
    detected samples
    6/6
  14. 14
    ENSOCUG00000020676
    log1p variance
    18.9937
    mean native value
    1,459.5
    detected samples
    3/6
  15. 15
    ENSOCUG00000020004
    log1p variance
    18.9433
    mean native value
    1,535.7
    detected samples
    2/6
  16. 16
    ENSOCUG00000002057
    log1p variance
    18.5035
    mean native value
    1,940.6
    detected samples
    6/6
  17. 17
    ENSOCUG00000024530
    log1p variance
    18.1264
    mean native value
    3,900.8
    detected samples
    5/6
  18. 18
    ENSOCUG00000022842
    log1p variance
    18.0779
    mean native value
    1,293.3
    detected samples
    2/6
  19. 19
    ENSOCUG00000019747
    log1p variance
    17.9330
    mean native value
    1,217.1
    detected samples
    2/6
  20. 20
    ENSOCUG00000023380
    log1p variance
    17.9096
    mean native value
    1,574.2
    detected samples
    6/6
  21. 21
    ENSOCUG00000020983
    log1p variance
    17.8684
    mean native value
    2,624.9
    detected samples
    5/6
  22. 22
    ENSOCUG00000023096
    log1p variance
    17.5786
    mean native value
    3,279.3
    detected samples
    6/6
  23. 23
    ENSOCUG00000028220
    log1p variance
    17.5586
    mean native value
    1,238.4
    detected samples
    3/6
  24. 24
    ENSOCUG00000019311
    log1p variance
    17.1816
    mean native value
    22,133.5
    detected samples
    5/6
  25. 25
    ENSOCUG00000024166
    log1p variance
    17.0846
    mean native value
    997.5267
    detected samples
    2/6
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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