Within-species exploratory view · GSE43013

Brown rat native expression

Rattus norvegicus

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
29,516
Expression unit
GEO-supplied FPKM
9 samples in this species view
29,516 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.

Brown rat GSE43013 PCA Scatter plot of 9 samples. Each point is keyboard focusable and labelled by accession and tissue. rno.lv.1 · Liver · PC1 -94.83 · PC2 -63.50 rno.lv.2 · Liver · PC1 -93.25 · PC2 -61.99 rno.lv.3 · Liver · PC1 -95.20 · PC2 -63.53 rno.kd.1 · Kidney · PC1 -37.50 · PC2 83.40 rno.kd.2 · Kidney · PC1 -34.24 · PC2 86.85 rno.kd.3 · Kidney · PC1 -35.73 · PC2 85.34 rno.br.1 · Brain · PC1 127.20 · PC2 -19.81 rno.br.2 · Brain · PC1 135.94 · PC2 -25.08 rno.br.3 · Brain · PC1 127.61 · PC2 -21.69
Observed ranges: PC1 -95.20 to 135.94; PC2 -63.53 to 86.85.

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
rno.lv.1 ↗ GSM1055025 Liver 16,878 7.284e+6 3.8988
rno.lv.2 ↗ GSM1055026 Liver 17,043 6.234e+6 4.1361
rno.lv.3 ↗ GSM1055027 Liver 16,601 7.065e+6 4.0480
rno.kd.1 ↗ GSM1055075 Kidney 17,760 6.297e+6 6.6777
rno.kd.2 ↗ GSM1055076 Kidney 18,138 4.819e+6 6.8811
rno.kd.3 ↗ GSM1055077 Kidney 17,657 3.741e+6 6.7660
rno.br.1 ↗ GSM1055120 Brain 18,417 3.435e+6 8.2122
rno.br.2 ↗ GSM1055121 Brain 17,995 3.041e+6 9.1939
rno.br.3 ↗ GSM1055122 Brain 18,122 2.677e+6 8.9453
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
    ENSRNOG00000041744
    log1p variance
    26.5275
    mean native value
    12,135.7
    detected samples
    3/9
  2. 02
    ENSRNOG00000032578
    log1p variance
    26.1773
    mean native value
    7,361.3
    detected samples
    4/9
  3. 03
    ENSRNOG00000037922
    log1p variance
    25.3026
    mean native value
    7,881.3
    detected samples
    3/9
  4. 04
    ENSRNOG00000037222
    log1p variance
    24.5607
    mean native value
    7,637.6
    detected samples
    5/9
  5. 05
    ENSRNOG00000043750
    log1p variance
    24.1970
    mean native value
    6,366.1
    detected samples
    3/9
  6. 06
    ENSRNOG00000043844
    log1p variance
    24.0215
    mean native value
    6,185.3
    detected samples
    3/9
  7. 07
    ENSRNOG00000043738
    log1p variance
    23.8296
    mean native value
    6,057.2
    detected samples
    3/9
  8. 08
    ENSRNOG00000029389
    log1p variance
    22.6894
    mean native value
    5,029.2
    detected samples
    5/9
  9. 09
    ENSRNOG00000029145
    log1p variance
    22.2349
    mean native value
    4,630.9
    detected samples
    5/9
  10. 10
    ENSRNOG00000002911
    log1p variance
    20.6696
    mean native value
    26,331.7
    detected samples
    9/9
  11. 11
    ENSRNOG00000034636
    log1p variance
    20.0169
    mean native value
    3,843.1
    detected samples
    3/9
  12. 12
    ENSRNOG00000034416
    log1p variance
    19.8859
    mean native value
    2,528.2
    detected samples
    3/9
  13. 13
    ENSRNOG00000016115
    log1p variance
    19.8463
    mean native value
    2,801.1
    detected samples
    5/9
  14. 14
    ENSRNOG00000041309
    log1p variance
    19.7378
    mean native value
    2,669.8
    detected samples
    3/9
  15. 15
    ENSRNOG00000041372
    log1p variance
    19.5438
    mean native value
    2,595.7
    detected samples
    5/9
  16. 16
    ENSRNOG00000043802
    log1p variance
    18.8767
    mean native value
    2,142.0
    detected samples
    5/9
  17. 17
    ENSRNOG00000043532
    log1p variance
    18.8413
    mean native value
    1,717.1
    detected samples
    4/9
  18. 18
    ENSRNOG00000041349
    log1p variance
    18.8046
    mean native value
    2,743.6
    detected samples
    5/9
  19. 19
    ENSRNOG00000040758
    log1p variance
    18.0654
    mean native value
    1,426.3
    detected samples
    4/9
  20. 20
    ENSRNOG00000035760
    log1p variance
    18.0083
    mean native value
    1,495.7
    detected samples
    4/9
  21. 21
    ENSRNOG00000005992
    log1p variance
    17.6485
    mean native value
    3,352.1
    detected samples
    8/9
  22. 22
    ENSRNOG00000042641
    log1p variance
    17.6372
    mean native value
    4,454.9
    detected samples
    9/9
  23. 23
    ENSRNOG00000016275
    log1p variance
    16.6689
    mean native value
    3,733.2
    detected samples
    9/9
  24. 24
    ENSRNOG00000043560
    log1p variance
    16.5587
    mean native value
    2,603.3
    detected samples
    6/9
  25. 25
    ENSRNOG00000028823
    log1p variance
    16.3519
    mean native value
    2,282.4
    detected samples
    8/9
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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