Within-species exploratory view · GSE50726

Damaraland mole rat native expression

Fukomys damarensis

Sample QC, log-transformed PCA, and the most variable source-native feature IDs from Multi-sample GEO-supplied RPKM matrix.

View PCA → Open Igf1 gene profile → Source samples → Open GEO ↗
Samples
14
Native features
21,082
Expression unit
GEO-supplied RPKM
14 samples in this species view
21,082 source-native feature IDs
GSE50726 GEO-supplied RPKM
4 Table S1 tissues represented
Exploratory ordination

PCA of log1p native expression

SVD PCA after feature-wise centering after log1p(GEO-supplied RPKM). Axes apply only to this species and dataset.

Damaraland mole rat GSE50726 PCA Scatter plot of 14 samples. Each point is keyboard focusable and labelled by accession and tissue. 3F_brain_front · Brain · PC1 -112.06 · PC2 -44.66 3F_kidney · Kidney · PC1 37.11 · PC2 -2.93 3F_liver · Liver · PC1 91.99 · PC2 -19.82 BF_brain_front · Brain · PC1 -113.65 · PC2 -44.90 BF_kidney · Kidney · PC1 37.30 · PC2 -3.79 BF_liver · Liver · PC1 93.26 · PC2 -14.10 BM_brain_front · Brain · PC1 -103.42 · PC2 -39.94 BM_kidney · Kidney · PC1 39.68 · PC2 -0.83 BM_liver · Liver · PC1 100.81 · PC2 -17.92 BM_testis · Testis · PC1 -47.71 · PC2 121.10 M5y_brain · Brain · PC1 -112.76 · PC2 -43.21 M5y_kidney · Kidney · PC1 43.39 · PC2 -1.50 M5y_liver · Liver · PC1 94.81 · PC2 -17.79 M5y_testis · Testis · PC1 -48.75 · PC2 130.29
Observed ranges: PC1 -113.65 to 100.81; PC2 -44.90 to 130.29.

Tissue legend

  • Brain4
  • Kidney4
  • Liver4
  • Testis2
Transform
log1p(GEO-supplied RPKM)
Feature policy
All feature rows retained from the native GSE50726 matrix.
Normalization
The source reports RPKM; 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 RPKM values—not read-depth QC metrics and not thresholds for sample exclusion.

Sample Tissue Detected native features Total GEO-supplied RPKM Median positive value
3F_brain_front ↗ GSM1227233 Brain 17,238 555,233.0 9.4881
3F_kidney ↗ GSM1227234 Kidney 16,625 649,608.9 9.4327
3F_liver ↗ GSM1227236 Liver 16,002 1.304e+6 9.5839
BF_brain_front ↗ GSM1227237 Brain 17,519 546,849.0 8.9835
BF_kidney ↗ GSM1227243 Kidney 17,170 681,080.4 9.0666
BF_liver ↗ GSM1227232 Liver 16,627 1.173e+6 9.6843
BM_brain_front ↗ GSM1227238 Brain 17,759 509,498.8 9.2118
BM_kidney ↗ GSM1227228 Kidney 17,116 638,614.3 9.4666
BM_liver ↗ GSM1227239 Liver 15,957 1.536e+6 9.9023
BM_testis ↗ GSM1227235 Testis 19,418 430,940.9 7.1881
M5y_brain ↗ GSM1227230 Brain 17,528 517,329.2 9.3005
M5y_kidney ↗ GSM1227231 Kidney 16,790 661,402.7 9.5990
M5y_liver ↗ GSM1227229 Liver 16,113 1.387e+6 9.6390
M5y_testis ↗ GSM1227240 Testis 19,755 486,415.3 7.2193
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
    DMR_10289
    log1p variance
    15.4018
    mean native value
    45,283.2
    detected samples
    14/14
  2. 02
    DMR_05574
    log1p variance
    14.0997
    mean native value
    11,473.5
    detected samples
    14/14
  3. 03
    DMR_09841
    log1p variance
    14.0241
    mean native value
    5,591.5
    detected samples
    14/14
  4. 04
    DMR_07419
    log1p variance
    13.6742
    mean native value
    3,785.0
    detected samples
    14/14
  5. 05
    DMR_13102
    log1p variance
    13.5967
    mean native value
    10,285.4
    detected samples
    14/14
  6. 06
    DMR_11088
    log1p variance
    13.5642
    mean native value
    2,161.4
    detected samples
    14/14
  7. 07
    DMR_20425
    log1p variance
    13.4283
    mean native value
    1,903.6
    detected samples
    14/14
  8. 08
    DMR_19350
    log1p variance
    13.2282
    mean native value
    3,538.7
    detected samples
    14/14
  9. 09
    DMR_01021
    log1p variance
    12.9135
    mean native value
    3,238.7
    detected samples
    14/14
  10. 10
    DMR_19765
    log1p variance
    12.9091
    mean native value
    1,499.8
    detected samples
    14/14
  11. 11
    DMR_03938
    log1p variance
    12.8228
    mean native value
    1,437.8
    detected samples
    14/14
  12. 12
    DMR_02975
    log1p variance
    12.8213
    mean native value
    1,782.0
    detected samples
    14/14
  13. 13
    DMR_05216
    log1p variance
    12.8120
    mean native value
    2,364.9
    detected samples
    14/14
  14. 14
    DMR_09078
    log1p variance
    12.6699
    mean native value
    5,973.5
    detected samples
    14/14
  15. 15
    DMR_20267
    log1p variance
    12.5436
    mean native value
    8,755.6
    detected samples
    14/14
  16. 16
    DMR_10615
    log1p variance
    12.4115
    mean native value
    1,896.1
    detected samples
    14/14
  17. 17
    DMR_13938
    log1p variance
    12.3613
    mean native value
    6,856.8
    detected samples
    14/14
  18. 18
    DMR_04718
    log1p variance
    12.2831
    mean native value
    1,596.2
    detected samples
    14/14
  19. 19
    DMR_07783
    log1p variance
    12.2670
    mean native value
    1,874.4
    detected samples
    14/14
  20. 20
    DMR_15238
    log1p variance
    12.2110
    mean native value
    1,374.6
    detected samples
    14/14
  21. 21
    DMR_14847
    log1p variance
    12.1804
    mean native value
    1,569.2
    detected samples
    14/14
  22. 22
    DMR_13940
    log1p variance
    11.7934
    mean native value
    5,252.6
    detected samples
    14/14
  23. 23
    DMR_02652
    log1p variance
    11.7162
    mean native value
    3,751.5
    detected samples
    14/14
  24. 24
    DMR_21794
    log1p variance
    11.7149
    mean native value
    1,585.4
    detected samples
    14/14
  25. 25
    DMR_17506
    log1p variance
    11.7002
    mean native value
    1,034.7
    detected samples
    14/14
Declared exclusions

Matrix samples outside the six-tissue universe

2 source-matrix samples are retained in provenance but excluded from this Table S1A-aligned view.

Reproducible boundary

What this page computes—and what it does not

Input

Multi-sample GEO-supplied RPKM matrix

The source reports RPKM; LACA applies log1p only for within-species PCA/QC.

Within-species computation

QC · PCA · variable features

All feature rows retained from the native GSE50726 matrix.

Not computed

No cross-species expression test

No matrix merge, differential-expression result, lifespan regression, or causal claim is presented here.

Source integrity

GSE50726_DMR.rpkm.txt.gz

SHA-256 89ad6940d0fba2a340034afaf6390fc4aa6d01262e0ba9f7f5558d61cdb824a5

Back to source records → All 41 mammals →