Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2630 to 2679 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
329 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked Divided 312 284 1.09859
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Measured 15999.1 19007.1 1.18801
serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129] Rooted Subtracted 124.41 117.043 7.367
330 60s ribosomal protein l32. [swissprot;acc:p02433] Divided 50.519 45.5497 1.1091
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Ranked 312 284 1.09859
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Subtracted 224.657 203.235 21.422
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] Measured 11773 10733.2 1039.8
huntingtin interacting protein c. [refseq;acc:nm_012272] Squared Divided 16203.4 20339.9 1.25529
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 19321 12542.6 6778.4
septin 6. [swissprot;acc:q14141] Measured Divided 15959.9 18957.1 1.1878
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted Subtracted 55.5965 62.9349 7.3384
331 apical-like protein (apxl protein). [swissprot;acc:q13796] Divided 60.6697 67.2802 1.10896
doc-1 related protein (doc-1r). [swissprot;acc:o75956] Ranked 312 284 1.09859
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Measured Subtracted 10246.1 11285.8 1039.7
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 19321 12542.6 6778.4
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 55.5965 62.9349 7.3384
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] Measured Divided 20287.2 17083.8 1.18751
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Squared 33100.3 41520.6 1.25439
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Ranked Subtracted 224.647 203.242 21.405
332 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared 19321 12542.6 6778.4
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] Ranked 224.633 203.251 21.382
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Rooted 59.0951 66.4332 7.3381
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Ranked Divided 312 284 1.09859
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Squared 14464.3 18142.8 1.25432
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Measured 5051.16 5975.51 1.183
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted 60.6732 67.2827 1.10894
vav-2 protein. [swissprot;acc:p52735] Measured Subtracted 6660.02 7697.78 1037.76
333 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Rooted 95.4476 102.785 7.3374
deltex 2. [refseq;acc:nm_020892] Measured 1618.84 2651.88 1033.04
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 19321 12542.6 6778.4
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked Divided 312 284 1.09859
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Measured 5039.63 5961.83 1.18299
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Rooted 49.0526 54.3781 1.10857
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Squared 14464.3 18142.8 1.25432
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked Subtracted 265.634 244.304 21.33
334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared Divided 64975.9 81151.2 1.24894
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured Subtracted 1629.21 2662.12 1032.91
e-1 enzyme. [refseq;acc:nm_021204] Squared 30903.8 37638.1 6734.3
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked Divided 312 284 1.09859
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 58.6096 64.9655 1.10844
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked Subtracted 232.473 211.207 21.266
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Measured Divided 14924.4 17655.2 1.18298
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted Subtracted 58.2964 65.5926 7.2962
335 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 50.4705 45.5342 1.10841
60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared Subtracted 30924.3 37652.3 6728
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked Divided 312 284 1.09859
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Rooted Subtracted 52.7146 60.0088 7.2942
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked 223.273 202.423 20.85
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Measured Divided 3494.31 4129.6 1.18181
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared 30651.3 38253.3 1.24802

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/