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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 7114 to 7163 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : Low confidence
Filtered  : 1
Rank
description
red
green
network_comparison
3886 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 204.522 201.949 1.01274
3887 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 202.018 199.477
3888 anion exchange protein 2 (non-erythroid band 3-like protein) (bnd3l). [swissprot;acc:p04920] 204.559 201.988 1.01273
3889 cop9 constitutive photomorphogenic homolog subunit 7b; likely ortholog of cop9 (constitutive photomorphogenic), subunit 7b (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 7b. [refseq;acc:nm_022730] 201.902 199.364
3890 ubiquinol-cytochrome c reductase complex 7.2 kda protein (ec 1.10.2.2) (cytochrome c1, nonheme 7 kda protein) (complex iii subunit x) (7.2 kda cytochrome c1-associated protein subunit) (hspc119). [swissprot;acc:q9udw1] 206.614 204.018 1.01272
3891 tbp-associated factor 1b; tata box binding protein (tbp)-associated factor, rna polymerase i, b, 63kd; sl1, 63kd subunit. [refseq;acc:nm_005680] 199.996 197.485 1.01271
3892 acyl-coenzyme a oxidase 3, peroxisomal (ec 1.3.3.6) (pristanoyl-coa oxidase). [swissprot;acc:o15254]
3893 neighbor of cox4. [swissprot;acc:o43402] 200.352 197.839 1.0127
3894 survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893] 202.516 199.978 1.01269
3895 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 199.187 196.692 1.01268
3896 block 23. [sptrembl;acc:q8nhw5] 202.202 199.673 1.01267
3897 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]
3898 dual specificity mitogen-activated protein kinase kinase 3 (ec 2.7.1.-) (map kinase kinase 3) (mapkk 3) (mapk/erk kinase 3). [swissprot;acc:p46734] 200.15 197.647 1.01266
3899 similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 202.201 199.675 1.01265
3900 rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565] 206.72 204.137
3901 nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658] 204.481 201.928 1.01264
3902 regulatory factor x4 isoform b; transcription factor nyd-sp10. [refseq;acc:nm_002920] 203.988 201.442
3903 mhc class ii regulatory factor rfx1 (rfx) (enhancer factor c) (ef-c). [swissprot;acc:p22670] 203.982 201.44 1.01262
3904 transcription factor rfx3. [swissprot;acc:p48380] 203.98 1.01261
3905 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 200.957 198.456 1.0126
3906 nadh-ubiquinone oxidoreductase 24 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3). [swissprot;acc:p19404] 203.49 200.959 1.01259
3907 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 199.53 197.05
3908 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 203.756 201.222
3909 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 199.123 196.65 1.01258
3910 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 199.122 196.649
3911 discs, large homolog 5 (placenta and prostate dlg) (discs large protein p-dlg). [swissprot;acc:q8tdm6] 207.449 204.872
3912 ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532] 201.842 199.334
3913 dna-binding protein rfx2. [swissprot;acc:p48378] 203.974 201.439
3914 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 207.449 204.872
3915 ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] 202.173 199.664 1.01257
3916 dentin sialophosphoprotein precursor [contains: dentin phosphoprotein (dentin phosphophoryn) (dpp); dentin sialoprotein (dsp)]. [swissprot;acc:q9nzw4] 203.899 201.369 1.01256
3917 lamin b2. [swissprot;acc:q03252] 200.356 197.87
3918 solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] 205.017 202.475 1.01255
3919 rho gdp-dissociation inhibitor 2 (rho gdi 2) (rho-gdi beta) (ly-gdi). [swissprot;acc:p52566] 206.691 204.129
3920 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 199.083 196.618 1.01254
3921 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] 203.414 200.897 1.01253
3922 hmba-inducible; likely ortholog of mouse cardiac lineage protein 1; menage a quatre 1. [refseq;acc:nm_006460] 203.133 200.622 1.01252
3923 ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177] 201.856 199.362 1.01251
3924 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 203.54 201.025
3925 phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2]
3926 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] 204.167 201.649 1.01249
3927 muts protein homolog 5. [swissprot;acc:o43196] 201.212 198.73
3928 solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] 205.011 202.483 1.01248
3929 vacuolar proton-atpase subunit. [sptrembl;acc:q8nhe4] 201.567 199.087 1.01246
3930 peroxisome assembly factor-1 (paf-1) (peroxin-2) (peroxisomal membrane protein 3) (35 kda peroxisomal membrane protein). [swissprot;acc:p28328] 202.271 204.792
3931 vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase m9.2 subunit) (v-atpase 9.2 kda membrane accessory protein). [swissprot;acc:o15342] 201.567 199.087
3932 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] 201.144 198.67 1.01245
3933 sphingomyelin phosphodiesterase precursor (ec 3.1.4.12) (acid sphingomyelinase) (asmase). [swissprot;acc:p17405] 201.905 199.423
3934 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] 201.144 198.67
3935 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] 207.287 209.867

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/