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 51 to 100 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
7 homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Divided High confidence 1 215 322 1.49767
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted Low confidence 0 22286 13216 9070
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] Divided Low confidence 1 318 240 1.325
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Subtracted 78
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] High confidence 288.754 212.554 76.2
8 hbs1-like. [refseq;acc:nm_006620] Divided 215 322 1.49767
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 0 22286 13216 1.68629
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted High confidence 9070
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 288 362 74
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided 0 11525 21888 1.89918
oxysterol binding protein-related protein 7 (osbp-related protein 7) (orp-7). [swissprot;acc:q9bzf2] Low confidence 1 318 240 1.325
thyroid receptor interacting protein 8 (trip-8) (fragment). [swissprot;acc:q15652] Subtracted 305.472 247.246 58.226
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] 0 10889.4 19873 8983.6
9 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Divided 1 58 44 1.31818
gbp protein isoform a. [refseq;acc:nm_017870] Subtracted 305.399 247.213 58.186
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0 22422 14964 7458
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 22286 13216 9070
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided Low confidence 1.68629
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Subtracted High confidence 1 288 362 74
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Divided 0 11525 21888 1.89918
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 212 309 1.45755
10 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 0 7509.39 14178.1 1.88805
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 22286 13216 1.68629
jumonji domain containing 1; zinc finger protein; testis-specific protein a. [refseq;acc:nm_018433] Subtracted 1 305.303 247.169 58.134
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided 58 44 1.31818
protein x 0004. [refseq;acc:nm_016301] High confidence 212 309 1.45755
ptd016 protein. [refseq;acc:nm_016125] Subtracted Low confidence 0 18050 11234 6816
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 20989 12479 8510
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] 1 288 362 74
11 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided Low confidence 0 13730.5 8257 1.66289
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 1 37.318 28.4944 1.30966
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] Subtracted High confidence 0 12170.7 20670.6 8499.9
db83 protein. [swissprot;acc:p57088] 1 288 362 74
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110] Divided 0 11627 6248 1.86092
rad50-interacting protein 1. [refseq;acc:nm_021930] 1 337 232 1.45259
serpin b12. [swissprot;acc:q96p63] Subtracted Low confidence 0 14604.2 21138.6 6534.4
trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] 1 304.548 246.824 57.724
12 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Divided 0 3190 1933 1.65028
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] High confidence 9429.18 5208.84 1.81023
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Subtracted 1 266.856 336.233 69.377
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Low confidence 0 14592 21113.7 6521.7
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Divided High confidence 1 337 232 1.45259
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 0 19403 11267 8136
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Low confidence 1 304.359 246.737 57.622
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Divided 37.3475 28.5242 1.30933
13 dystrophin. [swissprot;acc:p11532] Subtracted High confidence 0 10232.5 18054.8 7822.3
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Low confidence 20324.1 14746.1 5578
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] High confidence 1 266.856 336.233 69.377
heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Divided 0 5210.5 9264.5 1.77804

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/