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 4936 to 4985 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1234 similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Measured 5807.83 6300.47 1.08482
1235 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] Squared 22816.7 25898.2 1.13505
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Ranked 219.356 224.723 1.02447
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Rooted 61.5382 64.3268 1.04531
1236 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Ranked 219.354 224.699 1.02437
kinesin family member c3. [refseq;acc:nm_005550] Squared 26958 30597.1 1.13499
p10-binding protein. [refseq;acc:nm_024491] Measured 5594.18 6067.49 1.08461
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Rooted 64.9834 67.9275 1.04531
1237 keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062] Ranked 219.354 224.699 1.02437
myelin gene expression factor 2. [refseq;acc:nm_016132] Squared 26039.6 29551.2 1.13486
tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Measured 5873.56 6370.31 1.08457
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Rooted 62.6895 65.5272 1.04527
1238 60 kda heat shock protein, mitochondrial precursor (hsp60) (60 kda chaperonin) (cpn60) (heat shock protein 60) (hsp-60) (mitochondrial matrix protein p1) (p60 lymphocyte protein) (hucha60). [swissprot;acc:p10809] Squared 23538.3 26712.4 1.13485
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Ranked 219.354 224.699 1.02437
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Measured 5873.56 6370.31 1.08457
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Rooted 62.6896 65.5272 1.04526
1239 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Measured 5654.53 6132.76 1.08457
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Squared 26127.9 29648.4 1.13474
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Ranked 219.354 224.699 1.02437
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Rooted 60.3671 57.7552 1.04522
1240 cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 62.6939 65.5285 1.04521
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Ranked 219.354 224.7 1.02437
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Squared 26127.9 29648.4 1.13474
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Measured 5654.54 6132.69 1.08456
1241 26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [swissprot;acc:q13200] 6436.19 6980.13 1.08451
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Ranked 219.354 224.7 1.02437
surfeit locus protein 1. [swissprot;acc:q15526] Rooted 62.6939 65.5285 1.04521
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Squared 26204.1 29732 1.13463
1242 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Ranked 219.354 224.7 1.02437
seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] Rooted 62.6944 65.5286 1.04521
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Measured 11143.5 10276.3 1.08439
1243 cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] Rooted 62.6939 65.5285 1.04521
keratin associated protein 1.5. [refseq;acc:nm_031957] Ranked 219.354 224.699 1.02437
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Squared 19239.8 21829.3 1.13459
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Measured 11143.5 10276.3 1.08439
1244 myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572] Squared 26227.1 29756.6 1.13457
protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] Rooted 62.6939 65.5285 1.04521
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Measured 4835.55 5243.23 1.08431
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Ranked 219.354 224.7 1.02437
1245 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] Measured 4835.55 5243.23 1.08431
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Rooted 62.6947 65.5287 1.0452
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Ranked 219.354 224.699 1.02437
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Squared 13127 14892.9 1.13452
1246 dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] Rooted 62.6947 65.5287 1.0452
glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] Squared 20120.1 22818.6 1.13412
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Ranked 219.354 224.699 1.02437
p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] Measured 5346.11 5796.72 1.08429
1247 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Squared 20117.4 22815.3 1.13411

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/