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 2001 to 2050 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1001 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] Subtracted 221.28 214.409 6.871
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] Divided 225.167 217.922 1.03325
1002 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Subtracted 221.278 214.409 6.869
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Divided 225.167 217.922 1.03325
1003 pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Subtracted 211.071 204.205 6.866
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Divided 225.167 217.922 1.03325
1004 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 231.059 1.03318
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Subtracted 269.59 276.454 6.864
1005 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Divided 225.448 218.232 1.03307
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Subtracted 231.007 237.864 6.857
1006 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Divided 116.524 120.375 1.03305
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Subtracted 217.026 210.189 6.837
1007 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Divided 162.055 156.884 1.03296
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Subtracted 217.021 210.185 6.836
1008 dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] 222.364 215.535 6.829
wd-repeat protein bing4. [swissprot;acc:o15213] Divided 243.227 235.475 1.03292
1009 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 229.116 221.823 1.03288
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Subtracted 222.364 215.535 6.829
1010 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 228.105 221.293 6.812
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Divided 217.523 210.648 1.03264
1011 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Subtracted 228.105 221.293 6.812
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Divided 217.026 210.189 1.03253
1012 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Subtracted 217.369 210.561 6.808
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Divided 217.021 210.185 1.03252
1013 protein bap28. [swissprot;acc:q9h583] 244.312 236.647 1.03239
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Subtracted 217.365 210.558 6.807
1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Divided 243.045 235.422 1.03238
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] Subtracted 217.361 210.554 6.807
1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Divided 221.73 228.906 1.03236
exocyst complex component sec6. [swissprot;acc:o60645] Subtracted 207.186 200.398 6.788
1016 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Divided 217.369 210.561 1.03233
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Subtracted 221.183 214.406 6.777
1017 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] 211.908 218.627 6.719
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Divided 217.365 210.558 1.03233
1018 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 210.554
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] Subtracted 211.908 218.627 6.719
1019 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 6.695
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 221.302 214.409 1.03215
1020 dopachrome tautomerase precursor (ec 5.3.3.12) (dt) (dct) (dopachrome delta-isomerase) (tyrosinase-related protein 2) (trp-2) (trp2). [swissprot;acc:p40126] 221.28 1.03205
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 226.218 232.88 6.662
1021 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] Divided 221.278 214.409 1.03204
block 23. [sptrembl;acc:q8nhw5] Subtracted 226.205 232.858 6.653
1022 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] 226.203 232.855 6.652
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Divided 205.632 199.266 1.03195
1023 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Subtracted 202.027 195.386 6.641
transforming protein rhoc (h9). [swissprot;acc:p08134] Divided 205.632 199.266 1.03195
1024 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Subtracted 203.381 196.76 6.621
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Divided 205.632 199.266 1.03195
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
40s ribosomal protein s30. [swissprot;acc:q05472] Subtracted 223.44 216.875 6.565

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/