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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Gene Rank description Value Type Interaction Map red Network Comparison Type Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1980 to 2029 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
red
Network Comparison Type
green
network_comparison
990 atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301] 221.682 Subtracted 228.68 6.998
991 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] 203.381 Divided 196.76 1.03365
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] 198.494 Subtracted 205.466 6.972
992 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 218.468 Divided 211.357 1.03364
vinculin (metavinculin). [swissprot;acc:p18206] 215.92 Subtracted 208.95 6.97
993 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 251.863 258.829 6.966
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 211.071 Divided 204.205 1.03362
994 growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] 251.863 Subtracted 258.829 6.966
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 116.845 Divided 120.772 1.03361
995 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] 251.863 Subtracted 258.829 6.966
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 219.656 Divided 212.547 1.03345
996 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] 251.863 Subtracted 258.829 6.966
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 219.656 Divided 212.547 1.03345
997 growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] 251.863 Subtracted 258.829 6.966
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] 219.656 Divided 212.547 1.03345
998 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 225.557 218.271 1.03338
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 221.302 Subtracted 214.409 6.893
999 skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] 269.608 276.493 6.885
vinculin (metavinculin). [swissprot;acc:p18206] 215.92 Divided 208.95 1.03336
1000 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 217.523 Subtracted 210.648 6.875
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 225.167 Divided 217.922 1.03325
1001 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 Subtracted 214.409 6.871
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] 225.167 Divided 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] 221.278 Subtracted 214.409 6.869
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] 225.167 Divided 217.922 1.03325
1003 pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 211.071 Subtracted 204.205 6.866
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] 225.167 Divided 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] 269.59 Subtracted 276.454 6.864
1005 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 225.448 Divided 218.232 1.03307
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 231.007 Subtracted 237.864 6.857
1006 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 116.524 Divided 120.375 1.03305
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 217.026 Subtracted 210.189 6.837
1007 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 162.055 Divided 156.884 1.03296
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 217.021 Subtracted 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] 243.227 Divided 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] 222.364 Subtracted 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] 217.523 Divided 210.648 1.03264
1011 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 228.105 Subtracted 221.293 6.812
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 217.026 Divided 210.189 1.03253
1012 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 217.369 Subtracted 210.561 6.808
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 217.021 Divided 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] 217.365 Subtracted 210.558 6.807
1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 243.045 Divided 235.422 1.03238
importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 Subtracted 210.554 6.807
1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 221.73 Divided 228.906 1.03236

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/