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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Value Type Interaction Map Filtered Gene Rank green description red network_comparison Network Comparison Type
Results: HTML CSV LaTeX Showing element 986 to 1035 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
Rank
green
description
red
network_comparison
986 120.707 exocyst complex component sec5. [swissprot;acc:q96kp1] 116.771 1.03371
987 211.338 serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] 218.459 1.03369
988 211.343 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 218.461 1.03368
989 211.345 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 218.462 1.03367
990 235.373 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 243.297
991 196.76 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 1.03365
992 211.357 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 218.468 1.03364
993 204.205 pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] 211.071 1.03362
994 120.772 poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 116.845 1.03361
995 212.547 mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] 219.656 1.03345
996 mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
997 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
998 218.271 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 225.557 1.03338
999 208.95 vinculin (metavinculin). [swissprot;acc:p18206] 215.92 1.03336
1000 217.922 sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] 225.167 1.03325
1001 sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
1002 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]
1003 sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
1004 231.059 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 1.03318
1005 218.232 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 225.448 1.03307
1006 120.375 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 116.524 1.03305
1007 156.884 ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] 162.055 1.03296
1008 235.475 wd-repeat protein bing4. [swissprot;acc:o15213] 243.227 1.03292
1009 221.823 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 229.116 1.03288
1010 210.648 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] 217.523 1.03264
1011 210.189 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 217.026 1.03253
1012 210.185 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 217.021 1.03252
1013 236.647 protein bap28. [swissprot;acc:q9h583] 244.312 1.03239
1014 235.422 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 243.045 1.03238
1015 228.906 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 221.73 1.03236
1016 210.561 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 217.369 1.03233
1017 210.558 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 217.365
1018 210.554 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361
1019 214.409 tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 221.302 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
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] 221.278 1.03204
1022 199.266 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 205.632 1.03195
1023 transforming protein rhoc (h9). [swissprot;acc:p08134]
1024 thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
1026 transforming protein rhoa (h12). [swissprot;acc:p06749]
1027 218.627 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 1.03171
1028 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]
1029 215.535 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 1.03168
1030 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]
1031 235.518 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 242.978 1.03167
1032 180.943 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 186.664 1.03162
1033 214.406 tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] 221.183 1.03161
1034 180.837 steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] 186.551 1.0316
1035 228.68 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 1.03157

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/