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 2025 to 2074 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1013 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Low confidence 200.743 195.959 1.02441
protein bap28. [swissprot;acc:q9h583] High confidence 244.312 236.647 1.03239
1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 243.045 235.422 1.03238
methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898] Low confidence 182.56 178.211 1.0244
1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] High confidence 221.73 228.906 1.03236
kinesin family member c3. [refseq;acc:nm_005550] Low confidence 205.25 200.362 1.0244
1016 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] High confidence 217.369 210.561 1.03233
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Low confidence 201.283 196.49 1.02439
1017 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] 200.745 195.966
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] High confidence 217.365 210.558 1.03233
1018 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 217.361 210.554
similar to semaf cytoplasmic domain associated protein 3. [sptrembl;acc:q96cc2] Low confidence 204.339 199.475 1.02438
1019 homeodomain interacting protein kinase 3; homeodomain-interacting protein kinase 3. [refseq;acc:nm_005734] 202.352 197.536
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] High confidence 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
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Low confidence 200.421 205.306 1.02437
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] High confidence 221.278 214.409 1.03204
homeodomain-interacting protein kinase 2 (ec 2.7.1.-). [swissprot;acc:q9h2x6] Low confidence 202.351 197.537 1.02437
1022 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] High confidence 205.632 199.266 1.03195
homeodomain-interacting protein kinase 1; homeodomain interacting protein kinase 1-like protein; nuclear body associated kinase 2b. [refseq;acc:nm_152696] Low confidence 202.351 197.538 1.02436
1023 geal-6 membrane-associated high-copy suppressor 1; unc-50 related. [refseq;acc:nm_014044] 203.215 208.165
transforming protein rhoc (h9). [swissprot;acc:p08134] High confidence 205.632 199.266 1.03195
1024 mitochondrial import inner membrane translocase subunit tim9 a. [swissprot;acc:q9y5j7] Low confidence 205.995 201.097 1.02436
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] High confidence 205.632 199.266 1.03195
1025 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6] Low confidence 201.047 196.275 1.02431
1026 gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 206.781 201.874
transforming protein rhoa (h12). [swissprot;acc:p06749] High confidence 205.632 199.266 1.03195
1027 protein cgi-147. [swissprot;acc:q9y3e5] Low confidence 203.643 198.811 1.0243
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] High confidence 211.908 218.627 1.03171
1028 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Low confidence 203.574 198.744 1.0243
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] High confidence 211.908 218.627 1.03171
1029 apical-like protein (apxl protein). [swissprot;acc:q13796] Low confidence 204.847 199.989 1.02429
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] High confidence 222.364 215.535 1.03168
1030 nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] Low confidence 201.043 196.276 1.02429
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] High confidence 222.364 215.535 1.03168
1031 probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] 242.978 235.518 1.03167
thromboxane-a synthase (ec 5.3.99.5) (txa synthase) (txs). [swissprot;acc:p24557] Low confidence 203.998 199.161 1.02429
1032 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] High confidence 186.664 180.943 1.03162
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Low confidence 203.946 199.111 1.02428
1033 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 172.447 168.363 1.02426
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] High confidence 221.183 214.406 1.03161
1034 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Low confidence 202.723 197.922 1.02426
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] High confidence 186.551 180.837 1.0316
1035 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] 221.682 228.68 1.03157
nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209] Low confidence 201.037 196.277 1.02425
1036 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] High confidence 171.341 176.746 1.03155
ras-related protein rab-7. [swissprot;acc:p51149] Low confidence 199.336 194.616 1.02425
1037 l-3-phosphoserine phosphatase (ec 3.1.3.3) (psp) (o-phosphoserine phosphohydrolase) (pspase). [swissprot;acc:p78330] 195.067 190.451 1.02424
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] High confidence 228.412 235.609 1.03151

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/