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 Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 2001 to 2050 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1001 rna-binding protein s1, serine-rich domain; sr protein. [refseq;acc:nm_006711] Low confidence 206.276 201.339 1.02452
sprouty homolog 3 (spry-3). [swissprot;acc:o43610] High confidence 225.167 217.922 1.03325
1002 bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263] Low confidence 205.137 200.227 1.02452
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] High confidence 225.167 217.922 1.03325
1003 n-acetylglutamate synthase. [refseq;acc:nm_153006] Low confidence 191.663 187.077 1.02451
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] High confidence 225.167 217.922 1.03325
1004 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Low confidence 200.403 195.612 1.02449
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] High confidence 238.725 231.059 1.03318
1005 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 225.448 218.232 1.03307
ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974] Low confidence 204.271 199.392 1.02447
1006 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] 206.183 201.259
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] High confidence 116.524 120.375 1.03305
1007 electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Low confidence 198.075 193.349 1.02444
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] High confidence 162.055 156.884 1.03296
1008 src substrate cortactin (amplaxin) (oncogene ems1). [swissprot;acc:q14247] Low confidence 199.992 195.221 1.02444
wd-repeat protein bing4. [swissprot;acc:o15213] High confidence 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
lu1 protein. [refseq;acc:nm_032512] Low confidence 204.391 199.514 1.02444
1010 peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] High confidence 217.523 210.648 1.03264
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Low confidence 202.366 197.54 1.02443
1011 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] 208.97 214.075
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] High confidence 217.026 210.189 1.03253
1012 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 217.021 210.185 1.03252
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Low confidence 204.877 199.992 1.02443
1013 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 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

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/