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 3375 to 3424 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1688 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Subtracted 216.079 219.024 2.945
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Divided 228.523 231.703 1.01392
1689 ataxin 2-binding protein. [swissprot;acc:q9nwb1] Subtracted 218.514 215.577 2.937
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Divided 228.277 225.163 1.01383
1690 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] 224.091 227.184 1.0138
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Subtracted 217.624 214.69 2.934
1691 hskin17 protein. [refseq;acc:nm_012311]
translation initiation factor if-2. [swissprot;acc:o60841] Divided 217.263 214.315 1.01376
1692 carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Subtracted 217.624 214.69 2.934
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] Divided 218.515 215.551 1.01375
1693 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 218.937 215.971 1.01373
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Subtracted 217.624 214.69 2.934
1694 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Divided 218.937 215.971 1.01373
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Subtracted 217.624 214.69 2.934
1695 40s ribosomal protein s13. [swissprot;acc:q02546] 220.899 223.813 2.914
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Divided 218.937 215.971 1.01373
1696 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Subtracted 221.058 218.164 2.894
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Divided 217.624 214.69 1.01367
1697 hskin17 protein. [refseq;acc:nm_012311]
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Subtracted 177.834 180.725 2.891
1698 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 204.437 201.551 2.886
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Divided 217.624 214.69 1.01367
1699 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Subtracted 218.436 215.553 2.883
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Divided 217.624 214.69 1.01367
1700 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Subtracted 204.433 201.564 2.869
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Divided 217.624 214.69 1.01367
1701 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] 216.079 219.024 1.01363
hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Subtracted 182.378 185.241 2.863
1702 dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Divided 216.079 219.024 1.01363
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Subtracted 233.45 230.595 2.855
1703 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Divided 216.079 219.024 1.01363
myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [swissprot;acc:p05976] Subtracted 233.45 230.595 2.855
1704 ataxin 2-binding protein. [swissprot;acc:q9nwb1] Divided 218.514 215.577 1.01362
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Subtracted 233.45 230.595 2.855
1705 nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380]
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Divided 223.846 220.847 1.01358
1706 immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318]
myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Subtracted 233.45 230.595 2.855
1707 mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] Divided 221.283 218.334 1.01351
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Subtracted 233.45 230.595 2.855
1708 inositol polyphosphate multikinase. [refseq;acc:nm_152230] 217.676 220.53 2.854
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided 221.283 218.334 1.01351
1709 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Subtracted 217.676 220.53 2.854
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014] Divided 198.014 195.385 1.01346
1710 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Subtracted 217.676 220.53 2.854
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Divided 227.225 224.21 1.01345
1711 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 218.436 215.553 1.01337
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] Subtracted 194.516 197.364 2.848
1712 hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775]
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Divided 208.598 211.375 1.01331

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/