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 3358 to 3407 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1679 gtp binding protein 2. [refseq;acc:nm_019096] High confidence 216.899 213.889 1.01407
1680 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]
cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Low confidence 200.124 196.081 1.02062
1681 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 200.826 196.771 1.02061
dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135] High confidence 216.899 213.889 1.01407
1682 glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Low confidence 199.393 195.367 1.02061
sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691] High confidence 216.899 213.889 1.01407
1683 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Low confidence 200.836 196.78 1.02061
cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] High confidence 216.899 213.889 1.01407
1684 jm4 protein. [refseq;acc:nm_007213] Low confidence 203.43 199.322 1.02061
sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] High confidence 216.899 213.889 1.01407
1685 xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]
zinc finger-like protein 9. [refseq;acc:nm_033414] Low confidence 202.494 198.406 1.0206
1686 galactoside 2-alpha-l-fucosyltransferase 2 (ec 2.4.1.69) (gdp-l- fucose:beta-d-galactoside 2-alpha-l-fucosyltransferase 2) (alpha(1,2)ft 2) (fucosyltransferase 2) (secretor blood group alpha-2- fucosyltransferase) (secretor factor) (se) (se2). [swissprot;acc:q10981] 201.628 197.561 1.02059
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] High confidence 220.75 217.704 1.01399
1687 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 215.345 212.386 1.01393
galactoside 2-alpha-l-fucosyltransferase 1 (ec 2.4.1.69) (gdp-l- fucose:beta-d-galactoside 2-alpha-l-fucosyltransferase 1) (alpha(1,2)ft 1) (fucosyltransferase 1) (blood group h alpha 2- fucosyltransferase). [swissprot;acc:p19526] Low confidence 201.628 197.561 1.02059
1688 transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] High confidence 228.523 231.703 1.01392
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Low confidence 201.234 197.175 1.02059
1689 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] High confidence 228.277 225.163 1.01383
suppressor of ty 6 homolog; suppressor of ty (s.cerevisiae) 6 homolog. [refseq;acc:nm_003170] Low confidence 203.44 199.336 1.02059
1690 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] High confidence 224.091 227.184 1.0138
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Low confidence 207.138 202.959 1.02059
1691 glycylpeptide n-tetradecanoyltransferase 2 (ec 2.3.1.97) (peptide n- myristoyltransferase 2) (myristoyl-coa:protein n-myristoyltransferase 2) (nmt 2) (type ii n-myristoyltransferase). [swissprot;acc:o60551] 200.606 196.56 1.02058
translation initiation factor if-2. [swissprot;acc:o60841] High confidence 217.263 214.315 1.01376
1692 mll septin-like fusion; septin d1. [refseq;acc:nm_006640] Low confidence 201.617 197.553 1.02057
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] High confidence 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
neuronal-specific septin 3. [swissprot;acc:q9uh03] Low confidence 201.615 197.551 1.02057
1694 chromosome-associated kinesin kif4a (chromokinesin). [swissprot;acc:o95239] 201.131 197.077
gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] High confidence 218.937 215.971 1.01373
1695 homeobox protein hox-c8 (hox-3a). [swissprot;acc:p31273] Low confidence 203.127 199.033 1.02057
inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] High confidence 218.937 215.971 1.01373
1696 candidate tumor suppressor protein. [refseq;acc:nm_020381] Low confidence 201.941 197.873 1.02056
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] High confidence 217.624 214.69 1.01367
1697 acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] Low confidence 201.941 197.873 1.02056
hskin17 protein. [refseq;acc:nm_012311] High confidence 217.624 214.69 1.01367
1698 acyl-coa-binding protein (acbp) (diazepam binding inhibitor) (dbi) (endozepine) (ep). [swissprot;acc:p07108] Low confidence 201.941 197.873 1.02056
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] High confidence 217.624 214.69 1.01367
1699 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Low confidence 201.425 197.367 1.02056
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] High confidence 217.624 214.69 1.01367
1700 polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940]
supervillin isoform 1; membrane-associated f-actin binding protein p205; archvillin. [refseq;acc:nm_003174] Low confidence 201.941 197.873 1.02056
1701 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] 201.46 197.403 1.02055
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] High confidence 216.079 219.024 1.01363
1702 dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542]
pr-domain zinc finger protein 12. [swissprot;acc:q9h4q4] Low confidence 195.014 191.088 1.02055
1703 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] High confidence 216.079 219.024 1.01363
pr-domain zinc finger protein 7. [swissprot;acc:q9nqw5] Low confidence 195.014 191.088 1.02055
1704 ataxin 2-binding protein. [swissprot;acc:q9nwb1] High confidence 218.514 215.577 1.01362

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/