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 6736 to 6785 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1684 sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137] Ranked 216.899 213.889 1.01407
1685 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4] Squared 27060.6 29916.8 1.10555
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Measured 6088.07 6508.45 1.06905
homeobox protein dlx-2. [swissprot;acc:q07687] Rooted 56.5094 58.3923 1.03332
xap-5 protein (hxc-26 protein). [swissprot;acc:q14320] Ranked 216.899 213.889 1.01407
1686 dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273] Squared 27060.6 29916.8 1.10555
homeobox protein dlx-5. [swissprot;acc:p56178] Rooted 56.5094 58.3923 1.03332
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Ranked 220.75 217.704 1.01399
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Measured 6088.07 6508.45 1.06905
1687 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955] Squared 27060.6 29916.8 1.10555
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] Ranked 215.345 212.386 1.01393
fetal brain protein 239 (239fb). [swissprot;acc:q15777] Rooted 56.5094 58.3923 1.03332
serpin b12. [swissprot;acc:q96p63] Measured 5767.69 6165.87 1.06904
1688 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484] Squared 27060.6 29916.8 1.10555
homeobox protein dlx-3. [swissprot;acc:o60479] Rooted 56.5094 58.3923 1.03332
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Measured 5767.69 6165.87 1.06904
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Ranked 228.523 231.703 1.01392
1689 activated p21cdc42hs kinase. [refseq;acc:nm_005781] Rooted 56.5094 58.3923 1.03332
adp-ribosylation factor-like protein 3. [swissprot;acc:p36405] Squared 27060.6 29916.8 1.10555
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Ranked 228.277 225.163 1.01383
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Measured 5767.69 6165.87 1.06904
1690 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Ranked 224.091 227.184 1.0138
mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093] Rooted 56.5094 58.3923 1.03332
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Measured 5767.69 6165.87 1.06904
unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] Squared 27060.6 29916.8 1.10555
1691 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556]
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Rooted 49.7922 48.1871 1.03331
translation initiation factor if-2. [swissprot;acc:o60841] Ranked 217.263 214.315 1.01376
upf0183 protein. [swissprot;acc:q9bsu1] Measured 5767.69 6165.87 1.06904
1692 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Rooted 64.1296 66.2619 1.03325
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Squared 13040.7 14416.9 1.10553
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] Ranked 218.515 215.551 1.01375
1693 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Rooted 62.1092 64.1674 1.03314
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Squared 9190.5 10160.2 1.10551
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Ranked 218.937 215.971 1.01373
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Measured 5767.69 6165.87 1.06904
1694 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Ranked 218.937 215.971 1.01373
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Squared 26226.9 28993.4 1.10548
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Measured 5767.69 6165.87 1.06904
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Rooted 62.1123 64.1674 1.03309
1695 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Ranked 218.937 215.971 1.01373
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Measured 5767.69 6165.87 1.06904
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Squared 29823.4 32961.5 1.10522
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Rooted 63.9104 66.0131 1.0329
1696 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 56.6562 54.8538 1.03286
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Ranked 217.624 214.69 1.01367
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Squared 26211.3 28968.8 1.1052
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Measured 6304.22 6738.77 1.06893
1697 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Squared 26192.8 28939.3 1.10486

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/