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 4758 to 4807 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1190 spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] Squared 21634.8 24608.1 1.13743
ubiquitin. [swissprot;acc:p02248] Ranked 209.6 204.372 1.02558
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Rooted 61.4873 64.3719 1.04691
1191 probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Measured 6599.84 7174.29 1.08704
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Squared 21634.8 24608.1 1.13743
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Ranked 220.742 215.237 1.02558
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Rooted 61.4869 64.3691 1.04688
1192 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Squared 21639 24612.9 1.13743
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Measured 6599.84 7174.29 1.08704
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Ranked 220.742 215.237 1.02558
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Rooted 61.4866 64.3673 1.04685
1193 44050 protein. [refseq;acc:nm_178832] 108.34 103.501 1.04675
lbp-9. [refseq;acc:nm_014553] Ranked 220.742 215.237 1.02558
putative eukaryotic translation initiation factor 3 subunit (eif-3) (fragment). [swissprot;acc:o75153] Measured 5464.9 5940.16 1.08697
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Squared 21639 24612.9 1.13743
1194 nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Rooted 108.34 103.501 1.04675
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Squared 21634.8 24608.1 1.13743
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152] Ranked 220.742 215.237 1.02558
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Measured 8425.35 7751.57 1.08692
1195 40s ribosomal protein s30. [swissprot;acc:q05472] Squared 28134.5 31984.1 1.13683
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] Rooted 61.4842 64.3512 1.04663
similar to trna synthetase class ii. [refseq;acc:nm_152268] Measured 5439.56 5911.24 1.08671
skeletal muscle lim-protein 3 (slim 3) (lim-domain protein dral) (four and a half lim domains protein 2) (fhl-2). [swissprot;acc:q14192] Ranked 269.608 276.493 1.02554
1196 kappa b-ras 1. [refseq;acc:nm_020345] Measured 5721.19 6217.2 1.0867
kinesin protein. [refseq;acc:nm_032559] Ranked 224.858 219.264 1.02551
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Squared 20812.4 23659.7 1.13681
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Rooted 60.0873 62.8865 1.04659
1197 heat shock factor binding protein 1. [swissprot;acc:o75506] 62.6382 65.5533 1.04654
i-kappa-b-interacting ras-like protein 2. [refseq;acc:nm_017595] Measured 5721.19 6217.2 1.0867
mstp028 protein. [refseq;acc:nm_031954] Ranked 219.042 213.6 1.02548
serine/threonine-protein kinase nek1 (ec 2.7.1.37) (nima-related protein kinase 1) (ny-ren-55 antigen). [swissprot;acc:q96py6] Squared 26914.1 30594.2 1.13674
1198 homeobox protein otx2. [swissprot;acc:p32243] Rooted 56.0239 58.6274 1.04647
serine/threonine-protein kinase nek3 (ec 2.7.1.37) (nima-related protein kinase 3) (hspk 36). [swissprot;acc:p51956] Squared 26914.1 30594.2 1.13674
skeletal muscle lim-protein 2 (slim 2) (four and a half lim domains protein 3) (fhl-3). [swissprot;acc:q13643] Ranked 269.59 276.454 1.02546
snare associated protein snapin. [refseq;acc:nm_012437] Measured 5721.19 6217.2 1.0867
1199 n-myc proto-oncogene protein. [swissprot;acc:p04198] Squared 20816.6 23663.1 1.13674
pxr2b protein. [refseq;acc:nm_016559] Rooted 66.7327 69.832 1.04644
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] Measured 5449.48 5921.77 1.08667
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Ranked 241.496 235.508 1.02543
1200 glyceraldehyde 3-phosphate dehydrogenase, liver (ec 1.2.1.12) (gapdh). [swissprot;acc:p04406] Squared 26914.1 30594.2 1.13674
homeobox protein otx1. [swissprot;acc:p32242] Rooted 56.0736 58.677 1.04643
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Ranked 219.03 213.604 1.0254
xylulokinase homolog; xylulokinase (h. influenzae) homolog. [refseq;acc:nm_005108] Measured 5950.27 6465.72 1.08663
1201 cone-rod homeobox protein. [swissprot;acc:o43186] Rooted 56.0896 58.6931 1.04642
mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] Squared 19317.7 21958.6 1.13671
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Ranked 210.986 216.344 1.0254
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Measured 6042.31 6565.03 1.08651
1202 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] Ranked 227.274 233.041 1.02537
myb-related protein b (b-myb). [swissprot;acc:p10244] Rooted 60.1108 62.9002 1.0464
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Measured 4913.07 5337.95 1.08648

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.
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