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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 6836 to 6885 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1709 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] Rooted 61.6482 63.6574 1.03259
1710 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Measured 5916.13 6321.77 1.06857
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Ranked 227.225 224.21 1.01345
geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] Rooted 53.8424 55.5929 1.03251
guanine nucleotide-binding protein g(i), alpha-1 subunit (adenylate cyclase-inhibiting g alpha protein). [swissprot;acc:p04898] Squared 2614.02 2367 1.10436
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] Ranked 218.436 215.553 1.01337
guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754] Squared 2614.02 2367 1.10436
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Measured 5917.22 6322.72 1.06853
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Rooted 64.6674 66.7696 1.03251
1712 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Measured 5917.23 6322.73 1.06853
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Rooted 64.803 66.9076 1.03248
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Ranked 208.598 211.375 1.01331
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Squared 13649.9 15070.2 1.10405
1713 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Measured 5917.23 6322.73 1.06853
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Squared 16662.1 18391.9 1.10382
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Rooted 64.3126 66.4016 1.03248
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Ranked 206.823 204.111 1.01329
1714 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 206.549 203.844 1.01327
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Measured 5917.23 6322.73 1.06853
dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] Squared 24923.8 27509.9 1.10376
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Rooted 64.7728 66.8682 1.03235
1715 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Measured 5918.48 6323.83 1.06849
cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Rooted 62.744 64.7668 1.03224
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Ranked 206.549 203.844 1.01327
katanin p60 subunit a 1. [refseq;acc:nm_007044] Squared 16643.4 18369.3 1.1037
1716 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Rooted 62.7467 64.7695 1.03224
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Measured 6070.41 6485.85 1.06844
lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358] Squared 26316.4 29038 1.10342
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Ranked 206.522 203.818 1.01327
1717 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Rooted 62.7494 64.7722 1.03224
epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Squared 27288.3 30109.5 1.10338
inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Measured 6069.65 6484.94 1.06842
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Ranked 221.058 218.164 1.01327
1718 coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Measured 9720.64 9099.1 1.06831
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Squared 24291.6 26802.4 1.10336
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Ranked 206.251 203.553 1.01325
tcd37 homolog; prune. [refseq;acc:nm_021222] Rooted 62.7464 64.7691 1.03224
1719 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 62.7446 64.7674
helicase (fragment). [sptrembl;acc:q92771] Ranked 187.204 189.679 1.01322
lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2] Squared 24007.5 26484.7 1.10318
mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] Measured 5458.12 5830.76 1.06827
1720 beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Squared 59318.4 53788.1 1.10282
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Ranked 187.205 189.679 1.01322
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Rooted 70.2606 72.5203 1.03216
putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Measured 5458.12 5830.76 1.06827
1721 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Squared 59318.4 53788.1 1.10282
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] Ranked 227.125 224.164 1.01321
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] Rooted 68.8451 71.0582 1.03215
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Measured 5458.12 5830.76 1.06827
1722 40s ribosomal protein s13. [swissprot;acc:q02546] Ranked 220.899 223.813 1.01319

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/