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 7362 to 7411 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
921 metastasis-associated protein mta1. [swissprot;acc:q13330] Squared Subtracted 23321.7 26976.4 3654.7
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Measured 3831.17 4388.74 557.57
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Ranked Divided 236.741 245.547 1.0372
translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] Measured 6324.31 6948.5 1.0987
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Rooted 93.8375 88.6044 1.05906
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Subtracted 62.3617 66.0327 3.671
wd-repeat protein bing4. [swissprot;acc:o15213] Ranked 243.227 235.475 7.752
922 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] Squared Divided 27031.3 31257.4 1.15634
cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Subtracted 23659.9 27312.6 3652.7
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Measured 3893.85 4450.98 557.13
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Ranked Divided 236.741 245.547 1.0372
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Subtracted 215.665 207.942 7.723
tubulin-tyrosine ligase. [refseq;acc:nm_153712] Measured Divided 5511.2 6054.71 1.09862
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Rooted 62.0422 65.7019 1.05899
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Subtracted 62.3618 66.0328 3.671
923 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Squared 23659.2 27311.3 3652.1
elongation factor 2 (ef-2). [swissprot;acc:p13639] Divided 23598.8 27286.9 1.15628
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Measured 4057.54 4457.66 1.09861
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Ranked Subtracted 193.114 185.412 7.702
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Divided 236.741 245.547 1.0372
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Measured Subtracted 3790.11 4346.98 556.87
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Rooted Divided 62.0422 65.7019 1.05899
yeast sec31p homolog. [refseq;acc:nm_014933] Subtracted 62.3618 66.0328 3.671
924 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Measured 10243.4 9686.82 556.58
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Rooted Divided 62.0422 65.7019 1.05899
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Ranked 236.741 245.547 1.0372
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Squared 23598.8 27286.9 1.15628
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Measured 5406.5 5939.42 1.09857
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Ranked Subtracted 238.725 231.059 7.666
tcd37 homolog; prune. [refseq;acc:nm_021222] Squared 23659.1 27311.1 3652
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Rooted 62.3617 66.0327 3.671
925 delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Divided 62.0422 65.7019 1.05899
grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] Measured Subtracted 4134.77 4691.24 556.47
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Squared 23294.5 26946.3 3651.8
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Divided 23598.8 27286.9 1.15628
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Ranked 215.665 207.942 1.03714
protein bap28. [swissprot;acc:q9h583] Subtracted 244.312 236.647 7.665
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Rooted 62.3618 66.0328 3.671
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] Measured Divided 5637.43 6193.07 1.09856
926 cellular modulator of immune recognition. [refseq;acc:nm_145021] Rooted 62.0422 65.7019 1.05899
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] Squared Subtracted 23658.7 27310.2 3651.5
eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Divided 17373.9 20087.4 1.15618
ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] Rooted Subtracted 62.3618 66.0328 3.671
grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7] Measured 4134.77 4691.24 556.47
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Ranked Divided 217.942 210.139 1.03713
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Subtracted 212.952 205.292 7.66
[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Measured Divided 5637.45 6193.08 1.09856
927 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Squared Subtracted 23658.5 27309.8 3651.3
dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Rooted 62.3617 66.0327 3.671
dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [refseq;acc:nm_020868] Measured Divided 5638.64 6194.22 1.09853

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/