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 6591 to 6640 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1648 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Ranked 219.745 222.928 1.01448
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Rooted 64.6737 62.547 1.034
1649 neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730] Ranked 219.062 215.942 1.01445
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Measured 6079.19 6503.12 1.06973
ubiquitin. [swissprot;acc:p02248] Rooted 63.4301 65.5846 1.03397
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Squared 15603.4 17270.2 1.10682
1650 bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [refseq;acc:nm_001701] Rooted 62.0351 64.1375 1.03389
molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] Measured 6079.19 6503.12 1.06973
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] Squared 16089.8 17808 1.10679
ring finger protein 44. [refseq;acc:nm_014901] Ranked 219.062 215.942 1.01445
1651 cbf1 interacting corepressor. [refseq;acc:nm_004882] Measured 5944.24 6358.1 1.06962
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Ranked 219.062 215.942 1.01445
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Squared 16089.8 17808 1.10679
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] Rooted 62.1186 64.2224 1.03387
1652 down-regulated in metastasis. [refseq;acc:nm_014503] Squared 16089.8 17808 1.10679
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Measured 5944.24 6358.1 1.06962
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Rooted 62.0332 64.1338 1.03386
ring finger protein 38. [refseq;acc:nm_022781] Ranked 219.062 215.942 1.01445
1653 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Squared 14728.9 16301.3 1.10676
peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [refseq;acc:nm_152331] Rooted 62.0318 64.1312 1.03384
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Ranked 219.062 215.942 1.01445
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Measured 7433.73 7950.61 1.06953
1654 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Squared 14714.3 16284.1 1.10669
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Rooted 61.873 63.9658 1.03382
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Ranked 219.062 215.942 1.01445
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Measured 7433.73 7950.61 1.06953
1655 40s ribosomal protein s26. [swissprot;acc:p02383] 5488.7 5131.89
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Ranked 219.062 215.942 1.01445
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Squared 14714.1 16283.8 1.10668
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Rooted 64.6548 66.8408 1.03381
1656 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Squared 23451.3 25948.4 1.10648
importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Rooted 61.8671 63.9574 1.03379
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Measured 5488.7 5131.89 1.06953
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Ranked 219.062 215.942 1.01445
1657 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Measured 5488.7 5131.89 1.06953
cab2. [refseq;acc:nm_033419] Squared 23451.3 25948.4 1.10648
cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Ranked 219.314 216.195 1.01443
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Rooted 54.1965 56.0231 1.0337
1658 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Ranked 217.925 214.826 1.01443
dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Squared 23451.3 25948.4 1.10648
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] Rooted 54.1965 56.0231 1.0337
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Measured 7433.73 7950.61 1.06953
1659 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Ranked 217.925 214.826 1.01443
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Squared 23451.3 25948.4 1.10648
farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324] Rooted 54.1965 56.0231 1.0337
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Measured 5488.7 5131.89 1.06953
1660 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 7433.73 7950.61
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Ranked 228.654 231.933 1.01434
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Squared 23451.3 25948.4 1.10648
protocadherin 15 precursor. [swissprot;acc:q96qu1] Rooted 54.1965 56.0231 1.0337

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/