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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Value Type Filtered Rank Gene description green Interaction Map network_comparison Network Comparison Type red
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 19268 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
green
Interaction Map
network_comparison
Network Comparison Type
red
248 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 155.476 Low confidence 1.04682 Divided 162.755
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 201.076 1.0468 210.487
ns1-associated protein 1. [refseq;acc:nm_006372] 212.41 High confidence 1.11719 237.302
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 202.333 23.776 Subtracted 226.109
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 210.503 Low confidence 9.246 219.749
250 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 210.498 9.244 219.742
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 201.051 1.04671 Divided 210.443
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 212.41 High confidence 1.11719 237.302
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 186.95 23.743 Subtracted 210.693
251 40s ribosomal protein s20. [swissprot;acc:p17075] 267.21 23.71 243.5
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] 201.035 Low confidence 1.04666 Divided 210.415
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 166.661 High confidence 1.11707 186.172
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 210.484 Low confidence 9.238 Subtracted 219.722
252 cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] 201.035 1.04665 Divided 210.414
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 High confidence 1.11689 237.292
mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 23.667 Subtracted 228
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 193.53 Low confidence 9.124 202.654
253 mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 High confidence 1.11583 Divided 228
nadph oxidase 4. [refseq;acc:nm_016931] 201.035 Low confidence 1.04665 210.413
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 228.037 High confidence 23.642 Subtracted 251.679
parafibromin. [refseq;acc:nm_024529] 204.916 Low confidence 9.099 214.015
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 High confidence 23.642 227.999
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] 201.035 Low confidence 1.04665 Divided 210.414
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 209.763 9.022 Subtracted 218.785
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 179.88 High confidence 1.11569 Divided 200.691
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 23.633 Subtracted 227.999
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 201.035 Low confidence 1.04665 Divided 210.413
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 191.678 9.021 Subtracted 200.699
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 179.88 High confidence 1.11569 Divided 200.691
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 23.629 Subtracted 227.999
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 1.11569 Divided
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 190.521 Low confidence 1.04648 199.376
sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] 199.455 9.014 Subtracted 208.469
257 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 179.88 High confidence 1.11569 Divided 200.691
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] 209.71 Low confidence 9.005 Subtracted 218.715
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 192.404 1.04632 Divided 201.316
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 265.697 High confidence 23.557 Subtracted 242.14
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] 209.709 Low confidence 9.005 218.714
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 High confidence 1.11564 Divided 227.999
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] 192.427 Low confidence 1.04613 201.304
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 265.696 High confidence 23.556 Subtracted 242.14
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 1.11562 Divided 227.999
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] 209.709 Low confidence 9.005 Subtracted 218.714
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 202.482 1.04599 Divided 211.794
260 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 207.34 1.04589 216.855
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 High confidence 1.11394 219.421
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] 209.71 Low confidence 9.005 Subtracted 218.715
surfeit locus protein 5. [swissprot;acc:q15528] 265.696 High confidence 23.556 242.14
261 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 207.333 Low confidence 1.04588 Divided 216.845

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/