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 green Gene description Interaction Map network_comparison red Network Comparison Type
Results: HTML CSV LaTeX Showing element 3682 to 3731 of 19268 in total
Value Type  : Ranked
Filtered  : 1
Rank
green
description
Interaction Map
network_comparison
red
Network Comparison Type
248 267.527 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] High confidence 23.944 243.583 Subtracted
249 201.076 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Low confidence 1.0468 210.487 Divided
202.333 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] High confidence 23.776 226.109 Subtracted
210.503 transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Low confidence 9.246 219.749
212.41 ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 1.11719 237.302 Divided
250 186.95 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 23.743 210.693 Subtracted
201.051 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 1.04671 210.443 Divided
210.498 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 9.244 219.742 Subtracted
212.41 heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] High confidence 1.11719 237.302 Divided
251 166.661 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 1.11707 186.172
201.035 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence 1.04666 210.415
210.484 upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 9.238 219.722 Subtracted
267.21 40s ribosomal protein s20. [swissprot;acc:p17075] High confidence 23.71 243.5
252 193.53 u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Low confidence 9.124 202.654
201.035 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] 1.04665 210.414 Divided
204.333 mad protein (max dimerizer). [swissprot;acc:q05195] High confidence 23.667 228 Subtracted
212.457 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 1.11689 237.292 Divided
253 201.035 nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 1.04665 210.413
204.333 mad protein (max dimerizer). [swissprot;acc:q05195] High confidence 1.11583 228
204.916 parafibromin. [refseq;acc:nm_024529] Low confidence 9.099 214.015 Subtracted
228.037 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] High confidence 23.642 251.679
254 179.88 source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 1.11569 200.691 Divided
201.035 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence 1.04665 210.414
204.357 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] High confidence 23.642 227.999 Subtracted
209.763 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence 9.022 218.785
255 179.88 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 1.11569 200.691 Divided
191.678 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Low confidence 9.021 200.699 Subtracted
201.035 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 1.04665 210.413 Divided
204.366 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] High confidence 23.633 227.999 Subtracted
256 190.521 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Low confidence 1.04648 199.376 Divided
199.455 sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] 9.014 208.469 Subtracted
204.357 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] High confidence 1.11569 227.999 Divided
204.37 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 23.629 Subtracted
257 179.88 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] 1.11569 200.691 Divided
192.404 tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Low confidence 1.04632 201.316
209.71 jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] 9.005 218.715 Subtracted
265.697 ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] High confidence 23.557 242.14
258 192.427 tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 1.04613 201.304 Divided
204.366 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] High confidence 1.11564 227.999
209.709 jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] Low confidence 9.005 218.714 Subtracted
265.697 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] High confidence 23.557 242.14
259 202.482 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence 1.04599 211.794 Divided
204.37 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] High confidence 1.11562 227.999
209.709 myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 9.005 218.714 Subtracted
265.696 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] High confidence 23.556 242.14
260 196.978 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 1.11394 219.421 Divided
207.34 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] Low confidence 1.04589 216.855
209.71 myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] 9.005 218.715 Subtracted
265.696 surfeit locus protein 5. [swissprot;acc:q15528] High confidence 23.556 242.14
261 196.978 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 1.11394 219.421 Divided

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/