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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Gene Rank green Value Type description Network Comparison Type Interaction Map network_comparison Filtered red
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
green
description
Network Comparison Type
Interaction Map
network_comparison
red
251 166.661 oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Divided High confidence 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] Subtracted 9.238 219.722
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] Divided 1.04665 210.414
204.333 mad protein (max dimerizer). [swissprot;acc:q05195] Subtracted High confidence 23.667 228
212.457 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Divided 1.11689 237.292
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] Subtracted Low confidence 9.099 214.015
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] Divided 1.11569 200.691
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] Subtracted High confidence 23.642 227.999
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] Divided High confidence 1.11569 200.691
191.678 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Subtracted Low confidence 9.021 200.699
201.035 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Divided 1.04665 210.413
204.366 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Subtracted High confidence 23.633 227.999
256 190.521 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Divided Low confidence 1.04648 199.376
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] Subtracted 9.014 208.469
204.357 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided High confidence 1.11569 227.999
204.37 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Subtracted 23.629
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] Divided 1.11569 200.691
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] Subtracted 9.005 218.715
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] Divided Low confidence 1.04613 201.304
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] Subtracted Low confidence 9.005 218.714
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] Divided Low confidence 1.04599 211.794
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] Subtracted Low confidence 9.005 218.714
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] Divided 1.11394 219.421
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] Subtracted 9.005 218.715
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] Divided 1.11394 219.421
207.333 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Low confidence 1.04588 216.845
209.709 myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Subtracted 9.004 218.713
265.696 zinc finger protein 291. [swissprot;acc:q9by12] High confidence 23.556 242.14
262 196.978 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Divided 1.11394 219.421
199.44 ring finger protein 10. [refseq;acc:nm_014868] Subtracted Low confidence 8.997 208.437
207.332 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Divided 1.04587 216.842
265.696 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted High confidence 23.556 242.14
263 196.978 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided 1.11394 219.421
199.44 sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610] Subtracted Low confidence 8.996 208.436

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/