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 475 to 524 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
238 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Low confidence 200.699 191.678 1.04706
rd protein. [swissprot;acc:p18615] High confidence 227.357 254.15 1.11785
239 dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Low confidence 210.504 201.086 1.04684
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] High confidence 227.357 254.15 1.11785
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 162.755 155.476 1.04682
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] High confidence 227.357 254.15 1.11785
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Low confidence 162.755 155.476 1.04682
242 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]
j domain containing protein 1. [swissprot;acc:q9ukb3] High confidence 227.357 254.15 1.11785
243 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 162.755 155.476 1.04682
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] High confidence 227.357 254.15 1.11785
244 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 162.755 155.476 1.04682
245 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] High confidence 226.109 202.333 1.11751
246 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 237.312 212.363 1.11748
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 162.755 155.476 1.04682
247 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]
rna-binding protein. [refseq;acc:nm_019027] High confidence 237.302 212.41 1.11719
248 apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Low confidence 162.755 155.476 1.04682
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 210.487 201.076 1.0468
ns1-associated protein 1. [refseq;acc:nm_006372] High confidence 237.302 212.41 1.11719
250 diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Low confidence 210.443 201.051 1.04671
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] High confidence 237.302 212.41 1.11719
251 nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Low confidence 210.415 201.035 1.04666
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] High confidence 186.172 166.661 1.11707
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] Low confidence 210.414 201.035 1.04665
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] High confidence 237.292 212.457 1.11689
253 mad protein (max dimerizer). [swissprot;acc:q05195] 228 204.333 1.11583
nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 210.413 201.035 1.04665
254 nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] 210.414
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] High confidence 200.691 179.88 1.11569
255 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Low confidence 210.413 201.035 1.04665
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 200.691 179.88 1.11569
256 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 204.357
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Low confidence 199.376 190.521 1.04648
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] High confidence 200.691 179.88 1.11569
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] Low confidence 201.316 192.404 1.04632
258 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] High confidence 227.999 204.366 1.11564
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 201.304 192.427 1.04613
259 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] High confidence 227.999 204.37 1.11562
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence 211.794 202.482 1.04599
260 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 216.855 207.34 1.04589
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] High confidence 219.421 196.978 1.11394
261 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] Low confidence 216.845 207.333 1.04588
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] High confidence 219.421 196.978 1.11394
262 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Low confidence 216.842 207.332 1.04587
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] High confidence 219.421 196.978 1.11394

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/