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 description Value Type Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 9634 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Rank
description
Filtered
Interaction Map
red
green
network_comparison
251 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 0 High confidence 10551.6 11573.6 1.09686
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] 1 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
zinc finger protein 93 (zinc finger protein htf34) (fragment). [swissprot;acc:p35789] 0 Low confidence 4257.49 4854.46 1.14022
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] 1 210.414 201.035 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
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 10551.6 11573.5 1.09685
zinc finger protein zfp. [refseq;acc:nm_018651] Low confidence 4257.65 4854.63 1.14021
253 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] High confidence 10551.6 11573.5 1.09685
krab zinc finger protein. [sptrembl;acc:q96jc4] Low confidence 4257.65 4854.63 1.14021
mad protein (max dimerizer). [swissprot;acc:q05195] 1 High confidence 228 204.333 1.11583
nadph oxidase 4. [refseq;acc:nm_016931] Low confidence 210.413 201.035 1.04665
254 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 0 High confidence 10551.6 11573.5 1.09685
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] 1 Low confidence 210.414 201.035 1.04665
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] High confidence 200.691 179.88 1.11569
zinc finger protein loc163140 (fragment). [sptrembl;acc:q86wm6] 0 Low confidence 4257.81 4854.79 1.14021
255 nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 1 210.413 201.035 1.04665
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] High confidence 200.691 179.88 1.11569
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 0 10551.6 11573.5 1.09685
zinc finger protein 431. [swissprot;acc:q8tf32] Low confidence 4258.04 4855.04 1.14021
256 espin. [refseq;acc:nm_031475] High confidence 10551.6 11573.4 1.09684
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1 227.999 204.357 1.11569
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Low confidence 199.376 190.521 1.04648
zinc finger protein 267 (zinc finger protein hzf2). [swissprot;acc:q14586] 0 4258.04 4855.04 1.14021
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] 1 High confidence 200.691 179.88 1.11569
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 0 10552.2 11566.4 1.09611
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 1 Low confidence 201.316 192.404 1.04632
zinc finger protein 180 (hhz168). [swissprot;acc:q9ujw8] 0 4258.04 4855.04 1.14021
258 40s ribosomal protein s28. [swissprot;acc:p25112] High confidence 12967.1 14193.6 1.09459
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1 227.999 204.366 1.11564
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] Low confidence 201.304 192.427 1.04613
zinc finger protein 28 homolog (zfp-28) (kruppel-like zinc finger factor x6). [swissprot;acc:q8nhy6] 0 4257.81 4854.79 1.14021
259 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] High confidence 10438.3 9549.77 1.09304
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 1 227.999 204.37 1.11562
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Low confidence 211.794 202.482 1.04599
zinc finger protein 79 (znfpt7) (fragment). [swissprot;acc:q15937] 0 4258.04 4855.04 1.14021
260 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 12447.6 11392.6 1.0926
ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 1 Low confidence 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
zinc finger protein 463; c2h2-like zinc finger protein. [refseq;acc:nm_018555] 0 Low confidence 4258.35 4855.37 1.1402
261 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 12448.9 11393.9 1.09259
ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 1 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
zinc finger protein 126 (hzf-2) (fragment). [swissprot;acc:p35275] 0 Low confidence 4259.13 4856.2 1.14019
262 breast cancer antigen ny-br-1. [refseq;acc:nm_052997] 1 216.842 207.332 1.04587
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] High confidence 219.421 196.978 1.11394
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 0 3464 3778 1.09065
zinc finger protein 345 (zinc finger protein hzf10). [swissprot;acc:q14585] Low confidence 4259.67 4856.77 1.14018
263 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] High confidence 13573.3 14801.2 1.09046
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 1 219.421 196.978 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/