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 Value Type description Interaction Map red Network Comparison Type Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
red
Network Comparison Type
Filtered
green
network_comparison
251 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 Subtracted 1 267.21 23.71
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 12463.5 0 11482.6 980.9
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 10551.6 Divided 11573.6 1.09686
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 186.172 1 166.661 1.11707
252 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 237.292 212.457 1.11689
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 10551.6 0 11573.5 1.09685
mad protein (max dimerizer). [swissprot;acc:q05195] 228 Subtracted 1 204.333 23.667
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] 12748.1 0 11770.9 977.2
253 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 9586.97 10560 973.03
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] 10551.6 Divided 11573.5 1.09685
mad protein (max dimerizer). [swissprot;acc:q05195] 228 1 204.333 1.11583
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] 251.679 Subtracted 228.037 23.642
254 keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] 10551.6 Divided 0 11573.5 1.09685
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 227.999 Subtracted 1 204.357 23.642
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 17387.1 0 16427.3 959.8
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 200.691 Divided 1 179.88 1.11569
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 Subtracted 204.366 23.633
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 200.691 Divided 179.88 1.11569
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] 17387.1 Subtracted 0 16427.3 959.8
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] 10551.6 Divided 11573.5 1.09685
256 espin. [refseq;acc:nm_031475] 11573.4 1.09684
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 Subtracted 1 204.37 23.629
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided 204.357 1.11569
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 13981.5 Subtracted 0 13025.1 956.4
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] 200.691 Divided 1 179.88 1.11569
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] 10552.2 0 11566.4 1.09611
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 9379.47 Subtracted 8436.39 943.08
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 242.14 1 265.697 23.557
258 40s ribosomal protein s28. [swissprot;acc:p25112] 12967.1 Divided 0 14193.6 1.09459
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 242.14 Subtracted 1 265.697 23.557
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 227.999 Divided 204.366 1.11564
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 13687.7 Subtracted 0 12751.8 935.9
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 1 265.696 23.556
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 10438.3 Divided 0 9549.77 1.09304
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 9815.6 Subtracted 8889.93 925.67
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 227.999 Divided 1 204.37 1.11562
260 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 12447.6 0 11392.6 1.0926
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 1 196.978 1.11394
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 5797 Subtracted 0 4873 924
surfeit locus protein 5. [swissprot;acc:q15528] 242.14 1 265.696 23.556
261 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 12448.9 Divided 0 11393.9 1.09259
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 1 196.978 1.11394
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 13651 Subtracted 0 14572 921
zinc finger protein 291. [swissprot;acc:q9by12] 242.14 1 265.696 23.556
262 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 9984 0 9067 917
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 Divided 1 196.978 1.11394
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 242.14 Subtracted 265.696 23.556
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] 3464 Divided 0 3778 1.09065
263 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 13573.3 14801.2 1.09046
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 219.421 1 196.978 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/