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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Value Type Filtered Rank Gene description green 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
description
green
Interaction Map
network_comparison
red
Network Comparison Type
248 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 155.476 Low confidence 1.04682 162.755 Divided
249 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] 201.076 1.0468 210.487
ns1-associated protein 1. [refseq;acc:nm_006372] 212.41 High confidence 1.11719 237.302
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 202.333 23.776 226.109 Subtracted
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 210.503 Low confidence 9.246 219.749
250 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 210.498 9.244 219.742
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] 201.051 1.04671 210.443 Divided
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] 212.41 High confidence 1.11719 237.302
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 186.95 23.743 210.693 Subtracted
251 40s ribosomal protein s20. [swissprot;acc:p17075] 267.21 23.71 243.5
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] 201.035 Low confidence 1.04666 210.415 Divided
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 166.661 High confidence 1.11707 186.172
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] 210.484 Low confidence 9.238 219.722 Subtracted
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] 201.035 1.04665 210.414 Divided
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 212.457 High confidence 1.11689 237.292
mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 23.667 228 Subtracted
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] 193.53 Low confidence 9.124 202.654
253 mad protein (max dimerizer). [swissprot;acc:q05195] 204.333 High confidence 1.11583 228 Divided
nadph oxidase 4. [refseq;acc:nm_016931] 201.035 Low confidence 1.04665 210.413
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] 228.037 High confidence 23.642 251.679 Subtracted
parafibromin. [refseq;acc:nm_024529] 204.916 Low confidence 9.099 214.015
254 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 High confidence 23.642 227.999
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] 201.035 Low confidence 1.04665 210.414 Divided
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 209.763 9.022 218.785 Subtracted
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 179.88 High confidence 1.11569 200.691 Divided
255 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 23.633 227.999 Subtracted
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] 201.035 Low confidence 1.04665 210.413 Divided
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 191.678 9.021 200.699 Subtracted
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 179.88 High confidence 1.11569 200.691 Divided
256 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 23.629 227.999 Subtracted
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 204.357 1.11569 Divided
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 190.521 Low confidence 1.04648 199.376
sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908] 199.455 9.014 208.469 Subtracted
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] 179.88 High confidence 1.11569 200.691 Divided
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] 209.71 Low confidence 9.005 218.715 Subtracted
tropomyosin alpha 3 chain (tropomyosin 3) (tropomyosin gamma). [swissprot;acc:p06753] 192.404 1.04632 201.316 Divided
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 265.697 High confidence 23.557 242.14 Subtracted
258 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] 209.709 Low confidence 9.005 218.714
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 204.366 High confidence 1.11564 227.999 Divided
tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493] 192.427 Low confidence 1.04613 201.304
259 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 265.696 High confidence 23.556 242.14 Subtracted
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 204.37 1.11562 227.999 Divided
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] 209.709 Low confidence 9.005 218.714 Subtracted
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 202.482 1.04599 211.794 Divided
260 ankyrin repeat domain protein 7 (testis-specific protein tsa806). [swissprot;acc:q92527] 207.34 1.04589 216.855
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 High confidence 1.11394 219.421
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] 209.71 Low confidence 9.005 218.715 Subtracted
surfeit locus protein 5. [swissprot;acc:q15528] 265.696 High confidence 23.556 242.14
261 ba526d8.2 (novel protein similar to kiaa1074). [sptrembl;acc:q9h560] 207.333 Low confidence 1.04588 216.845 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/