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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4458 to 4507 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2229 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Divided 217.955 219.336 1.00634
2230 sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Subtracted 199.129 200.413 1.284
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Divided 217.955 219.336 1.00634
2231 clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Subtracted 199.129 200.413 1.284
hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] Divided 221.842 223.246 1.00633
2232 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 215.547 214.194 1.00632
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Subtracted 199.129 200.413 1.284
2233 lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]
tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] Divided 202.414 203.691 1.00631
2234 rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Subtracted 199.129 200.413 1.284
seven in absentia homolog 1. [refseq;acc:nm_003031] Divided 223.608 225.005 1.00625
2235 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 200.95 199.711 1.0062
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Subtracted 196.748 195.466 1.282
2236 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] 209.197 207.915
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 222.959 224.337 1.00618
2237 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] 222.965 224.343
integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Subtracted 209.197 207.915 1.282
2238 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885] Divided 222.959 224.337 1.00618
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Subtracted 209.197 207.915 1.282
2239 testis-specific bromodomain protein. [refseq;acc:nm_001726] Divided 222.958 224.336 1.00618
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Subtracted 193.787 195.064 1.277
2240 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679]
nag14 protein. [refseq;acc:nm_022143] Divided 222.959 224.337 1.00618
2241 bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] 222.96 224.338
tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] Subtracted 202.414 203.691 1.277
2242 integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Divided 209.197 207.915 1.00617
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Subtracted 193.787 195.064 1.277
2243 integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Divided 209.197 207.915 1.00617
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Subtracted 195.97 194.7 1.27
2244 integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Divided 209.197 207.915 1.00617
sipl protein. [refseq;acc:nm_018269] Subtracted 208.609 207.346 1.263
2245 e-1 enzyme. [refseq;acc:nm_021204] 208.315 207.061 1.254
fibulin-2 precursor. [swissprot;acc:p98095] Divided 191.618 190.448 1.00614
2246 leng5 protein. [refseq;acc:nm_024075] Subtracted 221.599 220.351 1.248
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Divided 223.58 224.943 1.0061
2247 sipl protein. [refseq;acc:nm_018269] 208.609 207.346 1.00609
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Subtracted 221.599 220.351 1.248
2248 kinesin-like protein kif3c. [swissprot;acc:o14782] Divided 219.045 220.377 1.00608
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Subtracted 221.599 220.351 1.248
2249 pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Divided 181.091 179.999 1.00607
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Subtracted 221.599 220.351 1.248
2250 likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Divided 164.064 165.058 1.00606
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted 221.599 220.351 1.248
2251 e-1 enzyme. [refseq;acc:nm_021204] Divided 208.315 207.061 1.00606
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Subtracted 212.563 211.315 1.248
2252 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] 200.95 199.711 1.239
delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716] Divided 217.185 218.498 1.00605
2253 kinesin-like protein kif3b (microtubule plus end-directed kinesin motor 3b) (hh0048). [swissprot;acc:o15066] 219.047 220.371 1.00604
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Subtracted 125.845 127.083 1.238
2254 type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210] 125.912 127.146 1.234

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/