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 10264 to 10313 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2566 thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Rooted 56.832 56.3214 1.00907
2567 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] 65.4023 64.8155 1.00905
kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Ranked 219.907 220.267 1.00164
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Squared 37433.4 35694.1 1.04873
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Measured 3964.71 4042.75 1.01968
2568 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Squared 29781 31226 1.04852
nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838] Rooted 72.5727 73.2274 1.00902
serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9] Ranked 219.907 220.267 1.00164
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Measured 3964.71 4042.75 1.01968
2569 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Squared 24789.5 23652.7 1.04806
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653] Rooted 72.5723 73.227 1.00902
serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965] Ranked 219.907 220.267 1.00164
2570 cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
homeobox protein barh-like 2. [swissprot;acc:q9umq3] Measured 3964.71 4042.75 1.01968
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653] Rooted 72.5726 73.2272 1.00902
tumor susceptibility gene 101 protein. [swissprot;acc:q99816] Squared 24493.1 25668.8 1.048
2571 b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749] Rooted 72.5769 73.2309 1.00901
kruppel-related zinc finger protein hckrox. [refseq;acc:nm_015872] Measured 7056.13 7194.65 1.01963
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Ranked 209.549 209.205 1.00164
transcription factor jun-b. [swissprot;acc:p17275] Squared 27675 26409.3 1.04793
2572 nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221] Rooted 72.6266 73.273 1.0089
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Squared 28829.8 30196.5 1.04741
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Ranked 203.953 204.285 1.00163
zinc finger protein 288 (dendritic-derived btb/poz zinc finger protein). [swissprot;acc:q9hc78] Measured 7056.42 7194.87 1.01962
2573 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] Squared 28829.8 30196.5 1.04741
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Ranked 213.347 213.005 1.00161
peroxisomal targeting signal 2 receptor (pts2 receptor) (peroxin-7). [swissprot;acc:o00628] Measured 7056.58 7194.99 1.01961
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Rooted 57.9415 57.4389 1.00875
2574 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Squared 23205.6 22155.5 1.0474
katanin p60 subunit a 1. [refseq;acc:nm_007044] Measured 4327.94 4248.77 1.01863
swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] Ranked 220.016 219.667 1.00159
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] Rooted 71.497 72.1196 1.00871
2575 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] Squared 24288.8 23193.7 1.04722
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Ranked 209.583 209.255 1.00157
rho interacting protein 3. [refseq;acc:nm_015134] Measured 5608.38 5712.59 1.01858
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Rooted 71.5006 72.1231 1.00871
2576 beta-1-syntrophin (59 kda dystrophin-associated protein a1, basic component 1) (dapa1b) (tax interaction protein 43) (tip-43) (syntrophin 2) (bsyn2). [swissprot;acc:q13884] Ranked 213.422 213.75 1.00154
m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] Squared 23815.1 22760.3 1.04634
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Measured 5608.22 5712.39 1.01857
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Rooted 71.5059 72.1283 1.0087
2577 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Squared 13530.9 14151.4 1.04586
ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Ranked 192.625 192.922 1.00154
delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Rooted 71.5023 72.1247 1.0087
translin. [swissprot;acc:q15631] Measured 4979.44 5071.53 1.01849
2578 40s ribosomal protein s26. [swissprot;acc:p02383] Squared 23172.9 22157.6 1.04582
beta-2-syntrophin (59 kda dystrophin-associated protein a1, basic component 2) (syntrophin 3) (snt3) (syntrophin-like) (sntl). [swissprot;acc:q13425] Ranked 213.422 213.75 1.00154
lamin b receptor (integral nuclear envelope inner membrane protein) (lmn2r). [swissprot;acc:q14739] Rooted 71.5023 72.1247 1.0087
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Measured 4979.44 5071.53 1.01849
2579 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Squared 23172.9 22157.6 1.04582

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/