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 4236 to 4285 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1059 uridine kinase-like 1. [swissprot;acc:q9nwz5] Rooted 61.1919 64.2955 1.05072
1060 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Squared 28800.8 33037.5 1.1471
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Ranked 218.162 211.648 1.03078
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Rooted 74.62 78.3934 1.05057
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Measured 5719.01 6248.6 1.0926
1061 elks protein. [refseq;acc:nm_015064] Ranked 218.162 211.648 1.03078
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Squared 59335 68062.6 1.14709
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Measured 5412.23 5913.4 1.0926
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Rooted 73.8603 77.5904 1.0505
1062 ammecr1 protein. [refseq;acc:nm_015365] Measured 5412.23 5913.4 1.0926
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Rooted 73.8553 77.585 1.0505
ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] Squared 17511.1 20085.3 1.147
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Ranked 269.963 278.239 1.03066
1063 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Measured 5412.23 5913.4 1.0926
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Rooted 73.8426 77.5711 1.05049
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Squared 2709.8 3107.78 1.14687
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Ranked 269.96 278.232 1.03064
1064 dead-box protein. [refseq;acc:nm_018665] Measured 5719.01 6248.6 1.0926
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Rooted 63.2949 66.4799 1.05032
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Squared 31583.4 36221.8 1.14686
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Ranked 269.955 278.221 1.03062
1065 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Measured 6393.81 6984.94 1.09245
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Squared 17134.4 19648.7 1.14674
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Rooted 63.2911 66.4734 1.05028
zinc finger protein 305. [swissprot;acc:o43309] Ranked 269.954 278.219 1.03062
1066 homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622] Rooted 63.2689 66.4479 1.05025
leucyl-trna synthetase. [refseq;acc:nm_020117] Measured 5417.06 5917.79 1.09244
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] Squared 17134.4 19648.7 1.14674
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Ranked 269.956 278.223 1.03062
1067 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Rooted 63.2689 66.4479 1.05025
farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324] Squared 17134.4 19648.7 1.14674
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Measured 5417.07 5917.79 1.09243
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Ranked 269.956 278.223 1.03062
1068 activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375] Rooted 63.2689 66.4479 1.05025
exocyst complex component sec15a. [swissprot;acc:q8tag9] Measured 6201.54 6774.35 1.09237
protocadherin 15 precursor. [swissprot;acc:q96qu1] Squared 17134.4 19648.7 1.14674
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Ranked 269.953 278.215 1.03061
1069 cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Rooted 63.2689 66.4479 1.05025
elongation factor 2 (ef-2). [swissprot;acc:p13639] Measured 5494.73 6001.08 1.09215
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Squared 17134.4 19648.7 1.14674
zinc finger protein 232. [swissprot;acc:q9uny5] Ranked 269.954 278.218 1.03061
1070 hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Rooted 63.2689 66.4479 1.05025
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Squared 17134.4 19648.7 1.14674
metabotropic glutamate receptor 2 precursor (mglur2). [swissprot;acc:q14416] Measured 5494.73 6001.08 1.09215
zinc finger protein 99. [refseq;acc:nm_032164] Ranked 269.954 278.218 1.03061
1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Measured 5494.73 6001.08 1.09215
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Rooted 63.2671 66.4459 1.05024
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Squared 17134.4 19648.7 1.14674
1072 prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Measured 5207.39 5687.2 1.09214

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/