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 4258 to 4307 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1065 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
suppressor of fused. [refseq;acc:nm_016169] Squared 17134.4 19648.7 1.14674
transducin-like enhancer protein 4. [swissprot;acc:q04727] Rooted 63.2297 66.4011 1.05016
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Ranked 269.954 278.217 1.03061
1073 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Rooted 82.3421 86.4631 1.05005
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Measured 5207.39 5687.2 1.09214
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] Ranked 216.901 210.485 1.03048
zinc finger protein gli3. [swissprot;acc:p10071] Squared 17134.4 19648.7 1.14674
1074 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Rooted 82.3408 86.4617 1.05005
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Ranked 174.387 179.697 1.03045
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Squared 17134.4 19648.7 1.14674
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Measured 5207.39 5687.2 1.09214
1075 aquaporin 5. [swissprot;acc:p55064] Rooted 82.3414 86.4623 1.05005
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Ranked 174.387 179.697 1.03045
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] Squared 17134.4 19648.7 1.14674
phosphatidate cytidylyltransferase 1 (ec 2.7.7.41) (cdp-diglyceride synthetase 1) (cdp-diglyceride pyrophosphorylase 1) (cdp- diacylglycerol synthase 1) (cds 1) (ctp:phosphatidate cytidylyltransferase 1) (cdp-dag synthase 1) (cdp-dg synthetase 1). [swissprot;acc:q92903] Measured 6441.56 7034.86 1.09211
1076 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Ranked 174.387 179.697 1.03045
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Rooted 82.3406 86.4614 1.05005
solute carrier family 13, member 4 (na+/sulfate cotransporter sut-1). [swissprot;acc:q9ukg4] Measured 6439.63 7032.19 1.09202
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Squared 17134.4 19648.7 1.14674
1077 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Ranked 174.387 179.697 1.03045
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Squared 59334.6 68040.1 1.14672
solute carrier family 13, member 3 (sodium-dependent high-affinity dicarboxylate transporter 2) (na(+)/dicarboxylate cotransporter 3) (nadc-3) (hnadc3). [swissprot;acc:q8wwt9] Measured 6439.66 7032.22 1.09202

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/