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 Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1513 to 1562 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
green
red
network_comparison
190 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared High confidence 96037.6 71389.9 1.34525
dimethylaniline monooxygenase [n-oxide forming] 5 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 5) (fmo 5) (dimethylaniline oxidase 5). [swissprot;acc:p49326] Ranked Low confidence 200.074 210.557 1.0524
Rooted 73.256 69.0062 1.06159
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] Measured High confidence 5864.86 4571.89 1.28281
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted 129.699 149.165 1.15009
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] Squared Low confidence 46446.1 51507.8 1.10898
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Measured 6966.05 6480.93 1.07485
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Ranked High confidence 198.444 226.582 1.14179
191 aquaporin 5. [swissprot;acc:p55064] Squared 96035.2 71388.5 1.34525
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] Rooted Low confidence 74.2189 69.9165 1.06154
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Ranked High confidence 198.444 226.582 1.14179
intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Squared Low confidence 50350.5 45402.8 1.10897
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Ranked 191.43 201.43 1.05224
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted High confidence 72.584 63.1192 1.14995
similar to atp/gtp-binding protein. [sptrembl;acc:q8nem8] Measured Low confidence 10086.4 9385.4 1.07469
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] High confidence 5923.4 4638.1 1.27712
192 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 14008 17757.5 1.26767
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] Squared 96033.4 71387.4 1.34524
leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] Low confidence 46445.8 51506.6 1.10896
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Ranked 206.571 217.341 1.05214
musashi 2 isoform a. [refseq;acc:nm_138962] High confidence 199.458 227.491 1.14055
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Rooted Low confidence 74.2187 69.9161 1.06154
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] High confidence 61.5862 53.6107 1.14877
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Measured Low confidence 10086.4 9385.4 1.07469
193 hbs1-like. [refseq;acc:nm_006620] Ranked 216.913 206.166 1.05213
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared High confidence 96032.5 71386.9 1.34524
musashi 1. [refseq;acc:nm_002442] Ranked 199.458 227.491 1.14055
nadph oxidase 4. [refseq;acc:nm_016931] Rooted Low confidence 74.219 69.9166 1.06154
nostrin. [refseq;acc:nm_052946] High confidence 51.9242 59.6399 1.1486
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 14007.3 17756.5 1.26766
star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5] Low confidence 7021.2 6534.34 1.07451
transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] Squared 46440.2 51484.4 1.10862
194 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] High confidence 95965.1 71346.6 1.34505
conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] Ranked Low confidence 205.046 215.723 1.05207
cyclin g2. [swissprot;acc:q16589] Measured High confidence 13995.7 17738.6 1.26743
eap30 subunit of ell complex. [refseq;acc:nm_007241] Rooted 51.9242 59.6399 1.1486
nadph oxidase 3; nadph oxidase catalytic subunit-like 3. [refseq;acc:nm_015718] Low confidence 74.2188 69.9164 1.06154
nuclear protein ukp68. [refseq;acc:nm_024824] Ranked High confidence 199.458 227.491 1.14055
transforming protein n-ras. [swissprot;acc:p01111] Squared Low confidence 46437.7 51474.3 1.10846
transmembrane protein tmp21 precursor (21 kda transmembrane trafficking protein) (p24delta) (s31iii125) (s31i125) (tmp-21-i). [swissprot;acc:p49755] Measured 12252.1 11403 1.07446
195 cyclin g1 (cyclin g). [swissprot;acc:p51959] High confidence 13995.6 17738.5 1.26743
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked Low confidence 222.623 211.679 1.0517
huntingtin interacting protein c. [refseq;acc:nm_012272] High confidence 200.417 227.971 1.13748
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 51.9242 59.6399 1.1486
nadph oxidase homolog 1 (nox-1) (noh-1) (nadh/nadph mitogenic oxidase subunit p65-mox) (mitogenic oxidase 1) (mox1). [swissprot;acc:q9y5s8] Low confidence 74.219 69.9166 1.06154
phosphatidylinositol glycan, class b. [refseq;acc:nm_004855] Measured 12252.1 11403 1.07446
septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] Squared 65242.4 58865.4 1.10833
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] High confidence 95488.9 71062.4 1.34373
196 calsyntenin-1 precursor. [swissprot;acc:o94985]
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Rooted Low confidence 72.2685 68.0822 1.06149

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/