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 901 to 950 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
113 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Measured Divided 4366.44 5899.76 1.35116
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Ranked 332.874 267.246 1.24557
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Squared 19321 12542.6 1.54043
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked Subtracted 194.372 234.204 39.832
114 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Squared 67438.6 40697 26741.6
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Ranked 229.818 267.265 37.447
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted Divided 80.4705 101.526 1.26165
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Measured Subtracted 13768.2 11466 2302.2
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Rooted 40.225 24.7051 15.5199
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured Divided 4300.47 5807.72 1.35048
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Ranked 332.874 267.246 1.24557
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 19321 12542.6 1.54043
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured 21185 28492 1.34491
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Rooted Subtracted 21.4476 36.9459 15.4983
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Squared Divided 19321 12542.6 1.54043
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Ranked Subtracted 277.546 240.461 37.085
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 267.246 1.24557
pnas-18. [sptrembl;acc:q9bzu3] Measured Subtracted 13680.5 11409.6 2270.9
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Squared 72886.3 98544.5 25658.2
spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted Divided 80.4705 101.526 1.26165
116 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Subtracted 40.6302 25.4452 15.185
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked Divided 268.565 334.483 1.24545
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Subtracted 208.52 171.595 36.925
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared Divided 19321 12542.6 1.54043
p66 alpha. [refseq;acc:nm_017660] Subtracted 81888.8 56306.5 25582.3
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured Divided 21185 28492 1.34491
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 13261.9 11017.8 2244.1
117 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared Divided 211446 137422 1.53866
guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0] Rooted Subtracted 40.5691 25.4263 15.1428
high-mobility group 20a. [refseq;acc:nm_018200] Ranked 208.588 171.778 36.81
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Measured 9276.47 7090.37 2186.1
neuralized-like. [refseq;acc:nm_004210] Ranked Divided 332.326 266.948 1.24491
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured 21185 28492 1.34491
transcription factor jun-b. [swissprot;acc:p17275] Rooted 63.4173 79.5311 1.25409
transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared Subtracted 81888.8 56306.5 25582.3
118 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured 9275.1 7089.65 2185.45
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted Divided 50.3065 62.9788 1.2519
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Ranked 284.753 228.934 1.24382
Rooted Subtracted 37.2205 52.2064 14.9859
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Ranked 274.027 237.79 36.237
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured Divided 21185 28492 1.34491
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared 210445 136779 1.53858
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted 81888.8 56306.5 25582.3
119 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Measured 12998.5 15138.2 2139.7
adiponectin receptor 2. [refseq;acc:nm_024551] Ranked 281.582 246.371 35.211
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 25391
exocyst complex component sec5. [swissprot;acc:q96kp1] Divided 210335 136716 1.53848
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Measured 21185 28492 1.34491
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Ranked 318.982 259.004 1.23157

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/