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 5286 to 5335 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1322 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Ranked 159.86 156.275 1.02294
histone h2b.s (h2b/s). [swissprot;acc:p57053] Squared 15254.5 17204.9 1.12786
scratch; scratch 1. [refseq;acc:nm_031309] Rooted 67.9472 70.8115 1.04215
1323 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Ranked 205.225 200.625 1.02293
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Rooted 67.9155 70.7734 1.04208
glycogen synthase kinase-3 alpha (ec 2.7.1.37) (gsk-3 alpha). [swissprot;acc:p49840] Measured 6439.79 6959.21 1.08066
histone h2b.d (h2b/d). [swissprot;acc:q99877] Squared 15254.5 17204.9 1.12786
1324 glycogen synthase kinase-3 beta (ec 2.7.1.37) (gsk-3 beta). [swissprot;acc:p49841] Measured 6439.79 6959.21 1.08066
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Ranked 159.993 156.421 1.02284
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Squared 15254.5 17204.9 1.12786
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Rooted 68.9332 71.8139 1.04179
1325 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
serine/threonine protein phosphatase 2b catalytic subunit, alpha isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, alpha isoform) (cam-prp catalytic subunit). [swissprot;acc:q08209] Measured 5656.79 6112.02 1.08047
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Squared 15254.5 17204.9 1.12786
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Ranked 217.133 212.289 1.02282
1326 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] 218.509 213.648 1.02275
histone h2b.e (h2b/e). [swissprot;acc:q99879] Squared 15254.5 17204.9 1.12786
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Measured 6222.8 6723.54 1.08047
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Rooted 68.9332 71.8139 1.04179
1327 cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] Squared 32117.3 36220.6 1.12776
p protein (melanocyte-specific transporter protein). [swissprot;acc:q04671] Measured 5656.8 6111.9 1.08045
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Rooted 68.9332 71.8139 1.04179
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Ranked 218.509 213.648 1.02275
1328 autoantigen ngp-1. [swissprot;acc:q13823] Squared 14345.8 16176.5 1.12761
calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Ranked 218.509 213.649 1.02275
leucyl-trna synthetase. [refseq;acc:nm_020117] Rooted 60.8452 63.3735 1.04155
serine/threonine protein phosphatase 2b catalytic subunit, beta isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, beta isoform) (cam-prp catalytic subunit). [swissprot;acc:p16299] Measured 5656.81 6111.84 1.08044
1329 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Ranked 218.509 213.648 1.02275
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Rooted 60.8453 63.3735 1.04155
serine/threonine protein phosphatase 2b catalytic subunit, gamma isoform (ec 3.1.3.16) (calmodulin-dependent calcineurin a subunit, gamma isoform) (calcineurin, testis-specific catalytic subunit) (cam-prp catalytic subunit). [swissprot;acc:p48454] Measured 5656.82 6111.8 1.08043
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Squared 14429.1 16268.2 1.12746
1330 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Ranked 218.508 213.648 1.02275
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Measured 5779.83 6244.56 1.08041
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Squared 15612.5 17598.4 1.1272
serine/threonine protein phosphatase 4 (ec 3.1.3.16) (pp4) (protein phosphatase x) (pp-x). [swissprot;acc:p33172] Rooted 59.8171 62.2984 1.04148
1331 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Ranked 218.509 213.649 1.02275
immunoglobulin-binding protein 1 (cd79a-binding protein 1) (b cell signal transduction molecule alpha 4) (alpha 4 protein). [swissprot;acc:p78318] Rooted 59.8171 62.2984 1.04148
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Squared 22156.3 24969.2 1.12696
transaldolase (ec 2.2.1.2). [swissprot;acc:p37837] Measured 5799.29 6265.2 1.08034
1332 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Ranked 220.681 215.78 1.02271
my016 protein. [sptrembl;acc:q9h3k6] Measured 4775.25 5158.86 1.08033
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Squared 22156.3 24969.2 1.12696
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Rooted 64.3618 67.0301 1.04146
1333 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Ranked 220.681 215.78 1.02271
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] Measured 5803.95 6269.44 1.0802
maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Rooted 64.4276 67.0936 1.04138
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Squared 22156.3 24969.2 1.12696
1334 15 kda selenoprotein precursor. [swissprot;acc:o60613] Rooted 64.5959 67.2624 1.04128
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Squared 15967.6 17992.4 1.12681
jm4 protein. [refseq;acc:nm_007213] Ranked 199.643 204.163 1.02264

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/