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 5308 to 5357 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1327 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
spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470] Measured 5804.75 6270.15 1.08018
1335 alpha-actinin 2 (alpha actinin skeletal muscle isoform 2) (f-actin cross linking protein). [swissprot;acc:p35609] Rooted 62.4303 65.0019 1.04119
coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Measured 10430.3 9656.4 1.08014
cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407] Ranked 199.771 204.287 1.02261
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Squared 15967.6 17992.4 1.12681
1336 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 20179.8 22738.2 1.12678
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Measured 6140.18 6632.24 1.08014
Rooted 62.9331 65.5249 1.04118
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Ranked 215.162 210.412 1.02257
1337 caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] Squared 18648.8 21012.8 1.12676
dual-specificity tyrosine-phosphorylation regulated kinase 1a (ec 2.7.1.-) (protein kinase minibrain homolog) (mnbh) (hp86) (dual specificity yak1-related kinase). [swissprot;acc:q13627] Rooted 62.4314 65.0015 1.04117
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Ranked 215.162 210.412 1.02257
gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Measured 4935.58 5329.93 1.0799
1338 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Squared 18648.8 21012.8 1.12676
elongation protein 4 homolog; pax6 neighbor gene; chromosome 11 open reading frame 19. [refseq;acc:nm_019040] Rooted 62.4314 65.0015 1.04117
megf6 (fragment). [sptrembl;acc:o75095] Measured 5980.41 6457.51 1.07978
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Ranked 215.162 210.412 1.02257
1339 6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209] Measured 5988.06 6464.94 1.07964
block of proliferation 1. [swissprot;acc:q14137] Squared 14644.8 16497.8 1.12653
dual-specificity tyrosine-phosphorylation regulated kinase 1b (ec 2.7.1.-) (mirk protein kinase). [swissprot;acc:q9y463] Rooted 62.4314 65.0015 1.04117
epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Ranked 205.204 200.71 1.02239
1340 alpha-actinin 1 (alpha-actinin cytoskeletal isoform) (non-muscle alpha-actinin 1) (f-actin cross linking protein). [swissprot;acc:p12814] Rooted 62.4319 65.0013 1.04116

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/