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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4358 to 4407 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1090 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Measured 5651.07 6164.55 1.09086
myb proto-oncogene protein (c-myb). [swissprot;acc:p10242] Squared 22799.9 26110 1.14518
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Ranked 226.218 232.88 1.02945
1091 block 23. [sptrembl;acc:q8nhw5] 226.205 232.858 1.02941
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Rooted 82.1701 86.2587 1.04976
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Squared 20273.7 23216.9 1.14517
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Measured 5791.05 6316.61 1.09075
1092 60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388] Ranked 226.203 232.855 1.02941
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Rooted 82.1685 86.2569 1.04976
hskin17 protein. [refseq;acc:nm_012311] Measured 5791.05 6316.61 1.09075
peptidyl-prolyl cis-trans isomerase nima-interacting 1 (ec 5.2.1.8) (rotamase pin1) (ppiase pin1). [swissprot;acc:q13526] Squared 20273.7 23216.9 1.14517
1093 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Rooted 67.3413 70.6881 1.0497
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Measured 5791.05 6316.61 1.09075
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Ranked 177.432 182.647 1.02939
iroquois-class homeodomain protein irx-4 (iroquois homeobox protein 4). [swissprot;acc:p78413] Squared 20273.7 23216.9 1.14517
1094 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Ranked 219.655 213.385 1.02938
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Squared 25151.8 28800.9 1.14508
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Measured 5791.05 6316.61 1.09075
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Rooted 58.6583 61.5643 1.04954
1095 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Squared 20093.1 23005.6 1.14495
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Ranked 213.552 207.463 1.02935
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Measured 5791.05 6316.61 1.09075
sestrin 3. [swissprot;acc:p58005] Rooted 61.5152 64.5624 1.04954
1096 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Squared 20093.1 23005.6 1.14495
kinesin protein. [refseq;acc:nm_032559] Measured 5356.23 5842.15 1.09072
nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] Ranked 212.345 206.339 1.02911
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Rooted 58.6583 61.5643 1.04954
1097 homolog of yeast maf1. [refseq;acc:nm_032272] Measured 6133.83 6690.18 1.0907
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Ranked 209.123 203.208 1.02911
sestrin 2 (hi95). [swissprot;acc:p58004] Rooted 61.5152 64.5624 1.04954
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Squared 19141.8 21912.9 1.14477
1098 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Ranked 217.323 211.185 1.02906
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Squared 20382.5 23332.8 1.14475
tumor differentially expressed protein 2. [refseq;acc:nm_178865] Measured 6133.83 6690.18 1.0907
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Rooted 58.6583 61.5643 1.04954
1099 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] Ranked 217.315 211.183 1.02904
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Rooted 61.5152 64.5623 1.04953
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Squared 20382.5 23332.8 1.14475
tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Measured 6133.83 6690.18 1.0907
1100 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Ranked 209.052 203.183 1.02889
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Rooted 61.5152 64.5623 1.04953
phospholipase d2 (ec 3.1.4.4) (pld 2) (choline phosphatase 2) (phosphatidylcholine-hydrolyzing phospholipase d2) (pld1c) (hpld2). [swissprot;acc:o14939] Squared 25180.2 28821.7 1.14462
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Measured 6133.83 6690.18 1.0907
1101 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Squared 26583.7 30425.2 1.14451
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Rooted 61.5152 64.5623 1.04953
d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175] Measured 6133.83 6690.18 1.0907
lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Ranked 220.291 226.584 1.02857
1102 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 235.974 1.02847
esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Squared 26583.7 30425.2 1.14451
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Rooted 61.5152 64.5623 1.04953

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/