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 description Rank Network Comparison Type Value Type network_comparison green Filtered Interaction Map red
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Network Comparison Type  : Divided
Value Type  : Ranked
description
Rank
network_comparison
green
Filtered
Interaction Map
red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 18 1.32082 245.247 1 High confidence 185.678
242 1.09822 13895.8 0 15260.6
629 1.02915 13590.3 Low confidence 13205.3
4130 1.01062 201.5 1 199.383
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 1038 1.03148 181.041 High confidence 186.741
1328 1.02218 194.038 Low confidence 198.342
1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 1032 1.03162 180.943 High confidence 186.664
1322 1.0222 194.014 Low confidence 198.322
1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] 588 1.03039 185.859 191.507
1048 1.031 182.308 High confidence 187.96
1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] 637 1.029 186.751 Low confidence 192.166
1043 1.03128 182.137 High confidence 187.834
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592] 3423 1.01523 196.707 Low confidence 199.702
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4 (ec 3.1.4.11) (phosphoinositide phospholipase c) (plc-beta-4) (phospholipase c-beta-4). [swissprot;acc:q15147] 3126 1 0.00001 High confidence 0.00001
3585 1.01447 199.628 Low confidence 202.517
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 1963 1.00978 213.703 High confidence 211.633
2659 1.0177 196.574 Low confidence 200.053
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 1873 1.01985 199.455 203.414
2922 1 0.00001 High confidence 0.00001
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704] 4255 1.00954 200.395 Low confidence 202.306
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 2076 1.01928 194.83 198.587
2439 1.00337 221.425 High confidence 220.681
14-3-3 protein epsilon (mitochondrial import stimulation factor l subunit) (protein kinase c inhibitor protein-1) (kcip-1) (14-3-3e). [swissprot;acc:p42655] 2864 1.01713 197.043 Low confidence 200.418
3088 1 0.00001 High confidence 0.00001
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] 2108 1.01923 194.902 Low confidence 198.65
2396 1.00375 221.51 High confidence 220.683
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 1044 1.02415 196.966 Low confidence 201.723
2366 1.00407 202.529 High confidence 203.353
15 kda selenoprotein precursor. [swissprot;acc:o60613] 1948 1.00984 212.432 214.522
4465 1.00907 201.104 Low confidence 202.928
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] 2855 1 0.00001 High confidence 0.00001
4126 1.01062 195.778 Low confidence 197.858
16.7kd protein. [refseq;acc:nm_016139] 3267 1.01575 195.864 198.949
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 1.03097 217.998 High confidence 211.449
1803 1.02012 195.655 Low confidence 199.592
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 627 1.02953 10050.9 0 10347.7
2142 1.01915 192.884 1 196.577
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664] 3846 1.01306 198.422 201.014
2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880] 4455 1.00928 205.097 207
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 941 1.02493 201.99 207.026
2007 1.00919 222.969 High confidence 225.019
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 994 1.02457 196.729 Low confidence 201.562
1160 1.02633 214.041 High confidence 208.55
2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] 1484 1.0191 202.726 198.927
4541 1.00806 201.202 Low confidence 202.824
2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 1389 1.02148 213.875 High confidence 218.47
1439 1.0217 198.891 Low confidence 203.206
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 183 1.153 198.011 High confidence 228.306
276 1.04421 191.474 Low confidence 199.939
25 kda brain-specific protein (p25-alpha). [swissprot;acc:o94811] 1085 1.02382 199.188 203.933

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/