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

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/