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

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/