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 Value Type description Network Comparison Type Filtered Rank green Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 38536 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Filtered
Rank
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] 0 37 934.348 High confidence 334.401 2.79409
131 851.77 Low confidence 645.504 1.31954
1 60 2765.82 High confidence 4489.19 1.6231
4914 7900.54 Low confidence 7853.62 1.00597
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] 509 8630.06 High confidence 7551.8 1.14278
885 8585.64 Low confidence 8255.95 1.03993
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] 508 8636.87 High confidence 7556.75 1.14293
880 8587.03 Low confidence 8256.68 1.04001
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] 237 9081.29 8530.51 1.06457
514 8532.02 High confidence 7477 1.1411
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] 252 9018.94 Low confidence 8492.92 1.06194
513 8543.66 High confidence 7485.08 1.14143
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592] 2035 8323.04 Low confidence 8065.05 1.03199
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] 2882 8175.27 7948.01 1.02859
3126 0.00001 High confidence 0.00001 1
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 1136 6303.92 5790.65 1.08864
2182 8386.58 Low confidence 8130.62 1.03148
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 1693 8246.34 7981.12 1.03323
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] 4071 8067.47 Low confidence 7896.47 1.02166
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 575 8965.49 8572.9 1.04579
1411 6262.07 High confidence 5812.02 1.07743
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] 3088 0.00001 0.00001 1
3095 8370.12 Low confidence 8144.39 1.02772
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] 591 8956.98 8566.17 1.04562
1415 6265.44 High confidence 5815.33 1.0774
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 993 8288.57 Low confidence 7982.87 1.03829
1600 6788.96 High confidence 6336.22 1.07145
15 kda selenoprotein precursor. [swissprot;acc:o60613] 1043 6933.36 6344.41 1.09283
3577 8083.96 Low confidence 7881.96 1.02563
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] 2067 8425.81 8165.8 1.03184
2855 0.00001 High confidence 0.00001 1
16.7kd protein. [refseq;acc:nm_016139] 4005 8483.17 Low confidence 8297.71 1.02235
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 8498.04 8189.31 1.0377
2521 6113.96 High confidence 5964.17 1.02511
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 0 778 4869.42 Low confidence 4825.89 1.00902
1 631 8689.28 8316.12 1.04487
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664] 4609 8354 8218.07 1.01654
2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880] 2443 7708.55 7480.51 1.03048
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 1393 6192.72 High confidence 5743.36 1.07824
1973 7938.52 Low confidence 7690.22 1.03229
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 1032 8332.97 8029.13 1.03784
2506 6362.25 High confidence 6200.39 1.0261
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] 2451 6957.34 6737.15 1.03268
3458 8054.46 Low confidence 7848.62 1.02623
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] 2288 6048.94 High confidence 5783.76 1.04585
4165 8033.99 Low confidence 7871.26 1.02067
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 107 5843.51 High confidence 4266.04 1.36977
234 8143.47 Low confidence 7647.22 1.06489
25 kda brain-specific protein (p25-alpha). [swissprot;acc:o94811] 863 8007.43 7697.01 1.04033

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/