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 Value Type Interaction Map Filtered Network Comparison Type red network_comparison green
Results: HTML CSV LaTeX Showing element 1 to 50 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Rank
Interaction Map
Filtered
red
network_comparison
green
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 37 High confidence 0 334.401 2.79409 934.348
60 1 4489.19 1.6231 2765.82
131 Low confidence 0 645.504 1.31954 851.77
4914 1 7853.62 1.00597 7900.54
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 High confidence 7551.8 1.14278 8630.06
885 Low confidence 8255.95 1.03993 8585.64
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 High confidence 7556.75 1.14293 8636.87
880 Low confidence 8256.68 1.04001 8587.03
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 8530.51 1.06457 9081.29
514 High confidence 7477 1.1411 8532.02
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 Low confidence 8492.92 1.06194 9018.94
513 High confidence 7485.08 1.14143 8543.66
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592] 2035 Low confidence 8065.05 1.03199 8323.04
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 7948.01 1.02859 8175.27
3126 High confidence 0.00001 1 0.00001
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 1136 5790.65 1.08864 6303.92
2182 Low confidence 8130.62 1.03148 8386.58
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 1693 7981.12 1.03323 8246.34
2922 High confidence 0.00001 1 0.00001
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704] 4071 Low confidence 7896.47 1.02166 8067.47
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 575 8572.9 1.04579 8965.49
1411 High confidence 5812.02 1.07743 6262.07
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 1 0.00001
3095 Low confidence 8144.39 1.02772 8370.12
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] 591 8566.17 1.04562 8956.98
1415 High confidence 5815.33 1.0774 6265.44
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 993 Low confidence 7982.87 1.03829 8288.57
1600 High confidence 6336.22 1.07145 6788.96
15 kda selenoprotein precursor. [swissprot;acc:o60613] 1043 6344.41 1.09283 6933.36
3577 Low confidence 7881.96 1.02563 8083.96
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] 2067 8165.8 1.03184 8425.81
2855 High confidence 0.00001 1 0.00001
16.7kd protein. [refseq;acc:nm_016139] 4005 Low confidence 8297.71 1.02235 8483.17
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 8189.31 1.0377 8498.04
2521 High confidence 5964.17 1.02511 6113.96
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 631 Low confidence 8316.12 1.04487 8689.28
778 0 4825.89 1.00902 4869.42
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664] 4609 1 8218.07 1.01654 8354
2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880] 2443 7480.51 1.03048 7708.55
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 1393 High confidence 5743.36 1.07824 6192.72
1973 Low confidence 7690.22 1.03229 7938.52
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 1032 8029.13 1.03784 8332.97
2506 High confidence 6200.39 1.0261 6362.25
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 6737.15 1.03268 6957.34
3458 Low confidence 7848.62 1.02623 8054.46
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 High confidence 5783.76 1.04585 6048.94
4165 Low confidence 7871.26 1.02067 8033.99
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 107 High confidence 4266.04 1.36977 5843.51
234 Low confidence 7647.22 1.06489 8143.47
25 kda brain-specific protein (p25-alpha). [swissprot;acc:o94811] 863 7697.01 1.04033 8007.43

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/