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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Value Type Gene description Interaction Map Network Comparison Type network_comparison green Rank Filtered red
Results: HTML CSV LaTeX Showing element 1 to 50 of 38536 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Interaction Map
network_comparison
green
Rank
Filtered
red
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] High confidence 1.6231 2765.82 60 1 4489.19
2.79409 934.348 37 0 334.401
Low confidence 1.00597 7900.54 4914 1 7853.62
1.31954 851.77 131 0 645.504
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] High confidence 1.14278 8630.06 509 1 7551.8
Low confidence 1.03993 8585.64 885 8255.95
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] High confidence 1.14293 8636.87 508 7556.75
Low confidence 1.04001 8587.03 880 8256.68
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] High confidence 1.1411 8532.02 514 7477
Low confidence 1.06457 9081.29 237 8530.51
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] High confidence 1.14143 8543.66 513 7485.08
Low confidence 1.06194 9018.94 252 8492.92
1-aminocyclopropane-1-carboxylate synthase. [refseq;acc:nm_032592] 1.03199 8323.04 2035 8065.05
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] High confidence 1 0.00001 3126 0.00001
Low confidence 1.02859 8175.27 2882 7948.01
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] High confidence 1.08864 6303.92 1136 5790.65
Low confidence 1.03148 8386.58 2182 8130.62
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] High confidence 1 0.00001 2922 0.00001
Low confidence 1.03323 8246.34 1693 7981.12
130 kda leucine-rich protein (lrp 130) (gp130) (leucine-rich ppr-motif containing protein). [swissprot;acc:p42704] 1.02166 8067.47 4071 7896.47
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] High confidence 1.07743 6262.07 1411 5812.02
Low confidence 1.04579 8965.49 575 8572.9
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] High confidence 1 0.00001 3088 0.00001
Low confidence 1.02772 8370.12 3095 8144.39
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] High confidence 1.0774 6265.44 1415 5815.33
Low confidence 1.04562 8956.98 591 8566.17
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] High confidence 1.07145 6788.96 1600 6336.22
Low confidence 1.03829 8288.57 993 7982.87
15 kda selenoprotein precursor. [swissprot;acc:o60613] High confidence 1.09283 6933.36 1043 6344.41
Low confidence 1.02563 8083.96 3577 7881.96
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] High confidence 1 0.00001 2855 0.00001
Low confidence 1.03184 8425.81 2067 8165.8
16.7kd protein. [refseq;acc:nm_016139] 1.02235 8483.17 4005 8297.71
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] High confidence 1.02511 6113.96 2521 5964.17
Low confidence 1.0377 8498.04 1051 8189.31
17-beta-hydroxysteroid dehydrogenase type vii-like. [refseq;acc:nm_182829] 1.00902 4869.42 778 0 4825.89
1.04487 8689.28 631 1 8316.12
2,4-dienoyl coa reductase 2, peroxisomal; peroxisomal 2,4-dienoyl-coa reductase. [refseq;acc:nm_020664] 1.01654 8354 4609 8218.07
2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (ec 2.4.1.45) (udp-galactose-ceramide galactosyltransferase) (ceramide udp-galactosyltransferase) (cerebroside synthase). [swissprot;acc:q16880] 1.03048 7708.55 2443 7480.51
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] High confidence 1.07824 6192.72 1393 5743.36
Low confidence 1.03229 7938.52 1973 7690.22
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] High confidence 1.0261 6362.25 2506 6200.39
Low confidence 1.03784 8332.97 1032 8029.13
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] High confidence 1.03268 6957.34 2451 6737.15
Low confidence 1.02623 8054.46 3458 7848.62
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] High confidence 1.04585 6048.94 2288 5783.76
Low confidence 1.02067 8033.99 4165 7871.26
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] High confidence 1.36977 5843.51 107 4266.04
Low confidence 1.06489 8143.47 234 7647.22
25 kda brain-specific protein (p25-alpha). [swissprot;acc:o94811] 1.04033 8007.43 863 7697.01

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/