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