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