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 Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 6456 in total
Value Type  : Measured
Filtered  : 1
Interaction Map  : High confidence
description
Rank
Network Comparison Type
red
green
network_comparison
1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 60 Divided 4489.19 2765.82 1.6231
164 Subtracted 1723.37
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] 310 7551.8 8630.06 1078.26
509 Divided 1.14278
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] 307 Subtracted 7556.75 8636.87 1080.12
508 Divided 1.14293
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] 319 Subtracted 7477 8532.02 1055.02
514 Divided 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] 318 Subtracted 7485.08 8543.66 1058.58
513 Divided 1.14143
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] 3126 0.00001 0.00001 1
Subtracted 0 0 0
10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] 1136 Divided 5790.65 6303.92 1.08864
1140 Subtracted 513.27
10-formyltetrahydrofolate dehydrogenase (ec 1.5.1.6) (10-fthfdh). [swissprot;acc:o75891] 2922 Divided 0.00001 0.00001 1
Subtracted 0 0 0
14-3-3 protein beta/alpha (protein kinase c inhibitor protein-1) (kcip-1) (protein 1054). [swissprot;acc:p31946] 1411 Divided 5812.02 6262.07 1.07743
1422 Subtracted 450.05
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 Divided 0.00001 0.00001 1
Subtracted 0 0 0
14-3-3 protein zeta/delta (protein kinase c inhibitor protein-1) (kcip-1) (factor activating exoenzyme s) (fas). [swissprot;acc:p29312] 1415 Divided 5815.33 6265.44 1.0774
1418 Subtracted 450.11
14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] 1404 6336.22 6788.96 452.74
1600 Divided 1.07145
15 kda selenoprotein precursor. [swissprot;acc:o60613] 865 Subtracted 6344.41 6933.36 588.95
1043 Divided 1.09283
15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428] 2855 0.00001 0.00001 1
Subtracted 0 0 0
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 2496 5964.17 6113.96 149.79
2521 Divided 1.02511
2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 1393 5743.36 6192.72 1.07824
1426 Subtracted 449.36
2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 2455 6200.39 6362.25 161.86
2506 Divided 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] 2344 Subtracted 6737.15 6957.34 220.19
2451 Divided 1.03268
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] 2239 Subtracted 5783.76 6048.94 265.18
2288 Divided 1.04585
20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 107 4266.04 5843.51 1.36977
179 Subtracted 1577.47
25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] 3079 Divided 0.00001 0.00001 1
Subtracted 0 0 0
26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] 1491 5938.56 6376.76 438.2
1521 Divided 1.07379
26s protease regulatory subunit 6a (tat-binding protein 1) (tbp-1) (proteasome subunit p50). [swissprot;acc:p17980] 1511 Subtracted 5926.76 6362.33 435.57
1527 Divided 1.07349
26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] 1567 5822.25 6242.94 1.07226
1628 Subtracted 420.69
26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998] 1539 Divided 5783.97 6207.5 1.07322
1622 Subtracted 423.53

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/