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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description Rank Gene Value Type Filtered green Network Comparison Type Interaction Map red network_comparison
Results: HTML CSV LaTeX Showing element 601 to 650 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
description
Rank
Filtered
green
red
network_comparison
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 954 1 5382.5 4906.33 1.09705
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 1035 5530.23 5054.73 1.09407
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1030 5523.85 5048.33 1.09419
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 0.00001 0.00001 1
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] 2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] 2901
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 1245 5243.23 4835.55 1.08431
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 851 4755.03 4307.12 1.10399
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 852
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 948 5084.24 4633.48 1.09728
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 616 9948.93 11222.2 1.12798
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 914 7161 6513.45 1.09942
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 2238 6181.21 5902.27 1.04726
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 2237 5902.26
caveolin-1. [swissprot;acc:q03135] 3099 0.00001 0.00001 1
caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779
cbf1 interacting corepressor. [refseq;acc:nm_004882] 1651 6358.1 5944.24 1.06962
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 507 7858.38 6875.08 1.14302
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 257 7858.12 6417.31 1.22452
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 137 4763.34 3620.77 1.31556
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 369 4194.95 3583.56 1.17061
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516] 3163 0.00001 0.00001 1
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] 2289 6048.94 5783.76 1.04585
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] 2958 0.00001 0.00001 1
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 141 0 891.114 1161.88 1.30385
3226 1 0.00001 0.00001 1
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9] 2890
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] 1445 5510.45 5117.85 1.07671
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] 2753 4521.87 4521.42 1.0001
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] 2755
cda11 protein. [refseq;acc:nm_032026] 1174 6387.23 5874.11 1.08735
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185] 1995 6538.73 6174.74 1.05895
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] 1611 5132.35 5497.73 1.07119
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 419 6350.19 5493.1 1.15603
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948] 3209 0.00001 0.00001 1
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735] 981 7296.51 6654.42 1.09649
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 279 0 610.424 545.902 1.11819
1660 1 7950.61 7433.73 1.06953
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 363 10876.4 12780.7 1.17509
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 2387 7940.87 8265.85 1.04092
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 361 10880.5 12787.6 1.17528
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 319 0 1268.19 1388.45 1.09483
359 1 10887.2 12798.9 1.17559
cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535] 2850 0.00001 0.00001 1
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336] 32 0 184 598 3.25
2990 1 0.00001 0.00001 1
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750] 2974
cellular modulator of immune recognition. [refseq;acc:nm_145021] 739 6434.78 5768.32 1.11554
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 623 7013.19 6228.39 1.126
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 629

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/