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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 8164 to 8213 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2041 rho-gtpase-activating protein 1 (gtpase-activating protein rhoogap) (rho-related small gtpase protein activator) (cdc42 gtpase-activating protein) (p50-rhogap). [swissprot;acc:q07960] Measured 6036.68 6379.44 1.05678
2042 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Squared 26513.8 28905.8 1.09022
kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6] Measured 6036.62 6379.38 1.05678
t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Ranked 210.586 208.803 1.00854
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Rooted 59.4136 61.0113 1.02689
2043 kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176] Measured 6036.68 6379.44 1.05678
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Squared 26521.7 28913.2 1.09017
thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Rooted 60.9498 62.5881 1.02688
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Ranked 196.837 195.173 1.00853
2044 26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686] Rooted 62.2342 63.9055 1.02686
adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203] Ranked 199.928 198.24 1.00851
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Squared 26521.7 28913.2 1.09017
kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282] Measured 6036.68 6379.44 1.05678
2045 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] Rooted 62.309 63.9809 1.02683
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Squared 26521.7 28913.2 1.09017
neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840] Measured 6036.68 6379.44 1.05678
ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Ranked 199.928 198.24 1.00851
2046 adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]
argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424] Rooted 62.6557 64.3308 1.02673
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Squared 26521.7 28913.2 1.09017
kinesin light chain 1 (klc 1). [swissprot;acc:q07866] Measured 6036.73 6379.48 1.05678
2047 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Squared 26530.8 28921.7 1.09012
epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] Rooted 62.5767 64.2492 1.02673
solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3] Ranked 224.124 226.003 1.00838
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Measured 6036.68 6379.44 1.05678
2048 cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] Squared 30902.9 33687.7 1.09011
exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Measured 6036.68 6379.44 1.05678
rna, u transporter 1; snurportin-1. [refseq;acc:nm_005701] Rooted 67.1288 68.9195 1.02668
solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64] Ranked 224.124 226.003 1.00838
2049 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281] Squared 30902.9 33687.7 1.09011
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Rooted 61.5981 63.2352 1.02658
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Measured 5634.94 5953.19 1.05648
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] Ranked 220.787 222.634 1.00837
2050 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Measured 5556.36 5870.11 1.05647
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] Rooted 61.5981 63.2352 1.02658
destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Squared 30902.9 33687.7 1.09011
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Ranked 218.79 216.981 1.00834
2051 60s ribosomal protein l26. [swissprot;acc:q02877] Measured 3601.97 3409.48 1.05646
oxidation resistance 1. [refseq;acc:nm_181354] Ranked 218.79 216.981 1.00834
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Rooted 63.6794 65.3664 1.02649
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Squared 30902.9 33687.7 1.09011
2052 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 29406 32054.3 1.09006
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Ranked 207.667 205.95 1.00834
polybromo 1. [refseq;acc:nm_018165] Measured 5634.8 5952.7 1.05642
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Rooted 62.5624 64.2199 1.02649
2053 lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Ranked 218.79 216.981 1.00834
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Measured 5634.8 5952.7 1.05642
toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Squared 29406 32054.3 1.09006
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Rooted 62.4286 64.0792 1.02644
2054 60s ribosomal protein l19. [swissprot;acc:p14118] Squared 12769 13918.3 1.09001

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/