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 8191 to 8240 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2048 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
glutamate carboxypeptidase-like protein 2 precursor. [swissprot;acc:q96kn2] Rooted 65.5449 67.2768 1.02642
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Ranked 207.665 205.948 1.00834
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] Measured 5634.8 5952.7 1.05642
2055 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Squared 26619 29013.9 1.08997
dymeclin. [refseq;acc:nm_017653] Ranked 218.79 216.981 1.00834
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Rooted 62.3777 64.0227 1.02637
possible global transcription activator snf2l1. [swissprot;acc:p28370] Measured 5634.8 5952.7 1.05642
2056 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Squared 26621.3 29016.2 1.08996
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Ranked 218.79 216.981 1.00834
tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Measured 5634.8 5952.7 1.05642
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Rooted 62.3777 64.0227 1.02637
2057 elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]
lats homolog 1. [refseq;acc:nm_004690] Ranked 218.79 216.981 1.00834
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Measured 5634.8 5952.7 1.05642
tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] Squared 24214.1 26392.2 1.08995
2058 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Measured 5552.69 5865.84 1.0564
beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] Rooted 74.9362 76.9113 1.02636
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277] Squared 25226.2 27492 1.08982
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Ranked 218.79 216.981 1.00834
2059 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Rooted 74.9362 76.9113 1.02636
adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Measured 5552.69 5865.84 1.0564
interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] Squared 24224.6 26398.4 1.08974
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782] Ranked 218.79 216.981 1.00834
2060 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Measured 5552.69 5865.84 1.0564
arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] Squared 24224.5 26398.4 1.08974
dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] Ranked 218.79 216.981 1.00834
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] Rooted 66.825 68.5831 1.02631

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/