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 4108 to 4157 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2054 tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Subtracted 5634.8 5952.7 317.9
2055 possible global transcription activator snf2l1. [swissprot;acc:p28370] Divided 1.05642
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Subtracted 317.9
2056 swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] 5634.63 5952.14 317.51
tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Divided 5634.8 5952.7 1.05642
2057 acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752] Subtracted 6946.38 7263.48 317.1
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Divided 5634.8 5952.7 1.05642
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] 5552.69 5865.84 1.0564
hydroxymethylglutaryl-coa synthase, mitochondrial precursor (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:p54868] Subtracted 6946.6 7263.68 317.08
2059 3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]
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] Divided 5552.69 5865.84 1.0564
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]
hydroxymethylglutaryl-coa synthase, cytoplasmic (ec 2.3.3.10) (hmg-coa synthase) (3-hydroxy-3-methylglutaryl coenzyme a synthase). [swissprot;acc:q01581] Subtracted 6946.6 7263.68 317.08
2061 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 6946.82 7263.87 317.05
adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Divided 5552.69 5865.84 1.0564
2062 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 5552.7 5865.85
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] Subtracted 5776.79 6092.77 315.98
2063 swi/snf-related matrix-associated actin-dependent regulator of chromatin c1; mammalian chromatin remodeling complex brg1-associated factor 155; swi/snf complex 155 kda subunit; chromatin remodeling complex baf155 subunit. [refseq;acc:nm_003074] Divided 5634.63 5952.14 1.05635
williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] Subtracted 5171.45 5486.96 315.51
2064 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Divided 5548.79 5861.31 1.05632
williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044] Subtracted 5171.45 5486.96 315.51
2065 60s ribosomal protein l35. [swissprot;acc:p42766] Divided 3602.25 3410.23 1.05631
williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158] Subtracted 5171.45 5486.96 315.51
2066 ataxin 2-binding protein. [swissprot;acc:q9nwb1] 5778.16 6093.65 315.49
similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6] Divided 5882.61 6213.34 1.05622
2067 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Subtracted 5195.3 5510.67 315.37
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Divided 3602.75 3411.18 1.05616
2068 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted 5391.27 5706.64 315.37
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Divided 3602.75 3411.17 1.05616
2069 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 4632.65 4892.66 1.05613
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Subtracted 5391.27 5706.64 315.37
2070 hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219]
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Divided 10178.5 9638.08 1.05607
2071 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 6437.24 6797.24 1.05592
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Subtracted 5859.1 6173.7 314.6
2072 enhancer of rudimentary homolog. [swissprot;acc:q14259] Divided 6437.24 6797.24 1.05592
oxidation resistance 1. [refseq;acc:nm_181354] Subtracted 5859.1 6173.7 314.6
2073 lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Divided 6083.39 6423.12 1.05585
2074 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 3614.91 3423.89 1.05579
dymeclin. [refseq;acc:nm_017653] Subtracted 5859.1 6173.7 314.6
2075 serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4] Divided 3614.91 3423.89 1.05579
sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368] Subtracted 5859.1 6173.7 314.6
2076 af-6 protein. [swissprot;acc:p55196] Divided 5746.65 6067.27 1.05579
lats homolog 1. [refseq;acc:nm_004690] Subtracted 5859.1 6173.7 314.6
2077 60s ribosomal protein l34. [swissprot;acc:p49207] Divided 3614.91 3423.89 1.05579
sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5] Subtracted 5859.1 6173.7 314.6
2078 nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3] Divided 3614.91 3423.89 1.05579
2079 dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125] Subtracted 5859.1 6173.7 314.6

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/