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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4130 to 4179 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2065 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
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Divided 3614.91 3423.89 1.05579
2080 r3h domain protein 1. [swissprot;acc:q15032] 5837.34 6162.91 1.05577
tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19] Subtracted 5859.1 6173.7 314.6
2081 paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367] Divided 6318.3 6670.1 1.05568
tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7] Subtracted 5859.1 6173.7 314.6
2082 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] 4783.49 5097.66 314.17
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792] Divided 5800.93 6123.38 1.05559
2083 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] Subtracted 5556.36 5870.11 313.75
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Divided 5799.84 6122.18 1.05558
2084 complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Subtracted 6344.31 6657.98 313.67
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Divided 5800.22 6122.6 1.05558
2085 channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700] 5835.4 6159.4 1.05552
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238] Subtracted 6344.31 6657.98 313.67
2086 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 5865.84 313.15
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352] Divided 5835.44 6159.45 1.05552
2087 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] Subtracted 5552.69 5865.84 313.15
presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796] Divided 5835.45 6159.46 1.05552
2088 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] Subtracted 5552.69 5865.84 313.15
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959] Divided 5835.15 6159.11 1.05552
2089 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] Subtracted 5552.69 5865.84 313.15
putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5] Divided 5775.22 6094.89 1.05535
2090 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Subtracted 5552.7 5865.85 313.15

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/