MK5 Microarray Data

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 2030 to 2079 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
2030	histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1]	5060.82	5350.93	1.05732
2031	eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]
2032	histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463]
2033	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	6101.12	6449.87	1.05716
2034	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	6920.71	7315.59	1.05706
2035	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
2036	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]
2037	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]
2038	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848]	7088.08	7492.23	1.05702
2039	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	3646.01	3449.54	1.05696
2040	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]	6036.68	6379.44	1.05678
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]
2042	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]	6036.62	6379.38
2043	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]	6036.68	6379.44
2044	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]
2045	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]
2046	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]	6036.73	6379.48
2047	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	6036.68	6379.44
2048	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
2049	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]	5634.94	5953.19	1.05648
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]	5556.36	5870.11	1.05647
2051	60s ribosomal protein l26. [swissprot;acc:q02877]	3601.97	3409.48	1.05646
2052	polybromo 1. [refseq;acc:nm_018165]	5634.8	5952.7	1.05642
2053	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]
2054	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]
2055	possible global transcription activator snf2l1. [swissprot;acc:p28370]
2056	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]
2057	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]
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
2059	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]
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]
2061	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]
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
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]	5634.63	5952.14	1.05635
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]	5548.79	5861.31	1.05632
2065	60s ribosomal protein l35. [swissprot;acc:p42766]	3602.25	3410.23	1.05631
2066	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	5882.61	6213.34	1.05622
2067	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	3602.75	3411.18	1.05616
2068	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]		3411.17
2069	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	4632.65	4892.66	1.05613
2070	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]	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
2072	enhancer of rudimentary homolog. [swissprot;acc:q14259]
2073	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	6083.39	6423.12	1.05585
2074	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	3614.91	3423.89	1.05579
2075	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]
2076	af-6 protein. [swissprot;acc:p55196]	5746.65	6067.27
2077	60s ribosomal protein l34. [swissprot;acc:p49207]	3614.91	3423.89
2078	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
2079	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]

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.