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.

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 [...,...].

Value Type	Rank	Gene	Hugo	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 2030 to 2079 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
2030	SUV39H2	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	EIF2S1	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	SUV39H1	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	no value	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	6101.12	6449.87	1.05716
2034	TOPBP1	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	6920.71	7315.59	1.05706
2035	ACOX1	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
2036	ATP5J2	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]
2037	DHX35	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]
2038	TAF6	transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848]	7088.08	7492.23	1.05702
2039	MRPL4	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	3646.01	3449.54	1.05696
2040	PRR5	rho-gtpase-activating protein 8. [swissprot;acc:q9nsg0]	6036.68	6379.44	1.05678
2041	ARHGAP1	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	KLC2	kinesin light chain 2 (klc 2). [swissprot;acc:q9h0b6]	6036.62	6379.38
2043	KIF5B	kinesin heavy chain (ubiquitous kinesin heavy chain) (ukhc). [swissprot;acc:p33176]	6036.68	6379.44
2044	KIF5C	kinesin heavy chain isoform 5c (kinesin heavy chain neuron-specific 2). [swissprot;acc:o60282]
2045	KIF5A	neuronal kinesin heavy chain (nkhc) (kinesin heavy chain isoform 5a) (kinesin heavy chain neuron-specific 1). [swissprot;acc:q12840]
2046	KLC1	kinesin light chain 1 (klc 1). [swissprot;acc:q07866]	6036.73	6379.48
2047	GTF3A	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	6036.68	6379.44
2048	EXOC1	exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
2049	SMARCC2	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	AP2B1	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	RPL26	60s ribosomal protein l26. [swissprot;acc:q02877]	3601.97	3409.48	1.05646
2052	PBRM1	polybromo 1. [refseq;acc:nm_018165]	5634.8	5952.7	1.05642
2053	SMARCA5	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]
2054	SMARCA4	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]
2055	SMARCA1	possible global transcription activator snf2l1. [swissprot;acc:p28370]
2056	BTAF1	tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981]
2057	SMARCA2	possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]
2058	no value	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	AP1G1	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	AP1S3	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	AP1S1	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	JPH4	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	SMARCC1	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	AP1B1	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	RPL35	60s ribosomal protein l35. [swissprot;acc:p42766]	3602.25	3410.23	1.05631
2066	GNPNAT1	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	5882.61	6213.34	1.05622
2067	no value	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	3602.75	3411.18	1.05616
2068	MRPL2	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]		3411.17
2069	no value	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	4632.65	4892.66	1.05613
2070	SFPQ	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	MRPS26	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	6437.24	6797.24	1.05592
2072	ERH	enhancer of rudimentary homolog. [swissprot;acc:q14259]
2073	PPIL4	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	no value	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	3614.91	3423.89	1.05579
2075	SRR	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]
2076	MLLT4	af-6 protein. [swissprot;acc:p55196]	5746.65	6067.27
2077	RPL34	60s ribosomal protein l34. [swissprot;acc:p49207]	3614.91	3423.89
2078	SEC61A2	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
2079	SEC61A1	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
- Hugo is the HGNC identifier if it exists
- 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.