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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 8241 to 8290 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
2061	Measured	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]	5552.69	5865.84	1.0564
	Ranked	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]	218.79	216.981	1.00834
	Squared	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	24225.6	26399	1.08972
	Rooted	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]	66.825	68.5831	1.02631
2062	Measured	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	1.0564
	Ranked	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]	218.79	216.981	1.00834
	Squared	zinc finger protein 258. [refseq;acc:nm_145310]	24225.6	26399	1.08972
	Rooted	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	66.825	68.5831	1.02631
2063	Measured	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
	Ranked	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	207.638	205.923	1.00833
	Squared	zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202]	24225.6	26399	1.08972
	Rooted	cytosolic nonspecific dipeptidase (glutamate carboxypeptidase-like protein 1). [swissprot;acc:q96kp4]	65.2079	66.9218	1.02628
2064	Measured	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
	Ranked	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	207.655	205.939	1.00833
	Squared	zinc finger protein 262; cell death inhibiting rna. [refseq;acc:nm_005095]	24225.6	26399	1.08972
	Rooted	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	62.2279	63.8594	1.02622
2065	Measured	60s ribosomal protein l35. [swissprot;acc:p42766]	3602.25	3410.23	1.05631
	Ranked	ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781]	214.328	212.561	1.00831
	Squared	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	24225.6	26399	1.08972
	Rooted	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]	61.0898	62.6908	1.02621
2066	Measured	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	5882.61	6213.34	1.05622
	Ranked	proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004]	229.102	231.001	1.00829
	Squared	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	24225.6	26399	1.08972
	Rooted	ring finger protein 20. [refseq;acc:nm_019592]	59.5914	61.1533	1.02621
2067	Measured	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	3602.75	3411.18	1.05616
	Ranked	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	193.226	191.639	1.00828
	Squared	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]	24225.6	26399	1.08972
	Rooted	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]	66.6886	68.4366	1.02621
2068	Measured	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	3602.75	3411.17	1.05616
	Ranked	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	220.8	222.61	1.0082
	Squared	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	24225.6	26399	1.08972
	Rooted	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]	59.5914	61.1533	1.02621
2069	Measured	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	4632.65	4892.66	1.05613
	Ranked	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	217.555	215.807	1.0081
	Squared	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	24225.6	26399	1.08972
	Rooted	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	55.9946	57.4614	1.0262
2070	Measured	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
	Ranked	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	223.199	225.008	1.0081
	Squared	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]	24225.6	26399	1.08972
	Rooted	polybromo 1. [refseq;acc:nm_018165]	61.089	62.6862	1.02615
2071	Measured	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]	6437.24	6797.24	1.05592
	Ranked	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	217.555	215.807	1.0081
	Squared	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]	24225.6	26399	1.08972
	Rooted	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	61.089	62.6862	1.02615
2072	Measured	enhancer of rudimentary homolog. [swissprot;acc:q14259]	6437.24	6797.24	1.05592
	Ranked	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]	217.555	215.807	1.0081
	Squared	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]	24225.6	26399	1.08972
	Rooted	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	61.089	62.6862	1.02615
2073	Measured	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
	Ranked	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	229.267	227.433	1.00806

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.