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

Results: HTML CSV LaTeX

Showing element 1875 to 1924 of 7460 in total

Value Type  : Measured
Interaction Map  : High confidence

description	Rank	Network Comparison Type	Filtered	red	network_comparison	green
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	348	Subtracted	0	1388.29	57.92	1330.37
	387	Divided			1.04354
	646	Subtracted	1	7273.78	717.94	7991.72
	920	Divided			1.0987
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	178		0	498.07	1.23523	615.233
	263	Subtracted			117.163
	1359	Divided	1	5657.71	1.0788	6103.54
	1446	Subtracted			445.83
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	174	Divided	0	488.43	1.25423	612.604
	257	Subtracted			124.174
	1357	Divided	1	5657.71	1.0788	6103.54
	1444	Subtracted			445.83
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	216		0	1658.07	147.29	1805.36
	329	Divided			1.08883
	2187		1	3586.31	1.05035	3414.41
	2433	Subtracted			171.9
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531]	753			6194.15	645.22	6839.37
	849	Divided			1.10417
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	340	Subtracted	0	1048.65	59.768	988.882
	369	Divided			1.06044
	2361		1	4674.38	1.04341	4877.31
	2366	Subtracted			202.93
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	339		0	1049.21	59.772	989.438
	370	Divided			1.06041
	2362		1	4673.96	1.04338	4876.71
	2367	Subtracted			202.75
dna excision repair protein ercc-1. [swissprot;acc:p07992]	3216	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	1525			5916.05	434.48	6350.53
	1529	Divided			1.07344
dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]	1527	Subtracted			434.48
	1531	Divided			1.07344
dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858]	3103			0.00001	1	0.00001
		Subtracted		0	0	0
dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917]	2808	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
dna methyltransferase 1-associated protein 1 (dnmt1-associated protein 1) (dnmap1). [swissprot;acc:q9npf5]	2796	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	423		0	1562.36	20.67	1541.69
	457	Divided			1.01341
	899	Subtracted	1	5859.25	572.78	6432.03
	938	Divided			1.09776
dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	618	Subtracted		6327.86	736.27	7064.13
	726	Divided			1.11635
dna mismatch repair protein msh2. [swissprot;acc:p43246]	3151			0.00001	1	0.00001
		Subtracted		0	0	0
dna mismatch repair protein msh6 (muts-alpha 160 kda subunit) (g/t mismatch binding protein) (gtbp) (gtmbp) (p160). [swissprot;acc:p52701]	3045	Divided		0.00001	1	0.00001
		Subtracted		0	0	0
dna polymerase delta p38 subunit. [refseq;acc:nm_015584]	1575	Divided		5106.13	1.07184	5472.96
	1876	Subtracted			366.83

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.