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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

description	Network Comparison Type	Rank	Value Type	Hugo	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]	Subtracted	1879	Ranked	no value	210.592	2.237	208.355
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Divided	1163	Rooted		61.4957	1.0477	64.429
		1329	Ranked		218.509	1.02275	213.648
		1359	Measured		5657.71	1.0788	6103.54
		2030	Squared		24791.1	1.09036	27031.1
	Subtracted	1164	Rooted		61.4957	2.9333	64.429
		1304	Ranked		218.509	4.861	213.648
		1446	Measured		5657.71	445.83	6103.54
		1838	Squared		24791.1	2240	27031.1
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Divided	1160	Rooted	CSMD1	61.4957	1.0477	64.429
		1326	Ranked		218.509	1.02275	213.648
		1357	Measured		5657.71	1.0788	6103.54
		2028	Squared		24791.1	1.09036	27031.1
	Subtracted	1161	Rooted		61.4957	2.9333	64.429
		1302	Ranked		218.509	4.861	213.648
		1444	Measured		5657.71	445.83	6103.54
		1836	Squared		24791.1	2240	27031.1
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Divided	339	Ranked	no value	243.583	1.0983	267.527
		408	Rooted		49.9856	1.09996	45.4432
		1932	Squared		12442.9	1.09355	13606.9
		2187	Measured		3586.31	1.05035	3414.41
	Subtracted	248	Ranked		243.583	23.944	267.527
		684	Rooted		49.9856	4.5424	45.4432
		2433	Measured		3586.31	171.9	3414.41
		2487	Squared		12442.9	1164	13606.9
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]	Divided	794		DDB1	29554.6	1.1646	34419.4
		849	Measured		6194.15	1.10417	6839.37
		908	Rooted		62.6851	1.06024	66.4615
		1029	Ranked		222.364	1.03168	215.535
	Subtracted	556	Squared		29554.6	4864.8	34419.4
		753	Measured		6194.15	645.22	6839.37
		885	Rooted		62.6851	3.7764	66.4615
		1008	Ranked		222.364	6.829	215.535
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]	Divided	906		no value	230.764	1.03838	239.62
		1427	Squared		18756.5	1.11999	21007.1
		2361	Measured		4674.38	1.04341	4877.31
		2595	Rooted		56.0046	1.008	55.5599
	Subtracted	839	Ranked		230.764	8.856	239.62
		1824	Squared		18756.5	2250.6	21007.1
		2366	Measured		4674.38	202.93	4877.31
		2621	Rooted		56.0046	0.4447	55.5599
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]	Divided	905	Ranked		230.768	1.03841	239.632
		1428	Squared		18753.6	1.11999	21003.9
		2362	Measured		4673.96	1.04338	4876.71
		2594	Rooted		56.0026	1.00804	55.5558
	Subtracted	834	Ranked		230.768	8.864	239.632
		1825	Squared		18753.6	2250.3	21003.9
		2367	Measured		4673.96	202.75	4876.71
		2618	Rooted		56.0026	0.4468	55.5558
dna excision repair protein ercc-1. [swissprot;acc:p07992]	Divided	3216	Measured	ERCC1	0.00001	1	0.00001

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.