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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Filtered  : 0

Rank	Value Type	description	Network Comparison Type	green	network_comparison	red	Interaction Map
1	Measured	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Subtracted	6410	6325	85	High confidence
							Low confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0.00001	36400000	364	High confidence
							Low confidence
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		15915	3.70633	4294	High confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Subtracted	21883	12977	8906
							Low confidence
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	Divided	14977	2.55362	5865
	Squared	cab2. [refseq;acc:nm_033419]		7.16592	716592	0.00001	High confidence
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		1.87479	187479		Low confidence
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	160184	72283	232467	High confidence
							Low confidence
	Rooted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		60.0707	50.8706	9.20014	High confidence
							Low confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	0.00001	1907880	19.0788	High confidence
							Low confidence
2	Measured	cab2. [refseq;acc:nm_033419]		174	17400000	0.00001	High confidence
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		89	8900000		Low confidence
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	6410	6325	85	High confidence
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		19621.3	4196.8	23818.1	Low confidence
	Ranked	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]		15915	11621	4294	High confidence
		mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	Divided	21883	2.45711	8906	Low confidence
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		14977	2.55362	5865	High confidence
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Subtracted	20617	11010	9607	Low confidence
	Squared	histone h4. [swissprot;acc:p02304]		345123	71500	273623	High confidence
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	1.87479	187479	0.00001	Low confidence
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]		0.00001	561325	5.61325	High confidence
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Subtracted	386144	28560	414704	Low confidence
	Rooted	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	9.43398	943398	0.00001
		lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Subtracted	60.0707	50.8706	9.20014	High confidence
		mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]		7.61577	21.6929	29.3087	Low confidence
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	0.00001	1240970	12.4097	High confidence
3	Measured	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		89	8900000	0.00001	Low confidence
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	19621.3	4196.8	23818.1	High confidence
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]		7500.75	2393.82	5106.93	Low confidence
		pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	Divided	109	10900000	0.00001	High confidence
	Ranked	cab2. [refseq;acc:nm_033419]	Subtracted	10950	10916	21866
		neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]	Divided	20617	2.14604	9607	Low confidence
		neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]	Subtracted		11010
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Divided	11083.9	2.47638	4475.84	High confidence
	Squared	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	Subtracted	170628	35348	135280
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	1.87479	187479	0.00001	Low confidence
		rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	Subtracted	197937	23051	220988
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	0.00001	561325	5.61325	High confidence
	Rooted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	Subtracted	6.85565	30.0631	36.9188
		anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]		66	20.3711	45.6289	Low confidence
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Divided	9.43398	943398	0.00001
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]		0.00001	1240970	12.4097	High confidence
4	Measured	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	Subtracted	4356	2274	2082	Low confidence
		homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	89	8900000	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
- 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.