Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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

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

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.

- http://analysis.yellowcouch.org/