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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

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Showing element 1 to 50 of 77072 in total

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

- http://analysis.yellowcouch.org/