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

- http://analysis.yellowcouch.org/