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 - 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.

Navigation/Query Panel:
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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1 to 50 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	Network Comparison Type	description	green	red	Filtered	network_comparison
1	Measured	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	364	0	36400000
		Divided	rad50-interacting protein 1. [refseq;acc:nm_021930]	2394.5	450.5	1	5.31521
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	85	0	6325
		Subtracted	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	33356.5	41482.5	1	8126
	Ranked	Divided	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	4294	0	3.70633
		Divided	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	24	10	1	2.4
		Subtracted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	322	215	1	107
		Subtracted	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	21883	8906	0	12977
	Squared	Divided	cab2. [refseq;acc:nm_033419]	7.16592	0.00001	0	716592
		Divided	rad50-interacting protein 1. [refseq;acc:nm_021930]	1357.07	48.0356	1	28.2513
		Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	160184	232467	0	72283
		Subtracted	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	322755	468498	1	145743
	Rooted	Divided	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	19.0788	0	1907880
		Divided	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	21.225	1	2.30547
		Subtracted	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	60.0707	9.20014	0	50.8706
		Subtracted	rad50-interacting protein 1. [refseq;acc:nm_021930]	48.9336	21.225	1	27.7086
2	Measured	Divided	cab2. [refseq;acc:nm_033419]	174	0.00001	0	17400000
		Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	2394.5	450.5	1	5.31521
		Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	33356.5	41482.5	1	8126
		Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	85	0	6325
	Ranked	Divided	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	28	15	1	1.86667
		Divided	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	14977	5865	0	2.55362
		Subtracted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	15915	4294	0	11621
		Subtracted	hbs1-like. [refseq;acc:nm_006620]	322	215	1	107
	Squared	Divided	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	5.61325	0	561325
		Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	1357.07	48.0356	1	28.2513
		Subtracted	histone h4. [swissprot;acc:p02304]	345123	273623	0	71500
		Subtracted	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	263351	407289	1	143938
	Rooted	Divided	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	0.00001	12.4097	0	1240970
		Divided	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	21.225	1	2.30547
		Subtracted	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	60.0707	9.20014	0	50.8706
		Subtracted	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	48.9336	21.225	1	27.7086
3	Measured	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	698.5	2597.5	1	3.71868
		Divided	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	0.00001	0	10900000
		Subtracted	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	33356.5	41482.5	1	8126
		Subtracted	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	23818.1	0	4196.8
	Ranked	Divided	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	28	15	1	1.86667
		Divided	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	11083.9	4475.84	0	2.47638
		Subtracted	cab2. [refseq;acc:nm_033419]	10950	21866	0	10916
		Subtracted	rad50-interacting protein 1. [refseq;acc:nm_021930]	232	337	1	105
	Squared	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	115.48	1596.92	1	13.8285
		Divided	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	5.61325	0	561325
		Subtracted	apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	170628	135280	0	35348
		Subtracted	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	263351	407289	1	143938
	Rooted	Divided	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	50.9657	1	1.92839
		Divided	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	0.00001	12.4097	0	1240970
		Subtracted	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	6.85565	36.9188	0	30.0631
		Subtracted	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	26.4292	50.9657	1	24.5365
4	Measured	Divided	hbs1-like. [refseq;acc:nm_006620]	698.5	2597.5	1	3.71868
4	Measured	Divided	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	0.00001	0	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/