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

Results: HTML CSV LaTeX

Showing element 2601 to 2650 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
651	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Ranked	233.725	220.751	1.05877	
651	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Measured	5168.43	4597.44	1.1242	
651	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [source:swissprot;acc:o75340]	Rooted	64.5685	69.6269	1.07834	
651	testis-specific chromodomain y protein 1. [source:swissprot;acc:q9y6f8]	Squared	29012.2	34163.9	1.17757	
652	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [source:refseq;acc:nm_020732]	Rooted	64.5672	69.6254	1.07834	
652	chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [source:refseq;acc:nm_004824]	Squared	29012.2	34163.9	1.17757	
652	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Measured	5168.43	4597.44	1.1242	
652	tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [source:refseq;acc:nm_014886]	Ranked	248.994	235.255	1.0584	
653	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [source:refseq;acc:nm_021069]	Rooted	64.4927	69.539	1.07825	
653	dok-like protein. [source:refseq;acc:nm_024872]	Ranked	216.504	204.622	1.05807	
653	methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [source:swissprot;acc:p56192]	Measured	5560.06	6248.27	1.12378	
653	testis-specific chromodomain protein y protein 2. [source:swissprot;acc:q9y6f7]	Squared	29012.4	34164	1.17757	
654	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [source:swissprot;acc:o60496]	Ranked	216.504	204.622	1.05807	
654	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Measured	4088.63	4593.43	1.12346	
654	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [source:swissprot;acc:o14936]	Rooted	59.9021	64.5838	1.07816	
654	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Squared	27174.1	31992.4	1.17731	
655	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Measured	4088.63	4593.43	1.12346	
655	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [source:swissprot;acc:q99704]	Ranked	216.504	204.622	1.05807	
655	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [source:refseq;acc:nm_152794]	Rooted	59.9021	64.5838	1.07816	
655	sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	Squared	27174.1	31992.4	1.17731	
656	apolipoprotein a-i binding protein; apoa-i binding protein. [source:refseq;acc:nm_144772]	Measured	6139.04	6893.7	1.12293	
656	single-minded homolog 1. [source:swissprot;acc:p81133]	Rooted	59.9021	64.5838	1.07816	
656	sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	Squared	27174.1	31992.4	1.17731	
656	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [source:swissprot;acc:p42685]	Ranked	216.504	204.622	1.05807	
657	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Measured	6079.26	6824.47	1.12258	
657	sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	Squared	27174.1	31992.4	1.17731	
657	synapsin iii. [source:swissprot;acc:o14994]	Ranked	229.072	216.576	1.0577	
657	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	Rooted	64.75	69.8065	1.07809	
658	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	Measured	6088.77	6834.87	1.12254	
658	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [source:refseq;acc:nm_032468]	Ranked	229.072	216.576	1.0577	
658	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [source:swissprot;acc:p55884]	Rooted	52.7523	56.8686	1.07803	
658	similar to trna synthetase class ii. [source:refseq;acc:nm_152268]	Squared	22293.8	26242.6	1.17713	
659	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [source:swissprot;acc:p82933]	Rooted	51.7081	47.9816	1.07767	
659	hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [source:swissprot;acc:q9y5j3]	Ranked	229.072	216.576	1.0577	
659	ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	Squared	24614	28973.4	1.17711	
659	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Measured	6089.21	6835.34	1.12253	
660	actin binding lim protein 2. [source:refseq;acc:nm_032432]	Ranked	229.072	216.576	1.0577	
660	fip1-like 1; rearranged in hypereosinophilia. [source:refseq;acc:nm_030917]	Rooted	133.216	123.627	1.07756	
660	nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [source:swissprot;acc:q9y6m9]	Squared	33024.9	38867.8	1.17692	
660	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	Measured	5575.18	6254.85	1.12191	
661	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [source:swissprot;acc:p13716]	Squared	22223.1	26152.4	1.17681	
661	hairy/enhancer-of-split related with yrpw motif-like. [source:refseq;acc:nm_014571]	Ranked	229.072	216.576	1.0577	
661	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	Rooted	68.8243	74.1496	1.07738	
661	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	Measured	5575.18	6254.85	1.12191	
662	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	Rooted	68.8237	74.1484	1.07737	
662	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Measured	6374.65	7145.59	1.12094	
662	synapsin ii. [source:swissprot;acc:q92777]	Ranked	229.072	216.576	1.0577	
662	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [source:swissprot;acc:p55855]	Squared	23947.4	28163.7	1.17607	
663	acrc protein; putative nuclear protein. [source:refseq;acc:nm_052957]	Squared	23947.7	28163.9	1.17606	
663	mitochondrial ribosome recycling factor. [source:refseq;acc:nm_138777]	Ranked	229.072	216.576	1.0577	

Legend:
- Rank is the rank after comparing the two networks
- 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/