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 2962 to 3011 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
741	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	Measured	5768.32	6434.78	1.11554	
741	multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [source:swissprot;acc:p22234]	Ranked	223.58	235.027	1.0512	
741	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Squared	23894.7	27894.5	1.16739	
742	brain protein 44. [source:swissprot;acc:o95563]	Ranked	126.215	120.078	1.05111	
742	eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [source:swissprot;acc:o75821]	Measured	4131.04	4607.9	1.11543	
742	homeobox protein engrailed-2 (hu-en-2). [source:swissprot;acc:p19622]	Squared	31406.6	36662.8	1.16736	
742	transcription factor btf3 (rna polymerase b transcription factor 3). [source:swissprot;acc:p20290]	Rooted	67.0234	71.5506	1.06755	
743	cpg binding protein (protein containing phd finger and cxxc domain 1). [source:swissprot;acc:q9p0u4]	Squared	31406.6	36662.8	1.16736	
743	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	Measured	4131.04	4607.9	1.11543	
743	katanin p60 subunit a 1. [source:refseq;acc:nm_007044]	Rooted	54.4988	51.0573	1.0674	
743	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	Ranked	126.215	120.078	1.05111	
744	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [source:refseq;acc:nm_013375]	Squared	31406.6	36662.8	1.16736	
744	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Measured	12515.4	11221.1	1.11535	
744	dynactin 4. [source:refseq;acc:nm_032486]	Rooted	55.2242	51.7372	1.0674	
744	septin 6. [source:swissprot;acc:q14141]	Ranked	126.604	120.463	1.05098	
745	cytokine-like nuclear factor n-pac. [source:refseq;acc:nm_032569]	Squared	31406.6	36662.8	1.16736	
745	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	Measured	4086.6	4557.68	1.11527	
745	solute carrier family 35, member b1; udp-galactose transporter related. [source:refseq;acc:nm_005827]	Ranked	214.679	225.568	1.05072	
745	transcription factor btf3 homolog 3. [source:swissprot;acc:q13892]	Rooted	67.0475	71.5566	1.06725	
746	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	Ranked	250.465	238.38	1.0507	
746	hect type e3 ubiquitin ligase. [source:refseq;acc:nm_015052]	Squared	31406.6	36662.8	1.16736	
746	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [source:refseq;acc:nm_005886]	Rooted	54.5195	51.084	1.06725	
746	rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [source:refseq;acc:nm_019555]	Measured	4086.6	4557.68	1.11527	
747	down-regulated in metastasis. [source:refseq;acc:nm_014503]	Measured	4086.6	4557.68	1.11527	
747	sr rich protein. [source:refseq;acc:nm_032870]	Rooted	61.4809	65.6088	1.06714	
747	transducin-like enhancer protein 3 (esg3). [source:swissprot;acc:q04726]	Squared	31401.8	36655.7	1.16731	
747	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	Ranked	250.465	238.38	1.0507	
748	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	Squared	23148.8	27021.5	1.1673	
748	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Measured	12503.3	11212	1.11517	
748	fibrillarin (34 kda nucleolar scleroderma antigen). [source:swissprot;acc:p22087]	Ranked	245.246	233.483	1.05038	
748	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [source:swissprot;acc:o75439]	Rooted	60.4376	64.4898	1.06705	
749	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [source:swissprot;acc:p54619]	Rooted	66.9737	71.4637	1.06704	
749	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm_001253]	Squared	23148.8	27021.5	1.1673	
749	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	Measured	4565.34	5085.92	1.11403	
749	exocyst complex component sec15b. [source:swissprot;acc:q9y2d4]	Ranked	221.968	211.326	1.05036	
750	exocyst complex component sec15a. [source:swissprot;acc:q8tag9]	Ranked	222.138	211.503	1.05028	
750	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [source:swissprot;acc:q10713]	Rooted	60.4385	64.49	1.06704	
750	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	Measured	4565.34	5085.92	1.11403	
750	n-acetyltransferase 5 (ec 2.3.1.-). [source:swissprot;acc:q9y6d2]	Squared	21678.4	25303.3	1.16721	
751	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [source:swissprot;acc:p54646]	Rooted	66.9738	71.4638	1.06704	
751	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [source:sptrembl;acc:q9nu36]	Squared	20305.9	23689.4	1.16663	
751	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	Measured	4565.34	5085.92	1.11403	
751	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [source:swissprot;acc:q15695]	Ranked	223.463	212.875	1.04974	
752	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [source:swissprot;acc:q13131]	Rooted	66.9736	71.4636	1.06704	
752	nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [source:swissprot;acc:o75380]	Measured	4565.34	5085.92	1.11403	
752	step ii splicing factor slu7. [source:refseq;acc:nm_006425]	Ranked	223.463	212.875	1.04974	
752	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [source:swissprot;acc:p09661]	Squared	20305.9	23689.4	1.16663	
753	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [source:swissprot;acc:o43741]	Rooted	66.9737	71.4637	1.06704	
753	biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [source:swissprot;acc:p50747]	Squared	24183.6	28211.1	1.16654	
753	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	Ranked	224.434	235.583	1.04968	

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/