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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 14920 in total

Filtered	0
Interaction Map	High confidence
Network Comparison Type	Divided

green	Value Type	description	Rank	network_comparison	red	
0.02001	Squared	cyclin h (mo15-associated protein) (p37) (p34). [source:swissprot;acc:p51946]	24	208.009	4.16226	
0.0289898	Squared	serpin b12. [source:swissprot;acc:q96p63]	19	813.196	23.5744	
0.0297673	Squared	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	20	789.312	23.4957	
0.0318343	Squared	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [source:swissprot;acc:q96jq0]	74	2.9145	0.092781	
0.0532544	Squared	protein transport protein sec24c (sec24-related protein c). [source:swissprot;acc:p53992]	22	225	0.000236686	
0.0766864	Squared	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [source:swissprot;acc:o00750]	16	7668.64	0.00001	
0.0854438	Squared	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source:swissprot;acc:p56559]	185	1.46537	0.125207	
0.104379	Squared	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [source:swissprot;acc:p15884]	53	4.39001	0.458225	
0.109658	Squared	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	27	39.2112	4.29982	
0.145878	Squared	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [source:swissprot;acc:p80404]	232	1.34278	0.108639	
0.344399	Squared	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [source:swissprot;acc:o15528]	26	128.828	44.3683	
0.344399	Squared	60s ribosomal protein l37a. [source:swissprot;acc:p12751]	25	128.828	44.3683	
0.365145	Squared	protein phosphatase inhibitor 2 (ipp-2). [source:swissprot;acc:p41236]	63	3.3984	1.24091	
0.426714	Squared	suppressor of actin 1. [source:refseq;acc:nm_014016]	179	1.49742	0.284967	
0.437633	Squared	methyltransferase like 2. [source:refseq;acc:nm_018396]	119	1.92403	0.227456	
0.437633	Squared	sedlin. [source:swissprot;acc:o14582]	11	43763.3	0.00001	
0.437633	Squared	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	12	43763.3	0.00001	
0.52284	Squared	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	18	841.001	439.709	
0.52284	Squared	glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [source:swissprot;acc:p46926]	38	9.25713	4.84	
0.591716	Squared	transcription initiation factor iie, beta subunit (tfiie-beta). [source:swissprot;acc:p29084]	78	2.77777	0.213018	
0.615621	Squared	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	352	1.12891	0.545325	
0.615621	Squared	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	348	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	361	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	362	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	350	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	360	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	351	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	349	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	356	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	353	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	358	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	357	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	363	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	359	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	354	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	364	1.12891	0.545325	
0.615621	Squared	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	355	1.12891	0.545325	
0.697197	Squared	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [source:refseq;acc:nm_003893]	34	15.9968	0.0435834	
0.742249	Squared	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [source:swissprot;acc:p50452]	139	1.77778	0.417515	
0.742249	Squared	heparan sulfate 6-o-sulfotransferase 2. [source:refseq;acc:nm_147174]	40	7.86	5.83408	
0.742249	Squared	maspin precursor (protease inhibitor 5). [source:swissprot;acc:p36952]	137	1.77778	0.417515	
0.742249	Squared	serpin b11. [source:swissprot;acc:q96p15]	138	1.77778	0.417515	
0.796213	Squared	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [source:swissprot;acc:q14849]	23	219.346	174.646	
0.823905	Squared	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [source:swissprot;acc:q9byb4]	10	82390.5	0.00001	
0.969467	Squared	lipopolysaccharide-binding protein precursor (lbp). [source:swissprot;acc:p18428]	132	1.80566	1.75053	
1.05706	Squared	spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	117	1.93793	0.545459	
1.18697	Rooted	serpin b12. [source:swissprot;acc:q96p63]	16	8.67149	10.2928	
1.2188	Rooted	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [source:swissprot;acc:q9uiv8]	17	8.45791	10.3085	
1.26833	Squared	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [source:swissprot;acc:p82650]	257	1.2661	1.60583	
1.44	Squared	sh2-b homolog; likely ortholog of mouse sh2 domain-containing putative adapter sh2-b; sh2-b gamma signaling protein; sh2-b alpha signaling protein. [source:refseq;acc:nm_015503]	124	1.88182	2.70982	

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/