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 2325 to 2374 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
582	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p18507]	Measured	6739.82	7644.62	1.13425	
582	homeobox protein barh-like 1. [source:swissprot;acc:q9hbu1]	Ranked	237.28	252.492	1.06411	
582	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Rooted	121.695	131.815	1.08316	
582	similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [source:refseq;acc:nm_033557]	Squared	23526.4	27879.3	1.18502	
583	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [source:swissprot;acc:o95154]	Squared	23526.4	27879.3	1.18502	
583	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [source:refseq;acc:nm_016123]	Measured	6739.81	7644.62	1.13425	
583	opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	Ranked	237.28	252.492	1.06411	
583	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Rooted	121.695	131.815	1.08316	
584	alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [source:refseq;acc:nm_138340]	Squared	23526.4	27879.3	1.18502	
584	gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p48169]	Measured	6739.82	7644.63	1.13425	
584	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Rooted	104.459	113.143	1.08313	
584	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [source:swissprot;acc:o43763]	Ranked	237.28	252.492	1.06411	
585	gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [source:swissprot;acc:p78334]	Measured	6739.82	7644.63	1.13425	
585	golgi membrane protein sb140; smooth muscle cell associated protein 5. [source:refseq;acc:nm_030799]	Squared	23526.4	27879.3	1.18502	
585	histone h3.3 (h3.a) (h3.b) (h3.3q). [source:swissprot;acc:p06351]	Rooted	51.5667	55.8498	1.08306	
585	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [source:swissprot;acc:p31314]	Ranked	237.28	252.492	1.06411	
586	alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [source:refseq;acc:nm_152870]	Squared	23526.4	27879.3	1.18502	
586	dj1099d15.1 (putative dnaj protein). [source:sptrembl;acc:q9h4j9]	Rooted	51.5667	55.8498	1.08306	
586	hect domain containing protein 1 (fragment). [source:swissprot;acc:q9ult8]	Ranked	237.28	252.492	1.06411	
586	phosphatidylserine receptor; phosphatidylserine receptor beta. [source:refseq;acc:nm_015167]	Measured	6739.81	7644.62	1.13425	
587	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [source:refseq;acc:nm_017647]	Rooted	51.7204	56.0156	1.08305	
587	gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p14867]	Measured	6739.83	7644.63	1.13425	
587	homeobox protein barh-like 2. [source:swissprot;acc:q9umq3]	Ranked	237.28	252.492	1.06411	
587	methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [source:swissprot;acc:q02252]	Squared	23526.5	27879.4	1.18502	
588	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [source:swissprot;acc:q04984]	Squared	23526.4	27879.3	1.18502	
588	gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [source:swissprot;acc:p34903]	Measured	6739.83	7644.63	1.13425	
588	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	Rooted	59.7294	64.6872	1.083	
588	shwachman-bodian-diamond syndrome protein (cgi-97). [source:swissprot;acc:q9y3a5]	Ranked	216.557	230.362	1.06375	
589	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Rooted	59.7294	64.6872	1.083	
589	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [source:swissprot;acc:p56556]	Measured	6739.85	7644.63	1.13424	
589	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [source:refseq;acc:nm_006423]	Squared	23526.4	27879.3	1.18502	
589	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [source:swissprot;acc:q9y333]	Ranked	228.215	214.546	1.06371	
590	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [source:swissprot;acc:q9y3b8]	Squared	23526.4	27879.3	1.18502	
590	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Ranked	217.215	204.279	1.06333	
590	similar to expressed sequence aa415817. [source:sptrembl;acc:q8n4q9]	Measured	6739.85	7644.63	1.13424	
590	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [source:swissprot;acc:p01116]	Rooted	108.671	100.365	1.08276	
591	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [source:swissprot;acc:p28329]	Squared	23526.5	27879.4	1.18502	
591	homeobox protein hox-d9 (hox-4c) (hox-5.2). [source:swissprot;acc:p28356]	Measured	6740.5	7644.76	1.13415	
591	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	Rooted	108.659	100.356	1.08274	
591	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [source:swissprot;acc:p78346]	Ranked	216.72	230.439	1.0633	
592	histone h2b.c (h2b/c). [source:swissprot;acc:q99880]	Measured	3946.32	4475.47	1.13409	
592	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Ranked	91.63	97.4011	1.06298	
592	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	Rooted	108.659	100.356	1.08274	
592	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [source:swissprot;acc:q13303]	Squared	23526.4	27879.3	1.18502	
593	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [source:swissprot;acc:o43488]	Squared	23526.4	27879.3	1.18502	
593	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Measured	3946.32	4475.47	1.13409	
593	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Ranked	232.118	218.406	1.06278	
593	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	Rooted	108.653	100.352	1.08272	
594	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [source:swissprot;acc:p16106]	Measured	3946.32	4475.47	1.13409	
594	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [source:swissprot;acc:p52294]	Squared	23517.1	27867.3	1.18498	

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/