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 727 to 776 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
727	60s ribosomal protein l24 (l30). [source:swissprot;acc:p38663]	7087.23	7911.25	1.11627	
728	hcv ns3-transactivated protein 1. [source:refseq;acc:nm_019048]	6000.23	6696.89	1.11611	
729	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [source:swissprot;acc:p38606]	6000.23	6696.89	1.11611	
730	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [source:swissprot;acc:p08243]	6000.23	6696.89	1.11611	
731	methyltransferase like 2. [source:refseq;acc:nm_018396]	13241.4	11864	1.1161	
732	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	13241.4	11864	1.1161	
733	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	13241.4	11864	1.1161	
734	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	13241.4	11864	1.1161	
735	vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [source:swissprot;acc:p27449]	5768.32	6434.78	1.11554	
736	sarcoglycan zeta; zeta-sarcoglycan. [source:refseq;acc:nm_139167]	5768.32	6434.78	1.11554	
737	golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [source:refseq;acc:nm_022735]	5768.32	6434.78	1.11554	
738	delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q92629]	5768.32	6434.78	1.11554	
739	cellular modulator of immune recognition. [source:refseq;acc:nm_145021]	5768.32	6434.78	1.11554	
740	vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [source:swissprot;acc:q99437]	5768.32	6434.78	1.11554	
741	gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [source:swissprot;acc:q13326]	5768.32	6434.78	1.11554	
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]	4131.04	4607.9	1.11543	
743	eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [source:swissprot;acc:q14152]	4131.04	4607.9	1.11543	
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]	12515.4	11221.1	1.11535	
745	neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [source:refseq;acc:nm_005863]	4086.6	4557.68	1.11527	
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]	4086.6	4557.68	1.11527	
747	down-regulated in metastasis. [source:refseq;acc:nm_014503]	4086.6	4557.68	1.11527	
748	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	12503.3	11212	1.11517	
749	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [source:swissprot;acc:q99447]	4565.34	5085.92	1.11403	
750	myosin light chain 1, skeletal muscle isoform (mlc1f) (a1 catalytic) (alkali). [source:swissprot;acc:p05976]	4565.34	5085.92	1.11403	
751	myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [source:swissprot;acc:p08590]	4565.34	5085.92	1.11403	
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]	4565.34	5085.92	1.11403	
753	myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [source:swissprot;acc:p14649]	4565.34	5085.92	1.11403	
754	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [source:swissprot;acc:p12829]	4565.34	5085.92	1.11403	
755	nucleolar rna-associated protein alpha isoform. [source:refseq;acc:nm_022917]	4079.81	4545.01	1.11402	
756	topoisomerase-related function protein 4-2. [source:refseq;acc:nm_022447]	4725.28	5261.06	1.11339	
757	signal recognition particle 68 kda protein (srp68). [source:swissprot;acc:q9uhb9]	5622.89	6260.02	1.11331	
758	dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [source:swissprot;acc:p56282]	3760.3	4185.82	1.11316	
759	6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [source:swissprot;acc:q01813]	4254.62	4736.03	1.11315	
760	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [source:refseq;acc:nm_152565]	5870.2	6533.39	1.11298	
761	translation initiation factor if-2. [source:swissprot;acc:o60841]	5811.51	6467.62	1.1129	
762	pms1 protein homolog 2 (dna mismatch repair protein pms2). [source:swissprot;acc:p54278]	6231.31	6933.9	1.11275	
763	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	4250.54	4729.67	1.11272	
764	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	4250.18	4729.12	1.11269	
765	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [source:refseq;acc:nm_006999]	4726.38	5258.95	1.11268	
766	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	6691.93	7445.09	1.11255	
767	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [source:swissprot;acc:q16851]	6691.21	7444.22	1.11254	
768	ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [source:refseq;acc:nm_003350]	6690.44	7443.29	1.11253	
769	vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [source:swissprot;acc:q16864]	5873.77	6532.44	1.11214	
770	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [source:swissprot;acc:o95670]	5874.74	6533.34	1.11211	
771	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	5874.74	6533.34	1.11211	
772	sec13-related protein. [source:swissprot;acc:p55735]	5874.76	6533.36	1.11211	
773	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [source:swissprot;acc:q96lb4]	5874.74	6533.34	1.11211	
774	yeast sec31p homolog. [source:refseq;acc:nm_014933]	5874.76	6533.36	1.11211	
775	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [source:swissprot;acc:o75348]	5874.74	6533.33	1.11211	
776	ganglioside-induced differentiation-associated protein 1-like 1. [source:refseq;acc:nm_024034]	5874.76	6533.36	1.11211	

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/