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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 3051 to 3100 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
763	putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [source:swissprot;acc:q9y5n5]	Ranked	228.78	218.091	1.04901	
763	tata-binding protein-associated phosphoprotein (down-regulator of transcription 1) (dr1 protein). [source:swissprot;acc:q01658]	Rooted	60.3269	64.3387	1.0665	
764	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	Measured	4250.18	4729.12	1.11269	
764	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [source:swissprot;acc:p35520]	Rooted	63.5181	67.7402	1.06647	
764	sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [source:swissprot;acc:q12772]	Squared	21186.4	24698.3	1.16576	
764	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	Ranked	222.082	211.707	1.04901	
765	hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [source:swissprot;acc:q9y5r4]	Ranked	229.045	218.343	1.04901	
765	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [source:refseq;acc:nm_006999]	Measured	4726.38	5258.95	1.11268	
765	sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [source:swissprot;acc:p36956]	Squared	21186.4	24698.3	1.16576	
765	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	Rooted	63.5181	67.7402	1.06647	
766	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p36542]	Squared	24509.4	28571.6	1.16574	
766	protein tara (trio-associated repeat on actin) (hrihfb2122). [source:swissprot;acc:q9h2d6]	Ranked	213.804	224.226	1.04875	
766	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	Rooted	63.5181	67.7402	1.06647	
766	ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [source:refseq;acc:nm_003349]	Measured	6691.93	7445.09	1.11255	
767	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	Rooted	63.5181	67.7402	1.06647	
767	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [source:swissprot;acc:p48047]	Squared	24509.4	28571.6	1.16574	
767	rho interacting protein 3. [source:refseq;acc:nm_015134]	Ranked	213.803	224.224	1.04874	
767	utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [source:swissprot;acc:q16851]	Measured	6691.21	7444.22	1.11254	
768	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [source:swissprot;acc:q9udy4]	Ranked	210.946	221.225	1.04873	
768	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Squared	12108.4	14114.6	1.16569	
768	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	Rooted	63.5181	67.7402	1.06647	
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]	Measured	6690.44	7443.29	1.11253	
769	60s ribosomal protein l39. [source:swissprot;acc:p02404]	Rooted	55.6817	59.3786	1.06639	
769	cab2. [source:refseq;acc:nm_033419]	Ranked	210.946	221.225	1.04873	
769	n-acetylglutamate synthase. [source:refseq;acc:nm_153006]	Squared	20943	24412.8	1.16568	
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]	Measured	5873.77	6532.44	1.11214	
770	60s ribosomal protein l18a. [source:swissprot;acc:q02543]	Rooted	55.6817	59.3786	1.06639	
770	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [source:swissprot;acc:o75953]	Ranked	210.946	221.225	1.04873	
770	fibulin-2 precursor. [source:swissprot;acc:p98095]	Squared	45189.6	52666.2	1.16545	
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]	Measured	5874.74	6533.34	1.11211	
771	40s ribosomal protein s19. [source:swissprot;acc:p39019]	Rooted	55.6817	59.3786	1.06639	
771	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [source:refseq;acc:nm_006595]	Measured	5874.74	6533.34	1.11211	
771	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [source:swissprot;acc:p25685]	Ranked	210.946	221.225	1.04873	
771	glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [source:refseq;acc:nm_018292]	Squared	24418	28453.7	1.16528	
772	60s ribosomal protein l31. [source:swissprot;acc:p12947]	Rooted	55.6817	59.3786	1.06639	
772	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [source:swissprot;acc:p46055]	Ranked	210.946	221.225	1.04873	
772	fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [source:swissprot;acc:o00519]	Squared	24418	28453.7	1.16528	
772	sec13-related protein. [source:swissprot;acc:p55735]	Measured	5874.76	6533.36	1.11211	
773	coactosin-like protein. [source:swissprot;acc:q14019]	Squared	24418	28453.7	1.16528	
773	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	Rooted	127.967	120.003	1.06637	
773	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [source:refseq;acc:nm_022553]	Ranked	210.946	221.225	1.04873	
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]	Measured	5874.74	6533.34	1.11211	
774	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [source:swissprot;acc:o60762]	Rooted	65.3248	69.648	1.06618	
774	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [source:refseq;acc:nm_139279]	Ranked	225.996	215.535	1.04854	
774	uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [source:swissprot;acc:p13051]	Squared	24418	28453.7	1.16528	
774	yeast sec31p homolog. [source:refseq;acc:nm_014933]	Measured	5874.76	6533.36	1.11211	
775	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	Rooted	62.2385	58.38	1.06609	
775	histone deacetylase 2 (hd2). [source:swissprot;acc:q92769]	Ranked	226.003	215.541	1.04854	
775	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [source:swissprot;acc:o75879]	Squared	24418	28453.7	1.16528	
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]	Measured	5874.74	6533.33	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/