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.

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 1327 to 1376 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
166	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Ranked	Subtracted	312	284	28	
166	nuclear protein ukp68. [source:refseq;acc:nm_024824]	Rooted	Subtracted	54.9787	66.2416	11.2629	
167	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [source:swissprot;acc:q01433]	Ranked	Subtracted	133	105	28	
167	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Squared	Subtracted	64975.9	81151.2	16175.3	
167	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [source:refseq;acc:nm_001457]	Rooted	Subtracted	55.6161	66.7332	11.1171	
167	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [source:swissprot;acc:q99259]	Ranked	Divided	209.299	249.187	1.19058	
167	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Squared	Divided	173408	242989	1.40126	
167	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Rooted	Divided	55.65	65.1448	1.17062	
167	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Measured	Divided	23693.7	18263	1.29736	
167	myosin xv (unconventional myosin-15). [source:swissprot;acc:q9ukn7]	Measured	Subtracted	4489.19	2765.82	1723.37	
168	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [source:refseq;acc:nm_181844]	Squared	Subtracted	69165.6	52992.1	16173.5	
168	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Ranked	Subtracted	312	284	28	
168	gaba-a receptor-associated protein. [source:sptrembl;acc:q9by60]	Ranked	Divided	82.5916	98.0548	1.18722	
168	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [source:swissprot;acc:p11217]	Measured	Subtracted	4489.19	2765.82	1723.37	
168	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Measured	Divided	23693.7	18263	1.29736	
168	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Squared	Divided	173408	242989	1.40126	
168	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [source:refseq;acc:nm_016316]	Rooted	Subtracted	55.6161	66.7332	11.1171	
168	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Rooted	Divided	56.3709	65.8949	1.16895	
169	apg3p; pc3-96 protein. [source:refseq;acc:nm_022488]	Ranked	Divided	82.5916	98.0548	1.18722	
169	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Rooted	Divided	62.762	53.7761	1.1671	
169	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Ranked	Subtracted	312	284	28	
169	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Measured	Subtracted	4245.52	5942.75	1697.23	
169	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Measured	Divided	23693.7	18263	1.29736	
169	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [source:refseq;acc:nm_015148]	Squared	Subtracted	69165	52991.7	16173.3	
169	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [source:swissprot;acc:q99873]	Rooted	Subtracted	55.6161	66.7332	11.1171	
169	symplekin. [source:swissprot;acc:q92797]	Squared	Divided	124118	88668.8	1.39979	
170	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [source:swissprot;acc:p41182]	Squared	Subtracted	69165	52991.7	16173.3	
170	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [source:refseq;acc:nm_015681]	Rooted	Divided	53.4993	45.9227	1.16499	
170	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [source:refseq;acc:nm_019857]	Squared	Divided	96730.5	69286.7	1.39609	
170	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Ranked	Subtracted	227.971	200.417	27.554	
170	huntingtin-interacting protein hypa/fbp11 (fragment). [source:sptrembl;acc:o75404]	Measured	Subtracted	4247.86	5941.88	1694.02	
170	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	Measured	Divided	23693.7	18263	1.29736	
170	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Ranked	Divided	227.199	192.715	1.17894	
170	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [source:swissprot;acc:q9nr22]	Rooted	Subtracted	55.6161	66.7332	11.1171	
171	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [source:swissprot;acc:p17812]	Squared	Divided	96602.7	69211.2	1.39577	
171	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Measured	Subtracted	4117.67	5801.04	1683.37	
171	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Rooted	Divided	61.6639	71.7355	1.16333	
171	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]	Measured	Divided	23693.7	18263	1.29736	
171	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Ranked	Divided	227.202	192.823	1.17829	
171	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4]	Ranked	Subtracted	201.478	228.784	27.306	
171	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621]	Rooted	Subtracted	55.6161	66.7332	11.1171	
171	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623]	Squared	Subtracted	69165	52991.7	16173.3	
172	c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363]	Squared	Subtracted	69123.3	52967	16156.3	
172	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	Ranked	Divided	174.667	205.556	1.17685	
172	ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6]	Ranked	Subtracted	201.515	228.752	27.237	
172	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333]	Rooted	Subtracted	55.6161	66.7332	11.1171	
172	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Squared	Divided	121579	87259.3	1.39331	
172	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Measured	Subtracted	4556.78	2945.26	1611.52	
172	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	Rooted	Divided	56.7592	65.9889	1.16261	
172	trophinin. [source:swissprot;acc:q12816]	Measured	Divided	23693.7	18263	1.29736	

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/