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 2208 to 2257 of 6456 in total 
Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1104	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [source:swissprot;acc:o60675]	Subtracted	7433.73	7950.61	516.88	
1105	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [source:refseq;acc:nm_006614]	Subtracted	7433.73	7950.61	516.88	
1105	synaptotagmin xii (sytxii). [source:swissprot;acc:q8iv01]	Divided	5460.49	5954.62	1.09049	
1106	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [source:swissprot;acc:p32004]	Subtracted	7433.73	7950.61	516.88	
1106	peptide methionine sulfoxide reductase (ec 1.8.4.6) (protein- methionine-s-oxide reductase) (peptide met(o) reductase). [source:swissprot;acc:q9uj68]	Divided	5489.99	5986.63	1.09046	
1107	phosphoserine aminotransferase (ec 2.6.1.52) (psat). [source:swissprot;acc:q9y617]	Divided	5489.99	5986.63	1.09046	
1107	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [source:swissprot;acc:q16594]	Subtracted	7433.73	7950.61	516.88	
1108	nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [source:swissprot;acc:q14494]	Subtracted	7433.73	7950.61	516.88	
1108	rrp5 protein homolog (programmed cell death protein 11). [source:swissprot;acc:q14690]	Divided	4846.16	5283.08	1.09016	
1109	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [source:refseq;acc:nm_004289]	Subtracted	7433.73	7950.61	516.88	
1109	rab3a interacting protein (rabin3)-like 1. [source:refseq;acc:nm_013401]	Divided	6545.19	7132.89	1.08979	
1110	mstp028 protein. [source:refseq;acc:nm_031954]	Subtracted	5838.87	6355.06	516.19	
1110	nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [source:swissprot;acc:p22570]	Divided	5947.53	6481.56	1.08979	
1111	putative sialoglycoprotease type 2. [source:refseq;acc:nm_022353]	Subtracted	5393.37	5909.47	516.1	
1111	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [source:refseq;acc:nm_022456]	Divided	6540.61	7127.41	1.08972	
1112	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [source:swissprot;acc:q8n0y7]	Divided	5910.54	6440.58	1.08968	
1112	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [source:swissprot;acc:q12824]	Subtracted	5840.01	6355.56	515.55	
1113	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [source:swissprot;acc:p18669]	Divided	5910.54	6440.58	1.08968	
1113	xylulokinase homolog; xylulokinase (h. influenzae) homolog. [source:refseq;acc:nm_005108]	Subtracted	5950.27	6465.72	515.45	
1114	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [source:swissprot;acc:p27708]	Subtracted	6021.21	6536.45	515.24	
1114	phosphoglycerate mutase 2 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme m) (pgam-m) (bpg-dependent pgam 2) (muscle-specific phosphoglycerate mutase). [source:swissprot;acc:p15259]	Divided	5910.54	6440.58	1.08968	
1115	5-methyltetrahydrofolate--homocysteine methyltransferase (ec 2.1.1.13) (methionine synthase, vitamin-b12 dependent) (ms). [source:swissprot;acc:q99707]	Divided	5795.13	6314.19	1.08957	
1115	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [source:swissprot;acc:q13829]	Subtracted	5840.65	6355.84	515.19	
1116	dynactin complex 50 kda subunit (50 kda dynein-associated polypeptide) (dynamitin) (dctn-50) (dynactin 2). [source:swissprot;acc:q13561]	Divided	5322.16	5798.38	1.08948	
1116	polymerase delta-interacting protein 1; tnfaip1-like. [source:refseq;acc:nm_178863]	Subtracted	5840.77	6355.89	515.12	
1117	adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [source:swissprot;acc:p12236]	Divided	5322.16	5798.38	1.08948	
1117	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [source:swissprot;acc:o43318]	Subtracted	6001.16	6515.9	514.74	
1118	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [source:swissprot;acc:p12235]	Divided	5322.16	5798.38	1.08948	
1118	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Subtracted	3658.76	3144.39	514.37	
1119	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [source:swissprot;acc:p05141]	Divided	5322.16	5798.38	1.08948	
1119	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	Subtracted	6230.49	6744.5	514.01	
1120	heat shock factor binding protein 1. [source:swissprot;acc:o75506]	Divided	5915.42	6443.77	1.08932	
1120	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	Subtracted	6230.38	6744.35	513.97	
1121	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [source:swissprot;acc:q9y2x3]	Divided	4338.49	4725.86	1.08929	
1121	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	Subtracted	6229.16	6742.79	513.63	
1122	importin alpha-6 subunit (karyopherin alpha-5 subunit). [source:swissprot;acc:o15131]	Subtracted	5792.08	6305.67	513.59	
1122	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	Divided	7937.72	8646.38	1.08928	
1123	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [source:swissprot;acc:p04424]	Divided	5857.48	6380.4	1.08927	
1123	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [source:swissprot;acc:q01167]	Subtracted	5651.07	6164.55	513.48	
1124	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	Subtracted	5946.33	6459.79	513.46	
1124	transducin-like enhancer protein 2 (esg2). [source:swissprot;acc:q04725]	Divided	6288.27	6846.97	1.08885	
1125	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	Subtracted	5946.33	6459.79	513.46	
1125	transducin-like enhancer protein 1 (esg1). [source:swissprot;acc:q04724]	Divided	6287.07	6845.28	1.08879	
1126	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	Subtracted	5946.33	6459.79	513.46	
1126	importin alpha-6 subunit (karyopherin alpha-5 subunit). [source:swissprot;acc:o15131]	Divided	5792.08	6305.67	1.08867	
1127	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	Subtracted	5946.33	6459.79	513.46	
1127	yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [source:refseq;acc:nm_020470]	Divided	5790.65	6303.92	1.08864	
1128	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [source:swissprot;acc:o43448]	Divided	5790.65	6303.94	1.08864	
1128	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [source:swissprot;acc:o43448]	Subtracted	5790.65	6303.94	513.29	
1129	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [source:swissprot;acc:p28329]	Subtracted	5790.66	6303.95	513.29	

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/