MK5 Microarray Data

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 1118 to 1167 of 3228 in total

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

Rank	description	red	green	network_comparison
1118	adp,atp carrier protein, heart/skeletal muscle isoform t1 (adp/atp translocase 1) (adenine nucleotide translocator 1) (ant 1). [swissprot;acc:p12235]	5322.16	5798.38	1.08948
1119	adp,atp carrier protein, fibroblast isoform (adp/atp translocase 2) (adenine nucleotide translocator 2) (ant 2). [swissprot;acc:p05141]
1120	heat shock factor binding protein 1. [swissprot;acc:o75506]	5915.42	6443.77	1.08932
1121	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	4338.49	4725.86	1.08929
1122	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	7937.72	8646.38	1.08928
1123	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	5857.48	6380.4	1.08927
1124	transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725]	6288.27	6846.97	1.08885
1125	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	6287.07	6845.28	1.08879
1126	importin alpha-6 subunit (karyopherin alpha-5 subunit). [swissprot;acc:o15131]	5792.08	6305.67	1.08867
1127	yip1 interacting factor homolog; yip1p-interacting factor; putative rab5-interacting protein; putative transmembrane protein 54tmp. [refseq;acc:nm_020470]	5790.65	6303.92	1.08864
1128	voltage-gated potassium channel beta-3 subunit (k+ channel beta-3 subunit) (kv-beta-3). [swissprot;acc:o43448]		6303.94
1129	voltage-gated potassium channel beta-1 subunit (k+ channel beta-1 subunit) (kv-beta-1). [swissprot;acc:q14722]		6303.92
1130	similar to putative transmembrane protein; homolog of yeast golgi membrane protein yif1p (yip1p-interacting factor). [refseq;acc:nm_033557]
1131	aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154]
1132	alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340]
1133	golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799]
1134	alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870]
1135	methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252]	5790.67	6303.95
1136	10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984]	5790.65	6303.92
1137	rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]
1138	oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8]
1139	choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	5790.66	6303.95
1140	voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303]	5790.65	6303.93
1141	aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
1142	importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294]	5789.07	6302.01	1.0886
1143	homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622]	6281.21	6837.61	1.08858
1144	cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4]
1145	40s ribosomal protein s30. [swissprot;acc:q05472]	5893.97	6416.07
1146	activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	6281.21	6837.61
1147	cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]
1148	hect type e3 ubiquitin ligase. [refseq;acc:nm_015052]
1149	transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726]	6280.74	6837.01	1.08857
1150	mstp028 protein. [refseq;acc:nm_031954]	5838.87	6355.06	1.08841
1151	alpha-centractin (centractin) (centrosome-associated actin homolog) (actin-rpv) (arp1). [swissprot;acc:p42024]	5322.74	5793.15	1.08838
1152	beta-centractin (actin-related protein 1b) (arp1b). [swissprot;acc:p42025]
1153	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824]	5840.01	6355.56	1.08828
1154	tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829]	5840.65	6355.84	1.08821
1155	transducin-like enhancer protein 4. [swissprot;acc:q04727]	6270.67	6823.73	1.0882
1156	polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	5840.77	6355.89	1.08819
1157	serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896]	5418.33	5895.2	1.08801
1158	delta-aminolevulinic acid dehydratase (ec 4.2.1.24) (porphobilinogen synthase) (aladh). [swissprot;acc:p13716]	5489.18	5972.09	1.08797
1159	kccr13l. [refseq;acc:nm_139179]	5538.8	6025.51	1.08787
1160	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
1161	n-acetyltransferase 5 (ec 2.3.1.-). [swissprot;acc:q9y6d2]	5315.76	5782.63	1.08783
1162	nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231]	5832.13	6343.59	1.0877
1163	elks protein. [refseq;acc:nm_015064]
1164	sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911]	6600.36	7178.84	1.08764
1165	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	6604.44	7183.07	1.08761
1166	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	6606.3	7185.01	1.0876
1167	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	6607.68	7186.45	1.08759

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.