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 1080 to 1129 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
135	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Rooted	Subtracted	49.2923	62.3969	13.1046
136	adiponectin receptor 2. [refseq;acc:nm_024551]	Rooted	Divided	41.8357	50.6469	1.21061
	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	Squared	Subtracted	71030.1	95434.8	24404.7
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Measured	Subtracted	12787.6	10880.5	1907.1
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	Divided	350	290	1.2069
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Ranked	Subtracted	263.215	231.407	31.808
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Measured	Divided	3620.77	4763.34	1.31556
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared	Divided	81888.8	56306.5	1.45434
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	Rooted	Subtracted	49.2923	62.3969	13.1046
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Measured	Divided	3620.77	4763.34	1.31556
	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	Divided	81606.8	56215.8	1.45167
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Ranked	Subtracted	263.191	231.394	31.797
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	Subtracted	12786.6	10879.9	1906.7
	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted	Divided	54.9787	66.2416	1.20486
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked	Divided	350	290	1.2069
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	Subtracted	69549	92953.5	23404.5
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted		49.2925	62.397	13.1045
138	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked		174.667	205.556	30.889
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Squared		70739	93908.8	23169.8
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Measured	Divided	2755.15	2094.3	1.31555
	musashi 1. [refseq;acc:nm_002442]	Rooted		54.9787	66.2416	1.20486
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared		468498	322755	1.45156
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Ranked		194.372	234.204	1.20493
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Measured	Subtracted	15182.5	13277.9	1904.6
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted	Subtracted	49.293	62.3973	13.1043
139	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Ranked	Divided	271.752	225.68	1.20415
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Measured	Subtracted	12780.7	10876.4	1904.3
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Ranked	Subtracted	287.41	256.835	30.575
	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Squared	Divided	81592.1	56211.1	1.45153
	nuclear protein ukp68. [refseq;acc:nm_024824]	Rooted		54.9787	66.2416	1.20486
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Measured		2759.61	2099.49	1.31442
	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	Squared	Subtracted	86861.5	65369.7	21491.8
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Rooted		49.3267	62.4167	13.09
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Ranked		228.306	198.011	30.295
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Squared	Divided	81527.6	56190.6	1.45091
	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. [refseq;acc:nm_001457]	Rooted	Divided	55.6161	66.7332	1.19989
	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Measured	Subtracted	2597.5	698.5	1899
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Measured	Divided	2760.28	2100.27	1.31425
	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]	Squared	Subtracted	86609.4	65234.5	21374.9
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Ranked	Divided	59	49	1.20408
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Rooted	Subtracted	39.9725	52.9973	13.0248
141	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Rooted		105.205	92.2415	12.9635
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Ranked		239.991	269.238	29.247
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Squared	Divided	81520.8	56188.5	1.45084
	hbs1-like. [refseq;acc:nm_006620]	Measured	Subtracted	2597.5	698.5	1899
	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	Squared	Subtracted	86600.9	65229.9	21371
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Ranked	Divided	59	49	1.20408
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Rooted		55.6161	66.7332	1.19989
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Measured		4405.4	5782.08	1.3125
142	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Squared		81478.9	56175.2	1.45044

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.

- http://analysis.yellowcouch.org/