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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1062 to 1111 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
133	PRSS16	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Squared	Subtracted	71062.2	95488.6	24426.4
	TMEM132A	gbp protein isoform a. [refseq;acc:nm_017870]	Squared	Divided	1182.25	1726.55	1.46039
	TOB1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Ranked		350	290	1.2069
134	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Measured		21785.2	16426.1	1.32626
	no value	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Ranked	Subtracted	226.884	194.79	32.094
	CCDC47	gk001 protein. [refseq;acc:nm_020198]	Squared		71062.2	95488.6	24426.4
	CCNB2	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Measured		12796.8	10886	1910.8
	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	Ranked	Divided	350	290	1.2069
	GATAD2A	p66 alpha. [refseq;acc:nm_017660]	Squared		81888.8	56306.5	1.45434
	POLE4	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Rooted		44.849	54.7964	1.2218
	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Rooted	Subtracted	54.8203	67.934	13.1137
135	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Measured	Divided	21785.2	16426.1	1.32626
	CACNG8	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
	CLSTN2	calsyntenin-2 precursor. [swissprot;acc:q9h4d0]	Squared	Subtracted	71033.4	95440.2	24406.8
	CPEB4	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Ranked	Divided	350	290	1.2069
	FOXP4	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Ranked	Subtracted	263.215	231.407	31.808
	GATAD2B	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Squared	Divided	81888.8	56306.5	1.45434
	JUNB	transcription factor jun-b. [swissprot;acc:p17275]	Measured	Subtracted	5579.18	7488.4	1909.22
	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Rooted	Divided	54.935	66.6101	1.21253
136	no value	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Squared		81888.8	56306.5	1.45434
	ADIPOR2	adiponectin receptor 2. [refseq;acc:nm_024551]	Rooted		41.8357	50.6469	1.21061
	CACNG3	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
	CDK2	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Measured		12787.6	10880.5	1907.1
	CLSTN3	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	Squared		71030.1	95434.8	24404.7
	CPEB3	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	Divided	350	290	1.2069
	FOXP1	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Ranked	Subtracted	263.215	231.407	31.808
	NFYC	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
137	CACNG2	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted	Subtracted	49.2925	62.397	13.1045
	CCNB1	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	Subtracted	12786.6	10879.9	1906.7
	CDK3	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	Squared	Divided	81606.8	56215.8	1.45167
	FOXP3	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Ranked	Subtracted	263.191	231.394	31.797
	MSI2	musashi 2 isoform a. [refseq;acc:nm_138962]	Rooted	Divided	54.9787	66.2416	1.20486
	NFYA	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		3620.77	4763.34	1.31556
	RASAL2	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked		350	290	1.2069
	SGTA	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	Subtracted	69549	92953.5	23404.5
138	CACNG4	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted		49.293	62.3973	13.1043
	HPRT1	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Squared		70739	93908.8	23169.8
	KCNIP1	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
	MSI1	musashi 1. [refseq;acc:nm_002442]	Rooted		54.9787	66.2416	1.20486
	PPP2CA	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
	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked	Subtracted	174.667	205.556	30.889
	TP53BP2	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
	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Squared	Divided	468498	322755	1.45156
139	APBA1	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
	CACNG5	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Rooted	Subtracted	49.3267	62.4167	13.09
	CCNB2	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Squared	Divided	81592.1	56211.1	1.45153
	CDC2	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
	CHRAC1	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
	KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Measured	Divided	2759.61	2099.49	1.31442
	STAM	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	Squared	Subtracted	86861.5	65369.7	21491.8

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
- Hugo is the HGNC identifier if it exists
- 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/