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 1768 to 1817 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
221	tubby protein homolog. [swissprot;acc:p50607]	Rooted	0	39.7788	45.0452	1.13239
222	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Ranked		12183	11013.2	1.10622
	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Measured		1499.4	1735.23	1.15728
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Rooted	1	52.7936	60.0592	1.13762
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Squared	0	410.662	561.35	1.36694
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	Measured	1	41482.5	33356.5	1.24361
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Ranked	1	112	126	1.125
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Rooted	0	58.6947	51.8401	1.13223
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Squared	1	86281	65058.3	1.32621
223	brain protein 16. [refseq;acc:nm_016458]	Rooted	0	38.9679	44.0549	1.13054
	cytohesin 4. [swissprot;acc:q9uia0]	Measured	1	41482.5	33356.5	1.24361
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	Measured	0	750.981	650.724	1.15407
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Ranked	1	112	126	1.125
	pnas-18. [sptrembl;acc:q9bzu3]	Ranked	0	12602.7	13939.6	1.10608
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Squared	0	952.068	697.024	1.3659
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Squared	1	40982.6	54272.3	1.32428
224	60s ribosomal protein l7. [swissprot;acc:p18124]	Measured	0	1915.27	2206.07	1.15183
	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Rooted		26.1198	23.1206	1.12972
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Ranked		9815.6	8889.93	1.10413
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Squared		399.199	542.77	1.35965
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	Measured	1	41482.5	33356.5	1.24361
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Rooted		137.446	120.823	1.13758
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Ranked		185.969	165.623	1.12285
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Squared		14943.9	19771.9	1.32307
225	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Rooted	0	23.1768	26.17	1.12915
	40s ribosomal protein s29. [swissprot;acc:p30054]	Ranked	0	11035.3	9997.71	1.10378
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	1	137.446	120.823	1.13758
	metaxin 1. [swissprot;acc:q13505]	Squared		60401.6	79875.7	1.32241
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Measured		9035	7279.6	1.24114
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Squared	0	399.199	542.77	1.35965
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Measured	0	8763	7608	1.15181
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Ranked	1	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Ranked	1	239.991	269.238	1.12187
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Measured	0	658.544	758.411	1.15165
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Measured		9035	7279.6	1.24114
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Squared		73510.2	55607.3	1.32195
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Ranked	0	15395.7	16992.9	1.10374
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Rooted		30.2675	34.1662	1.12881
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Squared		399.199	542.77	1.35965
227	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Squared		1662.68	2253.78	1.35551
	integral membrane protein cii-3b. [sptrembl;acc:o75609]	Rooted		19.6188	22.1086	1.12691
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Rooted	1	137.446	120.823	1.13758
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Measured		9035	7279.6	1.24114
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Squared		73995.1	56003.7	1.32125
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Ranked		239.99	269.234	1.12186
	tigger transposable element derived 6. [refseq;acc:nm_030953]	Ranked	0	12360	11200.2	1.10355
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Measured	0	424.258	369.011	1.14972
228	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Squared	1	57913.5	76336.3	1.31811

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/