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 873 to 922 of 7460 in total

Value Type

: Ranked
Interaction Map

: High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison
219	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Subtracted	1	242.339	266.986	24.647
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Divided	1	112	126	1.125
	myosin vi. [swissprot;acc:q9um54]	Subtracted	0	10121.5	11250.5	1129
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Divided	0	12196.2	11009.7	1.10777
220	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Subtracted	1	242.339	266.986	24.647
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Divided	1	112	126	1.125
	neurocalcin delta. [swissprot;acc:p29554]	Divided	0	13973.6	15473.5	1.10734
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Subtracted		5677.58	4549.85	1127.73
221	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Divided		12190.3	13497.2	1.10721
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Subtracted		5677.45	4550.87	1126.58
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Divided	1	112	126	1.125
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Subtracted	1	242.627	267.151	24.524
222	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Divided	0	12183	11013.2	1.10622
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Subtracted	1	242.153	266.673	24.52
	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	Divided	1	112	126	1.125
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Subtracted	0	5673.33	6797.56	1124.23
223	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Subtracted	0	14257.4	13134.5	1122.9
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Divided	1	112	126	1.125
	pnas-18. [sptrembl;acc:q9bzu3]	Divided	0	12602.7	13939.6	1.10608
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Subtracted	1	242.153	266.673	24.52
224	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]		0	14930.6	16053	1122.4
	60s ribosomal protein l34. [swissprot;acc:p49207]		1	242.153	266.673	24.52
	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Divided	0	9815.6	8889.93	1.10413
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]		1	185.969	165.623	1.12285
225	40s ribosomal protein s29. [swissprot;acc:p30054]		0	11035.3	9997.71	1.10378
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Subtracted	1	242.153	266.673	24.52
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Subtracted	0	8407.67	9516.92	1109.25
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Divided	1	226.471	201.769	1.12243
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Divided		239.991	269.238	1.12187
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Subtracted		242.153	266.673	24.52
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Divided	0	15395.7	16992.9	1.10374
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Subtracted	0	6755.71	7863.63	1107.92
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Subtracted	1	244.126	268.604	24.478
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Divided	1	239.99	269.234	1.12186
	tigger transposable element derived 6. [refseq;acc:nm_030953]	Divided	0	12360	11200.2	1.10355
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Subtracted	0	7879.3	6789.92	1089.38
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Subtracted	1	244.126	268.604	24.478
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Divided	1	226.411	202.088	1.12036
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Divided	0	10303.5	11370.4	1.10355
		Subtracted	0	10303.5	11370.4	1066.9
229	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Subtracted	1	242.195	266.663	24.468
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	1	226.401	202.094	1.12028
	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	Subtracted	0	15147.2	14091.9	1055.3
	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Divided	0	10899.4	9878.1	1.10339
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	Divided	1	239.35	267.915	1.11934
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Subtracted	0	15147.2	14091.9	1055.3
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Subtracted	1	242.694	267.017	24.323
	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	Divided	0	12364.7	11207.7	1.10323
231	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Subtracted	0	12447.6	11392.6	1055
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Divided	1	239.336	267.881	1.11927

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/