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 1723 to 1772 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
216	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	Squared	0	9.56237	6.91035	1.38378
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	Measured	1	16071.6	12886.8	1.24714
	maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708]	Ranked	0	10559.7	11732	1.11102
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Ranked	1	112	126	1.125
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Rooted		105.205	92.2415	1.14054
	protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156]	Squared		86600.9	65229.9	1.32763
217	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Ranked	0	7101.79	6406.18	1.10858
	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Rooted	0	9.37502	8.25148	1.13616
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Ranked	1	112	126	1.125
	peptidyl-prolyl cis-trans isomerase b precursor (ec 5.2.1.8) (ppiase) (rotamase) (cyclophilin b) (s-cyclophilin) (scylp) (cyp-s1). [swissprot;acc:p23284]	Squared		86600.9	65229.9	1.32763
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted		105.205	92.2415	1.14054
	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	Measured		16071.6	12886.8	1.24714
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Squared	0	9.56237	6.91035	1.38378
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured		903.967	771.309	1.17199
218	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	Rooted		19.7165	17.3602	1.13573
	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Rooted	1	46.1476	52.5742	1.13926
	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Ranked	0	19355	17469.2	1.10795
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Ranked	1	112	126	1.125
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	Squared	0	19.1247	13.8207	1.38377
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Measured	1	16070.4	12886	1.24712
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Measured	0	3645.5	3118.3	1.16907
	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]	Squared	1	86600.9	65229.9	1.32763
219	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]	Squared		86600.9	65229.9	1.32763
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Rooted		52.7146	60.0088	1.13837
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Ranked		112	126	1.125
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Measured	0	8852.4	7572.88	1.16896
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Rooted		31.7569	27.9904	1.13456
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Squared		3088.94	4269.96	1.38234
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Ranked		12196.2	11009.7	1.10777
	transforming protein n-ras. [swissprot;acc:p01111]	Measured	1	16069.8	12885.6	1.24711
220	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]	Squared		86600.9	65229.9	1.32763
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Measured		41482.5	33356.5	1.24361
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Rooted		52.7557	60.035	1.13798
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Ranked		112	126	1.125
	neurocalcin delta. [swissprot;acc:p29554]	Ranked	0	13973.6	15473.5	1.10734
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Rooted		24.1656	21.3198	1.13348
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Squared		19892.6	27221.2	1.36841
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Measured		18704	21730	1.16178
221	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Squared		1614.86	1181.19	1.36715
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Measured	1	41482.5	33356.5	1.24361
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Ranked	0	12190.3	13497.2	1.10721
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Squared	1	70739	93908.8	1.32754
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Ranked	1	112	126	1.125
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	Measured	0	1905.84	1643	1.15998
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Rooted	1	56.9506	64.7888	1.13763
	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

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/