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 1377 to 1426 of 25824 in total 
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
173	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Rooted	Divided	145.551	168.796	1.1597	
173	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Measured	Divided	4579.34	5940.64	1.29727	
173	methyltransferase like 2. [source:refseq;acc:nm_018396]	Squared	Subtracted	71576.8	56326.7	15250.1	
173	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Rooted	Subtracted	37.3005	48.4141	11.1136	
173	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Squared	Divided	82624.3	115061	1.39258	
173	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62]	Ranked	Subtracted	201.515	228.752	27.237	
173	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Ranked	Divided	227.032	193.056	1.17599	
173	uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48]	Measured	Subtracted	4556.79	2945.28	1611.51	
174	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763]	Squared	Subtracted	71576.8	56326.7	15250.1	
174	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8]	Ranked	Divided	335	286	1.17133	
174	luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019]	Ranked	Subtracted	228.1	200.968	27.132	
174	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Measured	Divided	4455.95	5774.03	1.2958	
174	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	Rooted	Divided	145.551	168.796	1.1597	
174	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	Rooted	Subtracted	37.3005	48.4141	11.1136	
174	sedlin. [source:swissprot;acc:o14582]	Squared	Divided	112820	157033	1.39189	
174	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	Measured	Subtracted	4556.83	2945.38	1611.45	
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653]	Ranked	Divided	199.949	234.187	1.17123	
175	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Rooted	Subtracted	37.3005	48.4141	11.1136	
175	fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263]	Squared	Subtracted	71576.8	56326.7	15250.1	
175	luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032]	Ranked	Subtracted	228.085	201.006	27.079	
175	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Measured	Divided	4456.67	5773.77	1.29553	
175	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	Rooted	Divided	145.551	168.796	1.1597	
175	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	Measured	Subtracted	4556.99	2945.8	1611.19	
175	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Squared	Divided	112820	157033	1.39189	
176	bet3 homolog. [source:swissprot;acc:o43617]	Squared	Divided	112820	157033	1.39189	
176	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Rooted	Subtracted	37.3005	48.4141	11.1136	
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Ranked	Divided	275.754	235.908	1.1689	
176	eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010]	Ranked	Subtracted	271.016	244.167	26.849	
176	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492]	Measured	Subtracted	10235.2	11830.8	1595.6	
176	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Measured	Divided	4456.93	5773.67	1.29544	
176	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	Rooted	Divided	145.551	168.796	1.1597	
176	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824]	Squared	Subtracted	71576.8	56326.7	15250.1	
177	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Squared	Subtracted	9924.76	25146.6	15221.8	
177	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2]	Ranked	Divided	229.406	196.695	1.1663	
177	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075]	Measured	Subtracted	4110.14	5694.99	1584.85	
177	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Measured	Divided	4457.06	5773.63	1.29539	
177	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Rooted	Divided	145.551	168.796	1.1597	
177	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Rooted	Subtracted	37.3005	48.4141	11.1136	
177	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Squared	Divided	78383	108483	1.38401	
177	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [source:refseq;acc:nm_015477]	Ranked	Subtracted	241.07	267.88	26.81	
178	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Squared	Subtracted	9924.76	25146.6	15221.8	
178	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Squared	Divided	25326.4	18354.1	1.37988	
178	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Rooted	Subtracted	37.3005	48.4141	11.1136	
178	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [source:swissprot;acc:o43583]	Ranked	Subtracted	241.07	267.88	26.81	
178	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [source:refseq;acc:nm_017892]	Ranked	Divided	226.887	194.72	1.1652	
178	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	Measured	Divided	21591.5	27904.5	1.29238	
178	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Measured	Subtracted	10908.6	12491.8	1583.2	
178	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Rooted	Divided	45.7414	52.932	1.1572	
179	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Measured	Subtracted	4266.04	5843.51	1577.47	
179	huntingtin interacting protein c. [source:refseq;acc:nm_012272]	Rooted	Subtracted	55.0737	66.0298	10.9561	

Legend:
- Rank is the rank after comparing the two networks
- 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/