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 900 to 949 of 6456 in total

Value Type	Measured
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
450	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Subtracted	5061.11	5950.22	889.11	
451	n-myc proto-oncogene protein. [source:swissprot;acc:p04198]	Divided	4889.71	5610.69	1.14745	
451	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	Subtracted	398.5	1281.5	883	
452	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	Subtracted	398.5	1281.5	883	
452	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Divided	3760.8	4315.06	1.14738	
453	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	Subtracted	398.5	1281.5	883	
453	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Divided	3760.8	4315.06	1.14738	
454	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	Subtracted	398.5	1281.5	883	
454	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Divided	3760.8	4315.06	1.14738	
455	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	Subtracted	398.5	1281.5	883	
455	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [source:swissprot;acc:q06546]	Divided	4890.51	5610.95	1.14731	
456	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [source:swissprot;acc:q06545]	Divided	4890.51	5610.95	1.14731	
456	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	Subtracted	398.5	1281.5	883	
457	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [source:swissprot;acc:o00217]	Divided	4890.51	5610.95	1.14731	
457	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Subtracted	4620.76	5501.94	881.18	
458	elongation of very long chain fatty acids protein 1 (cgi-88). [source:swissprot;acc:q9bw60]	Divided	4890.55	5610.96	1.14731	
458	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Subtracted	5986.65	6865.68	879.03	
459	myc proto-oncogene protein (c-myc). [source:swissprot;acc:p01106]	Divided	4892.16	5611.48	1.14704	
459	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	Subtracted	5082.66	5959.99	877.33	
460	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	Subtracted	1931.34	1057.39	873.95	
460	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	Divided	3790.11	4346.98	1.14693	
461	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Divided	5986.65	6865.68	1.14683	
461	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Subtracted	2353.63	3225.65	872.02	
462	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [source:swissprot;acc:o60858]	Divided	11383.2	9926.61	1.14674	
462	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]	Subtracted	2353.63	3225.65	872.02	
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [source:swissprot;acc:q9nvp1]	Divided	3720.18	4264.46	1.1463	
463	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]	Subtracted	2353.63	3225.65	872.02	
464	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Subtracted	2353.63	3225.65	872.02	
464	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [source:swissprot;acc:q16576]	Divided	4858.96	5568.85	1.1461	
465	presenilin 1 (ps-1) (s182 protein). [source:swissprot;acc:p49768]	Subtracted	2353.63	3225.65	872.02	
465	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Divided	3847.31	4409.22	1.14605	
466	cullin homolog 1 (cul-1). [source:swissprot;acc:q13616]	Subtracted	2353.63	3225.65	872.02	
466	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Divided	3847.31	4409.22	1.14605	
467	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	Subtracted	1926.69	1056.02	870.67	
467	metastasis-associated protein mta1. [source:swissprot;acc:q13330]	Divided	4864.25	5573.62	1.14583	
468	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). [source:swissprot;acc:q09028]	Divided	4869.15	5578.02	1.14558	
468	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [source:swissprot;acc:p51965]	Subtracted	11143.5	10276.3	867.2	
469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [source:swissprot;acc:p46087]	Divided	3831.17	4388.74	1.14554	
469	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [source:refseq;acc:nm_006357]	Subtracted	11143.5	10276.3	867.2	
470	block of proliferation 1. [source:swissprot;acc:q14137]	Divided	3796.24	4348.59	1.1455	
470	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	Subtracted	5367.04	6233.12	866.08	
471	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [source:swissprot;acc:p53778]	Divided	9649.61	11053.5	1.14549	
471	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Subtracted	5980.15	6843.48	863.33	
472	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [source:swissprot;acc:q12904]	Subtracted	5246.01	6109.31	863.3	
472	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	Divided	9649.61	11053.5	1.14549	
473	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Subtracted	5979.95	6842.78	862.83	
473	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]	Divided	9649.61	11053.5	1.14549	
474	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Subtracted	5979.94	6842.76	862.82	
474	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [source:swissprot;acc:q96qb1]	Divided	9649.61	11053.5	1.14549	
475	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Subtracted	5979.93	6842.72	862.79	

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/