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 151 to 200 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
151	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	4578.09	5939.91	1.29746	
152	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	23693.7	18263	1.29736	
153	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	23693.7	18263	1.29736	
154	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	23693.7	18263	1.29736	
155	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	23693.7	18263	1.29736	
156	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	23693.7	18263	1.29736	
157	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	23693.7	18263	1.29736	
158	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	23693.7	18263	1.29736	
159	necdin. [source:swissprot;acc:q99608]	23693.7	18263	1.29736	
160	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	23693.7	18263	1.29736	
161	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	23693.7	18263	1.29736	
162	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	23693.7	18263	1.29736	
163	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	23693.7	18263	1.29736	
164	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	23693.7	18263	1.29736	
165	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	23693.7	18263	1.29736	
166	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	23693.7	18263	1.29736	
167	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	23693.7	18263	1.29736	
168	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	23693.7	18263	1.29736	
169	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	23693.7	18263	1.29736	
170	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	23693.7	18263	1.29736	
171	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	23693.7	18263	1.29736	
172	trophinin. [source:swissprot;acc:q12816]	23693.7	18263	1.29736	
173	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	4579.34	5940.64	1.29727	
174	mad protein (max dimerizer). [source:swissprot;acc:q05195]	4455.95	5774.03	1.2958	
175	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	4456.67	5773.77	1.29553	
176	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	4456.93	5773.67	1.29544	
177	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	4457.06	5773.63	1.29539	
178	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	21591.5	27904.5	1.29238	
179	myosin vc (myosin 5c). [source:swissprot;acc:q9nqx4]	21591.5	27904.5	1.29238	
180	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [source:swissprot;acc:q9y4i1]	21591.5	27904.5	1.29238	
181	eukaryotic translation initiation factor 4 gamma, 3. [source:refseq;acc:nm_003760]	4068.56	5252.6	1.29102	
182	rna-binding protein. [source:refseq;acc:nm_019027]	4069.83	5252.17	1.29051	
183	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [source:refseq;acc:nm_014576]	4069.83	5252.17	1.29051	
184	ns1-associated protein 1. [source:refseq;acc:nm_006372]	4069.83	5252.17	1.29051	
185	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	4069.83	5252.17	1.29051	
186	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	4071.1	5251.75	1.29001	
187	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	4569.48	5885.79	1.28807	
188	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [source:refseq;acc:nm_178862]	4571.89	5864.86	1.28281	
189	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	4571.89	5864.86	1.28281	
190	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [source:swissprot;acc:p39656]	4571.89	5864.86	1.28281	
191	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	4638.1	5923.4	1.27712	
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	17757.5	14008	1.26767	
193	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	17756.5	14007.3	1.26766	
194	cyclin g2. [source:swissprot;acc:q16589]	17738.6	13995.7	1.26743	
195	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	17738.5	13995.6	1.26743	
196	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	17738.5	13995.7	1.26742	
197	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	17738.5	13995.7	1.26742	
198	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	17710.9	13977.7	1.26708	
199	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	4916.8	3888.18	1.26455	
200	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [source:swissprot;acc:p56945]	4808.79	6074.21	1.26315	

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/