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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 2130 to 2179 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
2130	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	221.248	222.788	1.00696	
2131	gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [source:swissprot;acc:p30793]	226.277	227.851	1.00696	
2132	protein sck (fragment). [source:swissprot;acc:p98077]	221.248	222.788	1.00696	
2133	orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	207.74	206.305	1.00696	
2134	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [source:swissprot;acc:p22626]	221.248	222.788	1.00696	
2135	nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	207.743	206.308	1.00696	
2136	ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	221.248	222.788	1.00696	
2137	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	221.248	222.788	1.00696	
2138	solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [source:swissprot;acc:q9ugh3]	221.248	222.788	1.00696	
2139	dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [source:swissprot;acc:o14733]	221.248	222.788	1.00696	
2140	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [source:swissprot;acc:p33240]	161.547	162.665	1.00692	
2141	orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	207.765	206.343	1.00689	
2142	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	206.443	207.864	1.00688	
2143	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	206.442	207.862	1.00688	
2144	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	206.443	207.864	1.00688	
2145	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [source:swissprot;acc:q9y2j2]	206.442	207.862	1.00688	
2146	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	206.443	207.864	1.00688	
2147	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	206.442	207.862	1.00688	
2148	ba271b5.1 (similar to ribosomal protein s7). [source:sptrembl;acc:q9h1s9]	217.871	219.366	1.00686	
2149	40s ribosomal protein s7 (s8). [source:swissprot;acc:p23821]	217.871	219.366	1.00686	
2150	26s proteasome-associated pad1 homolog. [source:refseq;acc:nm_005805]	217.871	219.366	1.00686	
2151	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [source:swissprot;acc:p04114]	217.871	219.366	1.00686	
2152	vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [source:swissprot;acc:p19065]	200.063	198.71	1.00681	
2153	vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [source:swissprot;acc:p23763]	200.063	198.71	1.00681	
2154	vesicule-associated membrane protein 4 (vamp-4). [source:swissprot;acc:o75379]	200.063	198.71	1.00681	
2155	cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [source:swissprot;acc:o14735]	200.063	198.71	1.00681	
2156	adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [source:swissprot;acc:q8n6t3]	200.063	198.71	1.00681	
2157	vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [source:swissprot;acc:q15836]	200.063	198.71	1.00681	
2158	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [source:swissprot;acc:p56470]	206.401	207.796	1.00676	
2159	mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [source:swissprot;acc:p27361]	215.921	214.474	1.00675	
2160	ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [source:swissprot;acc:p51812]	215.925	214.481	1.00673	
2161	calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [source:swissprot;acc:q13555]	215.925	214.481	1.00673	
2162	calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [source:swissprot;acc:q13557]	215.925	214.481	1.00673	
2163	mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [source:swissprot;acc:o95382]	215.925	214.481	1.00673	
2164	signal-induced proliferation-associated 1-like 1. [source:refseq;acc:nm_015556]	215.925	214.481	1.00673	
2165	ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [source:swissprot;acc:q15418]	215.925	214.481	1.00673	
2166	atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [source:swissprot;acc:p28288]	215.925	214.481	1.00673	
2167	glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [source:swissprot;acc:q92947]	215.925	214.481	1.00673	
2168	mitogen-activated protein kinase 1 (ec 2.7.1.37) (extracellular signal-regulated kinase 2) (erk-2) (mitogen-activated protein kinase 2) (map kinase 2) (mapk 2) (p42-mapk) (ert1). [source:swissprot;acc:p28482]	215.929	214.486	1.00673	
2169	histidine ammonia-lyase (ec 4.3.1.3) (histidase). [source:swissprot;acc:p42357]	215.925	214.481	1.00673	
2170	ribosomal protein s6 kinase alpha 6 (ec 2.7.1.37) (s6k-alpha 6) (90 kda ribosomal protein s6 kinase 6) (p90-rsk 6) (ribosomal s6 kinase 4) (rsk-4) (pp90rsk4). [source:swissprot;acc:q9uk32]	215.925	214.481	1.00673	
2171	ribosomal protein s6 kinase alpha 2 (ec 2.7.1.37) (s6k-alpha 2) (90 kda ribosomal protein s6 kinase 2) (p90-rsk 2) (ribosomal s6 kinase 3) (rsk-3) (pp90rsk3). [source:swissprot;acc:q15349]	215.925	214.481	1.00673	
2172	calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [source:swissprot;acc:q9uqm7]	215.925	214.481	1.00673	
2173	calcium/calmodulin-dependent protein kinase type ii beta chain (ec 2.7.1.123) (cam-kinase ii beta chain) (cam kinase ii beta subunit) (camk-ii beta subunit). [source:swissprot;acc:q13554]	215.925	214.481	1.00673	
2174	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	215.925	214.481	1.00673	
2175	26s proteasome non-atpase regulatory subunit 2 (26s proteasome regulatory subunit s2) (26s proteasome subunit p97) (tumor necrosis factor type 1 receptor associated protein 2) (55.11 protein). [source:swissprot;acc:q13200]	210.209	208.808	1.00671	
2176	serine/threonine-protein kinase plk (ec 2.7.1.-) (plk-1) (serine- threonine protein kinase 13) (stpk13). [source:swissprot;acc:p53350]	218.089	216.64	1.00669	
2177	peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [source:swissprot;acc:q9nr77]	210.961	209.563	1.00667	
2178	heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [source:swissprot;acc:p54652]	210.961	209.563	1.00667	
2179	heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [source:swissprot;acc:p08107]	210.961	209.563	1.00667	

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/