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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Gene description Rank Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 2663 to 2712 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
sperm tail protein shippo1; h-shippo 1. [source:refseq;acc:nm_053280]	2797	0.00001	0.00001	1	
spermatogenesis associated 6. [source:refseq;acc:nm_019073]	51	133	105	1.26667	
spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [source:swissprot;acc:p19623]	1471	221.412	217.199	1.0194	
spermine synthase (ec 2.5.1.22) (spermidine aminopropyltransferase) (spmsy). [source:swissprot;acc:p52788]	3118	0.00001	0.00001	1	
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [source:refseq;acc:nm_003676]	2648	213.169	213.417	1.00116	
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [source:swissprot;acc:o60906]	75	288	362	1.25694	
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	1264	171.231	167.177	1.02425	
sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [source:swissprot;acc:q9nra0]	1277	171.231	167.177	1.02425	
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [source:refseq;acc:nm_003901]	1744	219.423	222.215	1.01272	
spir-2 protein (fragment). [source:sptrembl;acc:q8wwl2]	2879	0.00001	0.00001	1	
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	393	225.719	207.072	1.09005	
splicing coactivator subunit srm300; rna binding protein; at-rich element binding factor. [source:refseq;acc:nm_016333]	2281	219.652	218.482	1.00536	
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [source:swissprot;acc:q15459]	938	220.246	212.618	1.03588	
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [source:swissprot;acc:q15428]	460	223.648	207.62	1.0772	
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [source:swissprot;acc:q12874]	937	220.246	212.618	1.03588	
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533]	265	225.217	202.459	1.11241	
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	578	224.606	210.944	1.06477	
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	317	224.445	204.044	1.09998	
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	1404	232.752	237.65	1.02104	
splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	201	240.133	211.382	1.13601	
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [source:swissprot;acc:q05519]	570	229.709	215.631	1.06529	
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [source:swissprot;acc:q01081]	2282	219.652	218.482	1.00536	
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [source:swissprot;acc:p26368]	2285	219.652	218.482	1.00536	
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [source:swissprot;acc:q07955]	636	228.639	242.258	1.05957	
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	1194	220.742	215.237	1.02558	
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [source:swissprot;acc:q12872]	824	206.068	197.471	1.04354	
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [source:swissprot;acc:p23246]	2538	190.765	191.163	1.00209	
sporulation-induced transcript 4-associated protein. [source:refseq;acc:nm_018312]	2318	194.834	195.794	1.00493	
sprouty homolog 1 (spry-1) (fragment). [source:swissprot;acc:o43609]	1002	225.167	217.922	1.03325	
sprouty homolog 2 (spry-2). [source:swissprot;acc:o43597]	1003	225.167	217.922	1.03325	
sprouty homolog 3 (spry-3). [source:swissprot;acc:o43610]	1001	225.167	217.922	1.03325	
sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	1000	225.167	217.922	1.03325	
spry domain-containing socs box protein ssb-1. [source:refseq;acc:nm_025106]	2814	0.00001	0.00001	1	
spry domain-containing socs box protein ssb-4. [source:refseq;acc:nm_080862]	2806	0.00001	0.00001	1	
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [source:swissprot;acc:q14534]	2199	193.787	195.064	1.00659	
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [source:swissprot;acc:p29508]	2420	218.2	218.984	1.00359	
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [source:refseq;acc:nm_005146]	488	225.026	209.798	1.07258	
sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	520	214.754	229.565	1.06897	
sr rich protein. [source:refseq;acc:nm_032870]	696	225.293	213.64	1.05455	
ss18-like protein 1 (syt homolog-1). [source:swissprot;acc:o75177]	2766	0.00001	0.00001	1	
ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [source:swissprot;acc:q15532]	2942	0.00001	0.00001	1	
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	1270	171.231	167.177	1.02425	
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [source:swissprot;acc:q96dr4]	1252	219.354	224.7	1.02437	
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	1247	219.354	224.7	1.02437	
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	1244	219.354	224.7	1.02437	
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	1271	171.231	167.177	1.02425	
ste20-like kinase; ste2-like kinase. [source:refseq;acc:nm_016281]	2980	0.00001	0.00001	1	
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	839	177.776	170.499	1.04268	
step ii splicing factor slu7. [source:refseq;acc:nm_006425]	752	223.463	212.875	1.04974	
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [source:refseq;acc:nm_015077]	1887	220.896	218.577	1.01061	

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/