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

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Showing element 2680 to 2729 of 3228 in total

Value Type

: Measured
Network Comparison Type

: Divided
Interaction Map

: High confidence
Filtered

: 1

description	Rank	red	green	network_comparison
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	207	4771.21	5961.43	1.24946
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427]	1224	4331.35	4700.91	1.08532
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	395	4532.73	5269.33	1.16251
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519]	1976	5939.85	6294.91	1.05978
splicing factor u2af 35 kda subunit (u2 auxiliary factor 35 kda subunit) (u2 snrnp auxiliary factor small subunit). [swissprot;acc:q01081]	1959	5448.35	5777.35	1.06039
splicing factor u2af 65 kda subunit (u2 auxiliary factor 65 kda subunit) (u2 snrnp auxiliary factor large subunit) (hu2af(65)). [swissprot;acc:p26368]	1961	5448.35	5777.35	1.06039
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]	2549	4725.79	4824.4	1.02087
splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152]	889	5903.18	6506.32	1.10217
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]	2267	9146.11	8743.98	1.04599
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). [swissprot;acc:p23246]	2070	10178.5	9638.08	1.05607
sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312]	1512	7234.61	7771.58	1.07422
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]	676	5549.2	6215.42	1.12006
sprouty homolog 2 (spry-2). [swissprot;acc:o43597]	677
sprouty homolog 3 (spry-3). [swissprot;acc:o43610]	675
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	674
spry domain-containing socs box protein ssb-1. [refseq;acc:nm_025106]	2814	0.00001	0.00001	1
spry domain-containing socs box protein ssb-4. [refseq;acc:nm_080862]	2806	0.00001	0.00001	1
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534]	2166	6952.66	7315.06	1.05212
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]	1694	5767.69	6165.87	1.06904
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. [refseq;acc:nm_005146]	310	4909.79	5878.79	1.19736
sqv-7-like protein (fragment). [sptrembl;acc:o95454]	2222	5309.65	5066.82	1.04793
sr rich protein. [refseq;acc:nm_032870]	2257	6245.32	6534.23	1.04626
ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]	2766	0.00001	0.00001	1
ssxt protein (synovial sarcoma, translocated to x chromosome) (syt protein). [swissprot;acc:q15532]	2942	0.00001	0.00001	1
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	478	9649.61	11053.5	1.14549
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	1870	6076.66	6463.13	1.0636
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	1865		6463.12
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	1862		6463.13
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	479	9649.61	11053.5	1.14549
ste20-like kinase; ste2-like kinase. [refseq;acc:nm_016281]	2980	0.00001	0.00001	1
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	486	10908.6	12491.8	1.14513
step ii splicing factor slu7. [refseq;acc:nm_006425]	661	5575.18	6254.85	1.12191
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077]	1621	5520.36	5911.98	1.07094
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	905	10230.1	11256.2	1.1003
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	875	10263.8	11318.6	1.10277
steroidogenic factor 1 (stf-1) (sf-1) (steroid hormone receptor ad4bp) (fushi tarazu factor homolog 1). [swissprot;acc:q13285]	2972	0.00001	0.00001	1
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	868	5595.65	6173.23	1.10322
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956]	712	5317.78	5944.25	1.11781
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772]	711	5317.78	5944.25	1.11781
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861]	2350	6480.27	6765.81	1.04406
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]	1804	4980.54	5307.81	1.06571
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]	1805	4980.54	5307.81	1.06571
stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	2607	6380.61	6476.19	1.01498
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	2614	6380.61	6476.19	1.01498
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	957	4483.26	4917.77	1.09692
succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor (integral membrane protein cii-3) (qps1) (qps-1) (succinate dehydrogenase complex subunit c) (succinate-ubiquinone oxidoreductase cytochrome b large subunit) (cybl). [swissprot;acc:q99643]	2510	6256.49	6415.21	1.02537
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	537	10603.5	12069.5	1.13826
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	2452	6042.36	6237.19	1.03224
succinate dehydrogenase [ubiquinone] iron-sulfur protein, mitochondrial precursor (ec 1.3.5.1) (ip) (iron-sulfur subunit of complex ii). [swissprot;acc:p21912]	2505	6237.83	6400.74	1.02612
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7]	2504	5996.06	6155.81	1.02664

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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/