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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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 [...,...].
Network Comparison Type Value Type Gene Rank Interaction Map green network_comparison description red Filtered
Results: HTML CSV LaTeX Showing element 25776 to 25825 of 77072 in total
Network Comparison Type  : Divided
Value Type  : Squared
Filtered  : 1
Rank
Interaction Map
green
network_comparison
description
red
2582 High confidence 22137 1.04382 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] 23107
Low confidence 43754.8 1.03804 sodium/calcium exchanger 3 precursor (na(+)/ca(2+)-exchange protein 3) (fragment). [swissprot;acc:p57103] 45419.2
2583 High confidence 32578.2 1.04345 transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] 31221.5
Low confidence 44607 1.03804 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 46303.8
2584 High confidence 34958.8 1.04214 insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] 36431.8
Low confidence 42715 1.03803 transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 44339.5
2585 High confidence 29412.6 1.04194 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 28228.7
Low confidence 42710.2 1.03803 transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] 44334.6
2586 High confidence 33907 1.04087 wd repeat domain 26. [refseq;acc:nm_025160] 32575.7
Low confidence 43784.4 1.03802 hamartin (tuberous sclerosis 1 protein). [swissprot;acc:q92574] 45449.1
2587 High confidence 35252 1.04076 insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663] 36688.8
Low confidence 43354.7 1.038 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 45002
2588 High confidence 36133.4 1.04066 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] 34721.5
Low confidence 41168.6 1.03799 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] 42732.6
2589 High confidence 20854.9 1.04048 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 20043.6
Low confidence 41168.6 1.03799 molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396] 42732.6
2590 High confidence 11074.7 1.04028 son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 11520.8
Low confidence 42036.3 1.03799 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] 43633.2
2591 High confidence 15351.1 1.04 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 15965.2
Low confidence 42573.1 1.03798 protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992] 44190.1
2592 High confidence 34704 1.0399 ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] 36088.6
Low confidence 43292.4 1.03796 ubiquilin 1 isoform 1. [refseq;acc:nm_013438] 44935.7
2593 High confidence 14111.2 1.03958 adiponectin receptor 2. [refseq;acc:nm_024551] 13573.9
Low confidence 44176.4 1.03795 midasin (midas-containing protein). [swissprot;acc:q9nu22] 45853.1
2594 High confidence 36386.7 1.0395 conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] 37823.8
Low confidence 44008.9 1.03794 hsgcn1 (fragment). [sptrembl;acc:q99736] 45678.7
2595 High confidence 32433.8 1.03811 rad50 homolog isoform 1. [refseq;acc:nm_005732] 33669.7
Low confidence 42505.9 1.03794 dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 44118.4
2596 High confidence 37901.1 1.03795 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] 36515.3
Low confidence 42611.6 1.03793 phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] 44228
2597 High confidence 37901.1 1.03795 mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] 36515.3
Low confidence 41784.5 1.03793 discs, large homolog 5 (placenta and prostate dlg) (discs large protein p-dlg). [swissprot;acc:q8tdm6] 43369.2
2598 High confidence 37901.1 1.03795 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] 36515.3
Low confidence 41784.5 1.03793 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 43369.2
2599 High confidence 37901.1 1.03795 mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] 36515.3
Low confidence 43610.7 1.03792 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 45264.2
2600 High confidence 37901.1 1.03795 histone deacetylase 11 (hd11). [swissprot;acc:q96db2] 36515.3
Low confidence 43797.9 1.03792 dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] 45458.8
2601 High confidence 37901.1 1.03795 ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] 36515.3
Low confidence 44386.8 1.03791 ubiquitin-conjugating enzyme e2 h (ec 6.3.2.19) (ubiquitin-protein ligase h) (ubiquitin carrier protein h) (ubch2) (e2-20k). [swissprot;acc:p37286] 46069.4
2602 High confidence 37901.1 1.03795 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] 36515.3
Low confidence 42216.2 1.0379 zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5] 43816.4
2603 High confidence 37901.1 1.03795 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] 36515.3
Low confidence 42837.6 1.0379 tumor antigen slp-8p. [refseq;acc:nm_016516] 44461.2
2604 High confidence 37901.1 1.03795 cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] 36515.3
Low confidence 42837.6 1.0379 cop9 complex subunit 4; likely ortholog of mouse cop9 (constitutive photomorphogenic), subunit 4 (arabidopsis); cop9 (constitutive photomorphogenic, arabidopsis, homolog) subunit 4. [refseq;acc:nm_016129] 44461.2
2605 High confidence 37901.1 1.03795 mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198] 36515.3
Low confidence 42837.6 1.0379 histone-lysine n-methyltransferase, h3 lysine-79 specific (ec 2.1.1.43) (histone h3-k79 methyltransferase) (h3-k79-hmtase) (dot1-like protein). [swissprot;acc:q8tek3] 44461.2
2606 High confidence 37901.1 1.03795 mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717] 36515.3
Low confidence 42636.4 1.03789 c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] 44251.9

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/