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 4936 to 4985 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2468 phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Subtracted 5114.15 5272.92 158.77
2469 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
homeobox protein meis1. [swissprot;acc:o00470] Divided 7765.3 8004 1.03074
2470 homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]
multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Subtracted 5114.15 5272.92 158.77
2471 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] Divided 7765.3 8004 1.03074
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] Subtracted 6256.49 6415.21 158.72
2472 integral membrane protein cii-3b. [sptrembl;acc:o75609] 6256.42 6415.04 158.62
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] Divided 7765.3 8004 1.03074
2473 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]
reticulon protein 3 (neuroendocrine-specific protein-like 2) (nsp-like protein ii) (nsplii). [swissprot;acc:o95197] Subtracted 6202.78 6360.79 158.01
2474 dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 3619.07 3461.21 157.86
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Divided 7765.3 8004 1.03074
2475 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 4998.72 5155.87 157.15
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Divided 3573.66 3682.14 1.03036
2476 reticulon protein 2 (neuroendocrine-specific protein-like 1) (nsp-like protein 1) (nspli). [swissprot;acc:o75298] Subtracted 6203.05 6360.18 157.13
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Divided 3569.07 3676.7 1.03016
2477 reticulon 1 (neuroendocrine-specific protein). [swissprot;acc:q16799] Subtracted 6204.25 6360.69 156.44
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Divided 3568.84 3676.43 1.03015
2478 eh-domain containing protein 1 (testilin) (hpast1). [swissprot;acc:q9h4m9] Subtracted 6203.92 6360.25 156.33
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 3568.96 3676.57 1.03015
2479 eh-domain containing protein 3. [swissprot;acc:q9nzn3] Subtracted 6203.94 6360.25 156.31
zinc finger protein 99. [refseq;acc:nm_032164] Divided 3568.99 3676.6 1.03015
2480 eh-domain containing protein 4 (eh domain-containing protein fksg7) (hepatocellular carcinoma-associated protein 10/11). [swissprot;acc:q9h223] Subtracted 6203.95 6360.24 156.29
zinc finger protein 305. [swissprot;acc:o43309] Divided 3568.95 3676.56 1.03015
2481 eh-domain containing protein 2. [swissprot;acc:q9nzn4] Subtracted 6203.96 6360.24 156.28
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 3568.8 3676.39 1.03015
2482 sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Subtracted 6204.15 6360.27 156.12
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Divided 3568.99 3676.61 1.03015
2483 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Subtracted 3496.21 3652.28 156.07
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Divided 3568.8 3676.38 1.03014
2484 pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [swissprot;acc:p29803] Subtracted 6669.22 6824.41 155.19
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided 3568.45 3675.97 1.03013
2485 40s ribosomal protein s5. [swissprot;acc:p46782] Subtracted 3672.17 3516.98 155.19
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Divided 3568.18 3675.65 1.03012
2486 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 3626.38 3734.8 1.0299
pyruvate dehydrogenase e1 component alpha subunit, somatic form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type i). [swissprot;acc:p08559] Subtracted 6672.69 6827.51 154.82
2487 reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] 6205.14 6359.44 154.3
tfiih basal transcription factor complex helicase subunit (ec 3.6.1.-) (dna-repair protein complementing xp-d cells) (xeroderma pigmentosum group d complementing protein) (cxpd) (dna excision repair protein ercc-2). [swissprot;acc:p18074] Divided 6963.12 7170.02 1.02971
2488 heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] 5637.59 5804.47 1.0296
protein cgi-147. [swissprot;acc:q9y3e5] Subtracted 6436.43 6283 153.43
2489 thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] 6452.33 6603.94 151.61
u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Divided 5637.59 5804.47 1.0296
2490 dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial precursor (ec 2.3.1.61) (e2) (e2k). [swissprot;acc:p36957] Subtracted 6452.33 6603.94 151.61
glutathione reductase, mitochondrial precursor (ec 1.8.1.7) (gr) (grase). [swissprot;acc:p00390] Divided 6294.37 6472.9 1.02836
2491 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Subtracted 3677.53 3526.65 150.88
hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] Divided 3436.65 3531.96 1.02773
2492 growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257]
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Subtracted 3677.53 3526.65 150.88
2493 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522] Divided 3436.65 3531.96 1.02773

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/