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 4958 to 5007 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2479 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
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Subtracted 5534.46 5684.97 150.51
2494 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 5964.17 6113.96 149.79
hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Divided 3436.65 3531.96 1.02773
2495 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Subtracted 5964.17 6113.96 149.79
growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Divided 3436.65 3531.96 1.02773
2496 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] Subtracted 5964.17 6113.96 149.79
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Divided 5534.46 5684.97 1.0272
2497 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 7002.3 7192.25 1.02713
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Subtracted 5964.17 6113.96 149.79
2498 helicase (fragment). [sptrembl;acc:q92771] Divided 7002.03 7191.88 1.02711
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Subtracted 6141.97 6291.08 149.11
2499 centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] Divided 8186.02 7971.27 1.02694
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Subtracted 3669.57 3520.86 148.71
2500 presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] 4751.74 4900.37 148.63
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Divided 3804.53 3705.05 1.02685
2501 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 6562.71 6738.23 1.02675
gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Subtracted 4751.74 4900.37 148.63
2502 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367] Divided 6562.71 6738.23 1.02675
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Subtracted 4751.74 4900.37 148.63
2503 succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] Divided 5996.06 6155.81 1.02664
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Subtracted 3690.79 3543.33 147.46
2504 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] Divided 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/