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 Rank Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
526 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Divided 10639.9 12117.4 1.13886
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9] Subtracted 5207.78 6010.45 802.67
527 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 4775.11 5438.18 1.13886
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Subtracted 4700.42 5492.63 792.21
528 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Divided 10635.3 12111.4 1.13879
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Subtracted 5244.71 6036.27 791.56
529 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Divided 8600.02 9792.49 1.13866
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Subtracted 5244.88 6036.38 791.5
530 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Divided 8600.02 9792.49 1.13866
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Subtracted 5246.38 6037.37 790.99
531 prohibitin. [swissprot;acc:p35232] 5773.45 6563.69 790.24
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Divided 4651.88 5296.78 1.13863
532 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Subtracted 5773.45 6563.69 790.24
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Divided 4651.88 5296.78 1.13863
533 epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099] Subtracted 11785.4 10995.3 790.1
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Divided 4651.88 5296.78 1.13863
534 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Subtracted 5233.86 6022.6 788.74
535 translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Divided 10603.5 12069.5 1.13826
vinculin (metavinculin). [swissprot;acc:p18206] Subtracted 5958.23 6743.37 785.14
536 calsyntenin-1 precursor. [swissprot;acc:o94985] Divided 10603.5 12069.5 1.13826
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Subtracted 6227.87 7012.9 785.03
537 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 6228.39 7013.19 784.8
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] Divided 10603.5 12069.5 1.13826
538 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Subtracted 6228.39 7013.19 784.8
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Divided 10603.5 12069.4 1.13825
539 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Subtracted 6228.39 7013.19 784.8
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Divided 10603.5 12069.4 1.13825
540 gk001 protein. [refseq;acc:nm_020198]
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Subtracted 6228.39 7013.19 784.8
541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Divided 10600.3 12065.2 1.13819
limkain b1. [refseq;acc:nm_019081] Subtracted 6228.39 7013.19 784.8
542 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2]
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Divided 3889.27 4426.74 1.13819
543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Subtracted 6228.39 7013.19 784.8
544 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886]
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Divided 3889.27 4426.74 1.13819
545 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Subtracted 6228.39 7013.19 784.8
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] Divided 3889.27 4426.74 1.13819
546 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Subtracted 6228.39 7013.19 784.8
zinc finger protein t86. [swissprot;acc:o00488] Divided 4052.77 4612.54 1.13812
547 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Subtracted 6228.39 7013.19 784.8
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Divided 5291.92 6020.19 1.13762
548 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] 8268.19 9405.85 1.13759
disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Subtracted 6228.39 7013.19 784.8
549 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Divided 5865.79 6671.23 1.13731
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Subtracted 6228.42 7013.21 784.79
550 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 6228.97 7013.53 784.56
prohibitin. [swissprot;acc:p35232] Divided 5773.45 6563.69 1.13687

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/