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 Hugo description Rank Value Type Interaction Map red green Network Comparison Type Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
Hugo  : no value
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] 1038 186.741 181.041 1.03148
15 kda selenoprotein precursor. [swissprot;acc:o60613] 1948 214.522 212.432 1.00984
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 1051 211.449 217.998 1.03097
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 2316 217.241 218.311 1.00493
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 2756 0.00001 0.00001 1
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060] 2802
3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 1852 196.008 198.154 1.01095
4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 1745 219.423 222.215 1.01272
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 304 242.339 266.986 1.1017
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 387 242.238 264.11 1.09029
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 344 241.625 265.136 1.0973
40s ribosomal protein s26. [swissprot;acc:p02383] 454 210.224 226.578 1.07779
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1102 229.442 235.974 1.02847
40s ribosomal protein s28. [swissprot;acc:p25112] 1982 200.343 198.427 1.00966
40s ribosomal protein s29. [swissprot;acc:p30054] 277 241.849 267.642 1.10665
40s ribosomal protein s3a. [swissprot;acc:p49241] 867 225.689 234.674 1.03981
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 288 240.758 266.078 1.10517
40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 789 224.244 234.511 1.04578
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 898 229.171 238.048 1.03874
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 357 243.12 266.661 1.09683
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 356 243.24 266.796 1.09684
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 338 243.583 267.528 1.0983
60s ribosomal protein l12. [swissprot;acc:p30050] 337 267.527
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 306 242.153 266.673 1.10126
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 281 241.808 267.335 1.10557
60s ribosomal protein l18a. [swissprot;acc:q02543] 860 234.025 224.958 1.04031
60s ribosomal protein l21. [swissprot;acc:p46778] 1054 223.958 217.263 1.03082
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 2205 199.129 200.413 1.00645
60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 293 240.782 265.717 1.10356
60s ribosomal protein l23a. [swissprot;acc:p29316] 323 241.884 265.945 1.09947
60s ribosomal protein l37a. [swissprot;acc:p12751] 2959 0.00001 0.00001 1
60s ribosomal protein l39. [swissprot;acc:p02404] 859 234.025 224.958 1.04031
60s ribosomal protein l7. [swissprot;acc:p18124] 297 235.727 259.984 1.1029
60s ribosomal protein l9. [swissprot;acc:p32969] 341 240.243 263.798 1.09805
acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] 2019 215.799 213.865 1.00904
adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 1595 222.134 225.731 1.01619
adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367] 2046 199.928 198.24 1.00851
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 1049 211.449 217.998 1.03097
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 348 242.14 265.696 1.09728
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 1186 218.402 212.904 1.02582
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 2428 192.871 193.555 1.00355
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 1189 209.649 204.406 1.02565
alpha-nac protein. [sptrembl;acc:q9h009] 889 212.028 204.053 1.03908
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 1249 219.354 224.7 1.02437
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 248 237.302 212.41 1.11719
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 1111 217.99 212.123 1.02766
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] 2291 200.158 201.213 1.00527
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 658 229.072 216.576 1.0577
ataxin 2-binding protein. [swissprot;acc:q9nwb1] 1704 218.514 215.577 1.01362
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 1059 228.105 221.293 1.03078

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
- Hugo is the HGNC identifier if it exists
- 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/