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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Hugo description Gene red Rank Value Type Network Comparison Type Interaction Map green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 3228 in total
Hugo  : no value
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
red
Rank
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] 186.741 1038 181.041 1.03148
15 kda selenoprotein precursor. [swissprot;acc:o60613] 214.522 1948 212.432 1.00984
17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] 211.449 1051 217.998 1.03097
26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 217.241 2316 218.311 1.00493
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 0.00001 2756 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] 196.008 1852 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] 219.423 1745 222.215 1.01272
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 242.339 304 266.986 1.1017
40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] 242.238 387 264.11 1.09029
40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 241.625 344 265.136 1.0973
40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 454 226.578 1.07779
40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 229.442 1102 235.974 1.02847
40s ribosomal protein s28. [swissprot;acc:p25112] 200.343 1982 198.427 1.00966
40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 277 267.642 1.10665
40s ribosomal protein s3a. [swissprot;acc:p49241] 225.689 867 234.674 1.03981
40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 288 266.078 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] 224.244 789 234.511 1.04578
60s acidic ribosomal protein p1. [swissprot;acc:p05386] 229.171 898 238.048 1.03874
60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 357 266.661 1.09683
60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 356 266.796 1.09684
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 338 267.528 1.0983
60s ribosomal protein l12. [swissprot;acc:p30050] 337 267.527
60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 242.153 306 266.673 1.10126
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 281 267.335 1.10557
60s ribosomal protein l18a. [swissprot;acc:q02543] 234.025 860 224.958 1.04031
60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 1054 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] 199.129 2205 200.413 1.00645
60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 293 265.717 1.10356
60s ribosomal protein l23a. [swissprot;acc:p29316] 241.884 323 265.945 1.09947
60s ribosomal protein l37a. [swissprot;acc:p12751] 0.00001 2959 0.00001 1
60s ribosomal protein l39. [swissprot;acc:p02404] 234.025 859 224.958 1.04031
60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 297 259.984 1.1029
60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 341 263.798 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] 215.799 2019 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] 222.134 1595 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] 199.928 2046 198.24 1.00851
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 211.449 1049 217.998 1.03097
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 348 265.696 1.09728
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 218.402 1186 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] 192.871 2428 193.555 1.00355
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 209.649 1189 204.406 1.02565
alpha-nac protein. [sptrembl;acc:q9h009] 212.028 889 204.053 1.03908
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 219.354 1249 224.7 1.02437
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] 237.302 248 212.41 1.11719
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 217.99 1111 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] 200.158 2291 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] 229.072 658 216.576 1.0577
ataxin 2-binding protein. [swissprot;acc:q9nwb1] 218.514 1704 215.577 1.01362
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 228.105 1059 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/