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 green Value Type Rank Filtered Network Comparison Type network_comparison description Interaction Map red
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 38536 in total
Network Comparison Type  : Divided
green
Value Type
Rank
Filtered
network_comparison
description
Interaction Map
red
26.7764 Rooted 497 0 1.05597 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Low confidence 28.2752
26.7806 375 1.0399 germ cell-less. [refseq;acc:nm_022471] High confidence 27.8491
26.8089 467 1.01107 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 26.5153
26.8141 357 1.04688 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] 28.0711
26.8253 206 1.12901 testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Low confidence 30.2859
26.8271 207 1.12898 testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] 30.2872
26.828 66 1.4185 elongation of very long chain fatty acids protein 2. [swissprot;acc:q9nxb9] 18.9129
26.8335 185 1.14291 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] High confidence 30.6682
26.8342 183 1.14342 ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Low confidence 30.6827
26.838 481 1.06061 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 25.3044
26.8697 273 1.09235 vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] High confidence 24.598
26.8784 209 1.12826 chromodomain y-like protein 2. [refseq;acc:nm_152342] Low confidence 30.3257
26.8952 582 1.03818 60s ribosomal protein l9. [swissprot;acc:p32969] 25.906
26.9186 227 1.1178 jm5 protein. [refseq;acc:nm_007075] 24.0817
26.9306 312 1.0652 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] High confidence 25.2821
313 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]
26.9488 182 1.14353 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Low confidence 30.8167
26.9708 501 1.05422 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 25.5837
26.9929 320 1.06334 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] High confidence 28.7027
27.0433 412 1.0793 dead-box protein 3, y-chromosomal. [swissprot;acc:o15523] Low confidence 29.1877
518 1.05095 60s ribosomal protein l21. [swissprot;acc:p46778] 25.7322
519 solute carrier family 26 member 6 (pendrin-like protein 1) (pendrin l1). [swissprot;acc:q9bxs9]
27.0924 73 1.3649 nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483] 19.8494
27.1011 614 1.03299 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 27.9952
27.182 655 1.02686 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 27.912
27.1942 836 1.00023 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 27.188
27.2079 415 1.07835 nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 29.3397
27.2466 748 1.01359 60s ribosomal protein l12. [swissprot;acc:p30050] 26.8813
27.2528 746 1.01368 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 26.8851
27.2559 744 1.01372 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 26.8871
27.2805 Squared 5 1 11.544 junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 314.926
6 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]
7 sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]
8 db83 protein. [swissprot;acc:p57088]
27.2883 Rooted 609 0 1.03345 dna-crosslink repair gene snm1. [refseq;acc:nm_014881] Low confidence 28.2011
610 t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283]
27.3392 828 1.00128 ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] 27.3043
27.3399 599 1.03553 ubiquitin and ribosomal protein s27a precursor; ubiquitin carboxyl extension protein 80; 40s ribosomal protein s27a; ubiquitin; ubiquitin-cep80. [refseq;acc:nm_002954] 26.4018
27.399 416 1.07826 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 25.4103
27.4107 713 1.01833 rna binding protein. [refseq;acc:nm_032509] 26.9172
27.4116 256 1.10462 glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434] High confidence 24.8155
27.4612 587 1.03756 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Low confidence 28.4926
27.5154 127 1.21624 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 33.4653
27.6157 524 1.05043 ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] 26.2898
27.6396 467 1.06384 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5] 25.9809
27.662 635 1.02912 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 28.4675
27.6672 516 1.05127 integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 26.3179
27.6684 766 1.01076 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 27.3739
27.6917 449 1.06742 protein phosphatase methylesterase-1. [refseq;acc:nm_016147] 25.9427
27.7265 248 1.10868 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] High confidence 30.7397

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/