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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1280 to 1329 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
640 intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Divided 217.67 230.596 1.05938
641 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Subtracted 244.842 232.577 12.265
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided 217.67 230.596 1.05938
642 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Subtracted 228.944 216.745 12.199
643 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Divided 217.67 230.596 1.05938
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 206.078 12.149
644 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided 217.67 230.596 1.05938
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted 226.497 214.355 12.142
645 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Divided 217.67 230.596 1.05938
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Subtracted 226.497 214.355 12.142
646 short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Divided 216.731 229.549 1.05914
single-minded homolog 1. [swissprot;acc:p81133] Subtracted 226.497 214.355 12.142
647 dynein light chain 2. [refseq;acc:nm_080677] Divided 216.731 229.549 1.05914
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Subtracted 214.257 202.125 12.132
648 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 202.132 12.125
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Divided 218.227 206.078 1.05895
649 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 233.725 220.751 1.05877
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 214.257 202.132 12.125
650 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 202.135 12.122
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Divided 228.986 216.276 1.05877
651 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 233.725 220.751
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Subtracted 214.256 202.139 12.117
652 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Divided 248.994 235.255 1.0584
653 dok-like protein. [refseq;acc:nm_024872] 216.504 204.622 1.05807
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Subtracted 214.256 202.139 12.117
654 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Divided 216.504 204.622 1.05807
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Subtracted 214.256 202.139 12.117
655 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Divided 216.504 204.622 1.05807
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Subtracted 214.256 202.14 12.116
656 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Divided 216.504 204.622 1.05807
657 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Subtracted 214.256 202.14 12.116
synapsin iii. [swissprot;acc:o14994] Divided 229.072 216.576 1.0577
658 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Subtracted 214.256 202.14 12.116
659 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Divided 229.072 216.576 1.0577
660 actin binding lim protein 2. [refseq;acc:nm_032432]
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Subtracted 214.256 202.14 12.116
661 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Divided 229.072 216.576 1.0577
662 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Subtracted 214.256 202.14 12.116
synapsin ii. [swissprot;acc:q92777] Divided 229.072 216.576 1.0577
663 mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Subtracted 214.256 202.141 12.115
664 peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Divided 229.072 216.576 1.0577
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Subtracted 214.256 202.141 12.115
665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Divided 229.072 216.576 1.0577

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/