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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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1286 to 1335 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
643 MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 206.078 12.149
644 C16orf35 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided 217.67 230.596 1.05938
CASK 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 HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]
HTATSF1 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
646 SCOC short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] 216.731 229.549 1.05914
SIM1 single-minded homolog 1. [swissprot;acc:p81133] Subtracted 226.497 214.355 12.142
647 DYNLL2 dynein light chain 2. [refseq;acc:nm_080677] Divided 216.731 229.549 1.05914
HOXA10 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Subtracted 214.257 202.125 12.132
648 HOXB9 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 202.132 12.125
MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Divided 218.227 206.078 1.05895
649 EIF4E 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
HOXA9 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 214.257 202.132 12.125
650 no value u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Divided 228.986 216.276 1.05877
HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Subtracted 214.257 202.135 12.122
651 BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Divided 233.725 220.751 1.05877
GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Subtracted 214.256 202.139 12.117
652 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Divided 248.994 235.255 1.0584
FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Subtracted 214.256 202.139 12.117
653 no value dok-like protein. [refseq;acc:nm_024872] Divided 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 DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Divided 216.504 204.622 1.05807
JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Subtracted 214.256 202.139 12.117
655 DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Divided 216.504 204.622 1.05807
GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Subtracted 214.256 202.14 12.116
656 FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Divided 216.504 204.622 1.05807
GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Subtracted 214.256 202.14 12.116
657 GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445]
SYN3 synapsin iii. [swissprot;acc:o14994] Divided 229.072 216.576 1.0577
658 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Subtracted 214.256 202.14 12.116
659 GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169]
HEY1 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 ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432]
GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Subtracted 214.256 202.14 12.116
661 GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867]
HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Divided 229.072 216.576 1.0577
662 GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Subtracted 214.256 202.14 12.116
SYN2 synapsin ii. [swissprot;acc:q92777] Divided 229.072 216.576 1.0577
663 MRRF mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
NDUFA6 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 PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9]
PEX5 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
665 HEY2 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Subtracted 214.254 202.166 12.088
666 EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 250.465 238.38 12.085
HES1 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] Divided 229.072 216.576 1.0577
667 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Subtracted 250.465 238.38 12.085
ECH1 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Divided 229.072 216.576 1.0577
668 ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]

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/