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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2477 to 2526 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
620 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Divided High confidence 214.256 202.14 1.05994
microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Subtracted 206.274 218.792 12.518
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Divided Low confidence 203.68 197.868 1.02937
Subtracted 5.812
621 60s acidic ribosomal protein p2. [swissprot;acc:p05387] High confidence 231.92 244.435 12.515
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Divided 214.256 202.14 1.05994
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Low confidence 203.68 197.868 1.02937
Subtracted 5.812
622 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Divided High confidence 214.256 202.14 1.05994
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] Low confidence 204.479 198.65 1.02934
probable rna-binding protein kiaa0682. [swissprot;acc:q9y4c8] Subtracted 206.001 200.193 5.808
synapsin iii. [swissprot;acc:o14994] High confidence 229.072 216.576 12.496
623 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] Divided 214.256 202.14 1.05994
jumonji protein. [swissprot;acc:q92833] Low confidence 207.726 201.813 1.0293
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Subtracted 204.369 198.564 5.805
624 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] High confidence 229.072 216.576 12.496
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Divided 214.256 202.139 1.05994
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Low confidence 205.16 199.322 1.02929
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Subtracted 204.369 198.564 5.805
625 actin binding lim protein 2. [refseq;acc:nm_032432] High confidence 229.072 216.576 12.496
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Divided Low confidence 203.853 198.057 1.02926
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] High confidence 214.256 202.14 1.05994
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Subtracted Low confidence 204.369 198.564 5.805
626 gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Divided High confidence 214.256 202.14 1.05994
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Subtracted 229.072 216.576 12.496
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Divided Low confidence 204.239 198.436 1.02924
Subtracted 5.803
627 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] 204.234 198.433 5.801
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Divided High confidence 214.256 202.139 1.05994
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Low confidence 204.369 198.564 1.02923
synapsin ii. [swissprot;acc:q92777] Subtracted High confidence 229.072 216.576 12.496
628 cullin homolog 1 (cul-1). [swissprot;acc:q13616] Low confidence 203.853 198.057 5.796
gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Divided High confidence 214.256 202.14 1.05994
histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106] Low confidence 204.234 198.433 1.02923
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Subtracted High confidence 229.072 216.576 12.496
629 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] Divided 214.256 202.14 1.05994
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Subtracted Low confidence 204.242 198.448 5.794
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] High confidence 229.072 216.576 12.496
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Divided Low confidence 204.369 198.564 1.02923
630 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Subtracted 204.242 198.448 5.794
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] High confidence 229.072 216.576 12.496
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Divided 214.256 202.141 1.05993
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Low confidence 204.369 198.564 1.02923
631 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 204.242 198.448 1.0292
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] High confidence 214.256 202.141 1.05993
similar to s. cerevisiae ssm4. [refseq;acc:nm_005885] Subtracted Low confidence 207.662 201.876 5.786
transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] High confidence 229.072 216.576 12.496
632 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided Low confidence 204.242 198.448 1.0292

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/