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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Network Comparison Type Gene Value Type red Rank description green Interaction Map network_comparison Filtered
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 29840 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
red
Rank
description
green
network_comparison
228.496 1670 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] 231.729 1.01415
1671 nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]
1672 ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153]
1673 dna replication licensing factor mcm5 (cdc46 homolog) (p1-cdc46). [swissprot;acc:p33992]
1674 survival of motor neuron protein-interacting protein 1 (smn- interacting protein 1) (component of gems 2) (gemin2). [swissprot;acc:o14893]
1675 probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]
228.513 1467 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] 232.983 1.01956
228.523 1688 transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] 231.703 1.01392
228.563 819 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 238.668 1.04421
228.599 845 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 219.399 1.04193
228.611 1620 transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 225.185 1.01521
1621 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
1622 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]
1623 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
228.639 635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 242.258 1.05957
636 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
637 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
638 sorting nexin 17. [swissprot;acc:q15036]
228.642 1359 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 223.726 1.02197
228.644 1362 peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 223.736 1.02194
1365 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]
1368 polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]
1369 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]
228.646 1371 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 223.744 1.02191
228.654 1660 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] 231.933 1.01434
228.78 763 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 218.091 1.04901
228.932 1766 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 231.732 1.01223
228.944 677 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] 216.745 1.05628
228.953 977 prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] 221.421 1.03402
978 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
228.986 650 u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 216.276 1.05877
229.045 765 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 218.343 1.04901
229.072 657 synapsin iii. [swissprot;acc:o14994] 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]
659 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]
660 actin binding lim protein 2. [refseq;acc:nm_032432]
661 hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571]
662 synapsin ii. [swissprot;acc:q92777]
663 mitochondrial ribosome recycling factor. [refseq;acc:nm_138777]
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]
665 hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259]
666 transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469]
667 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011]
668 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]
669 synapsin i (brain protein 4.1). [swissprot;acc:p17600]
229.102 2066 proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 231.001 1.00829
229.116 1009 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 221.823 1.03288
229.171 898 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 238.048 1.03874
899 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
900 thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]

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/