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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2551 to 2600 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
638 Squared homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 32183.5 37955.7 1.17935
Rooted transcription factor hes-1 (hairy and enhancer of split 1) (hairy- like) (hhl) (hairy homolog). [swissprot;acc:q14469] 60.0129 64.7371 1.07872
639 Measured nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] 7753.59 8728.13 1.12569
Ranked nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 217.67 230.596 1.05938
Squared bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 17618.8 20776.8 1.17924
Rooted delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] 60.0129 64.7371 1.07872
640 Measured glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 4811.02 5414.64 1.12547
Ranked intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] 217.67 230.596 1.05938
Squared nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] 22848.5 26941.5 1.17914
Rooted actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] 60.0129 64.7371 1.07872
641 Measured peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 4810.85 5414.21 1.12542
Ranked pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 217.67 230.596 1.05938
Squared u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 18364.9 21653.8 1.17909
Rooted synapsin i (brain protein 4.1). [swissprot;acc:p17600] 60.0129 64.7371 1.07872
642 Measured atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] 4810.85 5414.23 1.12542
Ranked intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] 217.67 230.596 1.05938
Squared 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 16123.9 19009.7 1.17898
Rooted ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 64.4857 69.5606 1.0787
643 Measured polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] 4810.85 5414.23 1.12542
Ranked hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] 217.67 230.596 1.05938
Squared 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 16126.5 19012.6 1.17897
Rooted autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 87.4586 81.0798 1.07867
644 Measured cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 4810.85 5414.22 1.12542
Ranked cgthba protein (-14 gene protein). [swissprot;acc:q12980] 217.67 230.596 1.05938
Squared 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 16156.3 19046 1.17886
Rooted rna polymerase i associated factor 53. [refseq;acc:nm_022490] 51.1896 47.4617 1.07855
645 Measured glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 4810.71 5413.89 1.12538
Ranked hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] 217.67 230.596 1.05938
Squared nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 22722.5 26786.5 1.17885
Rooted preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] 63.1463 68.1044 1.07852
646 Measured fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 4019.88 4522.61 1.12506
Ranked short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] 216.731 229.549 1.05914
Squared 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 27898 32866.2 1.17808
Rooted dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] 63.1463 68.1044 1.07852
647 Measured short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 5167.88 4594.43 1.12481
Ranked dynein light chain 2. [refseq;acc:nm_080677] 216.731 229.549 1.05914
Squared cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 33384.2 39324.9 1.17795
Rooted calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 64.5657 69.6237 1.07834
648 Measured splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] 5248.07 5901.72 1.12455
Ranked methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 218.227 206.078 1.05895
Squared retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 29174 34363.5 1.17788
Rooted swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] 64.5685 69.6269 1.07834
649 Measured splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] 5248.07 5901.72 1.12455
Ranked 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
Squared retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 29173.8 34362.7 1.17786
Rooted grancalcin. [swissprot;acc:p28676] 64.5659 69.624 1.07834
650 Measured golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 8362.81 9402.7 1.12435
Ranked u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] 228.986 216.276 1.05877
Squared chromodomain y-like protein 2. [refseq;acc:nm_152342] 29016.1 34169.2 1.17759
Rooted sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 64.566 69.6241 1.07834

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/