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.


Navigation/Query Panel:
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 description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1625 to 1674 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
813 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Divided 221.785 212.386 1.04425
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Subtracted 219.399 228.599 9.2
814 synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Divided 221.785 212.386 1.04425
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Subtracted 234.96 244.155 9.195
815 eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 237.223 246.354 9.131
syntaxin 1b. [swissprot;acc:q15531] Divided 221.785 212.386 1.04425
816 eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Subtracted 237.223 246.354 9.131
melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Divided 221.785 212.386 1.04425
817 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Subtracted 101.613 110.689 9.076
818 60s ribosomal protein l39. [swissprot;acc:p02404] 224.958 234.025 9.067
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 161.452 168.592 1.04422
819 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted 224.958 234.025 9.067
dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Divided 238.668 228.563 1.04421
820 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 224.958 234.025 9.067
mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Divided 231.501 221.716 1.04413
821 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 224.958 234.025 9.067
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Divided 231.453 221.676 1.0441
822 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 232.805 243.067 1.04408
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Subtracted 46 55 9
823 myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
transcription factor iib. [refseq;acc:nm_013242] Divided 197.471 206.068 1.04354
824 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] Subtracted 46 55 9
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Divided 197.471 206.068 1.04354
825 40s ribosomal protein s3a. [swissprot;acc:p49241] Subtracted 234.674 225.689 8.985
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Divided 197.614 206.214 1.04352
826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 213.912 223.186 1.04335
dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Subtracted 239.785 230.811 8.974
827 jm1 protein. [refseq;acc:nm_014008] 210.806 219.762 8.956
loh1cr12. [refseq;acc:nm_058169] Divided 220.579 230.087 1.0431
828 ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 144.041 135.087 8.954
unr protein. [swissprot;acc:o75534] Divided 220.579 230.087 1.0431
829 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Subtracted 261.821 252.873 8.948
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Divided 130.259 135.844 1.04288
830 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 222.222 231.734 1.0428
wd-repeat protein 3. [swissprot;acc:q9unx4] Subtracted 234.96 243.896 8.936
831 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 238.048 229.171 8.877
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Divided 222.222 231.734 1.0428
832 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Subtracted 238.048 229.171 8.877
833 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Divided 222.222 231.734 1.0428
thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Subtracted 238.048 229.171 8.877
834 60s ribosomal protein l8. [swissprot;acc:p25120] Divided 222.222 231.734 1.0428
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Subtracted 239.632 230.768 8.864
835 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Divided 222.222 231.734 1.0428
heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] Subtracted 233.272 224.413 8.859
836 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Divided 222.222 231.734 1.0428
u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Subtracted 233.272 224.413 8.859
837 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Divided 222.222 231.734 1.0428
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Subtracted 228.762 237.62 8.858

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/