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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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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green 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
Hugo
description
Network Comparison Type
red
green
network_comparison
813 C20orf3 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9] Divided 212.386 221.785 1.04425
LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Subtracted 228.599 219.399 9.2
814 SNAP29 synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Divided 212.386 221.785 1.04425
TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] Subtracted 244.155 234.96 9.195
815 EIF3G eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 246.354 237.223 9.131
STX1B syntaxin 1b. [swissprot;acc:q15531] Divided 212.386 221.785 1.04425
816 EIF3A eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Subtracted 246.354 237.223 9.131
MRPL28 melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084] Divided 212.386 221.785 1.04425
817 CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Subtracted 110.689 101.613 9.076
RFXANK dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593] Divided 212.386 221.785 1.04425
818 no value 60s ribosomal protein l39. [swissprot;acc:p02404] Subtracted 234.025 224.958 9.067
RGL1 ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Divided 168.592 161.452 1.04422
819 no value 60s ribosomal protein l18a. [swissprot;acc:q02543] Subtracted 234.025 224.958 9.067
POLR2I dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] Divided 228.563 238.668 1.04421
820 MRPS2 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] 221.716 231.501 1.04413
RPS19 40s ribosomal protein s19. [swissprot;acc:p39019] Subtracted 234.025 224.958 9.067
821 IMP4 u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Divided 221.676 231.453 1.0441
RPL31 60s ribosomal protein l31. [swissprot;acc:p12947] Subtracted 234.025 224.958 9.067
822 EIF3B eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Divided 243.067 232.805 1.04408
MYO5B myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Subtracted 55 46 9
823 C16orf80 transcription factor iib. [refseq;acc:nm_013242] Divided 206.068 197.471 1.04354
MYO5C myosin vc (myosin 5c). [swissprot;acc:q9nqx4] Subtracted 55 46 9
824 no value myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Divided 206.068 197.471 1.04354
825 no value 40s ribosomal protein s3a. [swissprot;acc:p49241] Subtracted 225.689 234.674 8.985
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Divided 206.214 197.614 1.04352
826 HTATIP 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 223.186 213.912 1.04335
POLR2J dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435] Subtracted 230.811 239.785 8.974
827 CCDC22 jm1 protein. [refseq;acc:nm_014008] 219.762 210.806 8.956
LOH12CR1 loh1cr12. [refseq;acc:nm_058169] Divided 230.087 220.579 1.0431
828 no value ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 135.087 144.041 8.954
CSDE1 unr protein. [swissprot;acc:o75534] Divided 230.087 220.579 1.0431
829 ERCC5 dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] Subtracted 252.873 261.821 8.948
SEPT4 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 135.844 130.259 1.04288
830 PARK2 parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] 231.734 222.222 1.0428
WDR3 wd-repeat protein 3. [swissprot;acc:q9unx4] Subtracted 243.896 234.96 8.936
831 no value 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 229.171 238.048 8.877
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Divided 231.734 222.222 1.0428
832 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
TXNDC2 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243] Subtracted 229.171 238.048 8.877
833 PSIP1 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Divided 231.734 222.222 1.0428
TXN thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599] Subtracted 229.171 238.048 8.877
834 no value 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] 230.768 239.632 8.864
RPL8 60s ribosomal protein l8. [swissprot;acc:p25120] Divided 231.734 222.222 1.0428
835 HDGF hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]
HNRPK heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244] Subtracted 224.413 233.272 8.859
836 HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Divided 231.734 222.222 1.0428
PRPF4 u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172] Subtracted 224.413 233.272 8.859
837 DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Divided 231.734 222.222 1.0428
SSRP1 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 237.62 228.762 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
- 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/