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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1664 to 1713 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
832 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
838 SUPT16H chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] Divided 231.734 222.222 1.0428
839 no value dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Subtracted 230.764 239.62 8.856
CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Divided 177.776 170.499 1.04268
840 DEAF1 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Subtracted 236.741 245.547 8.806
TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Divided 198.781 190.66 1.04259
841 PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]
RIOK1 rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Subtracted 236.741 245.547 8.806
842 CCDC22 jm1 protein. [refseq;acc:nm_014008] Divided 219.762 210.806 1.04248
MARK1 map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Subtracted 236.741 245.547 8.806
843 GART trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Divided 218.521 227.796 1.04244
MARK2 map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Subtracted 236.741 245.547 8.806
844 CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Divided 178.033 170.82 1.04223
SPO11 meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Subtracted 236.741 245.547 8.806
845 HAO2 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 232.512 241.288 8.776
LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Divided 228.599 219.399 1.04193
846 no value methyltransferase like 2. [refseq;acc:nm_018396] 147.211 153.371 1.04184
CDC73 parafibromin. [refseq;acc:nm_024529] Subtracted 239.704 230.991 8.713
847 DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Divided 147.211 153.371 1.04184
MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Subtracted 227.604 219.001 8.603
848 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Divided 147.211 153.371 1.04184
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Subtracted 206.214 197.614 8.6
849 C16orf80 transcription factor iib. [refseq;acc:nm_013242] 206.068 197.471 8.597
PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Divided 147.211 153.371 1.04184
850 CPSF4 cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] 107.842 112.329 1.04161
SFRS8 splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Subtracted 206.068 197.471 8.597
851 KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Divided 107.842 112.329 1.04161
MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Subtracted 227.601 219.008 8.593
852 GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 227.596 219.017 8.579
HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Divided 193.114 185.412 1.04154
853 no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Subtracted 227.596 219.017 8.579
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Divided 108.289 112.772 1.0414
854 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Subtracted 227.596 219.017 8.579
855 CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Divided 178.514 171.42 1.04138
ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Subtracted 227.596 219.018 8.578
856 MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 227.585 219.037 8.548
XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Divided 215.028 206.623 1.04068
857 MDN1 midasin (midas-containing protein). [swissprot;acc:q9nu22] Subtracted 237.218 228.698 8.52

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/