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 3341 to 3390 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
836 no value keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Squared 31100.2 36086.5 1.16033
DDX52 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Measured 4049 4477.43 1.10581
HDGFL1 pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Ranked 231.734 222.222 1.0428
PARD6G partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Rooted 65.0565 69.1533 1.06297
837 no value keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Squared 31100.2 36086.5 1.16033
CIRH1A cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Measured 4063.64 4492.98 1.10565
DDX6 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Ranked 231.734 222.222 1.0428
TUB tubby protein homolog. [swissprot;acc:p50607] Rooted 65.0565 69.1533 1.06297
838 no value keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Squared 31100.1 36086.4 1.16033
PRKCI protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Rooted 65.0565 69.1533 1.06297
RSL1D1 pbk1 protein. [sptrembl;acc:o76021] Measured 4064.23 4493.36 1.10559
TMEM131 rw1 protein (fragment). [swissprot;acc:q92545] Ranked 231.734 222.222 1.0428
839 no value keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Squared 31100.1 36086.4 1.16033
CLEC11A stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Ranked 177.776 170.499 1.04268
NUMB numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Rooted 65.0565 69.1533 1.06297
RARS2 arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320] Measured 7093.86 7842.67 1.10556
840 no value keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Squared 31100.1 36086.4 1.16033
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Measured 5786.67 6395.78 1.10526
TBC1D5 tbc1 domain family member 5. [swissprot;acc:q92609] Rooted 65.0565 69.1533 1.06297
TOMM20 mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Ranked 198.781 190.66 1.04259
841 no value keratin associated protein 1.5. [refseq;acc:nm_031957] Squared 31100.2 36086.5 1.16033
MTO1 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Measured 5786.67 6395.78 1.10526
PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Ranked 198.781 190.66 1.04259
TULP1 tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Rooted 65.0565 69.1533 1.06297
842 CCDC22 jm1 protein. [refseq;acc:nm_014008] Ranked 219.762 210.806 1.04248
LOH12CR1 loh1cr12. [refseq;acc:nm_058169] Measured 5195.48 5741.63 1.10512
STARD6 star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Squared 31100.1 36086.4 1.16033
VPS29 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Rooted 65.0565 69.1533 1.06297
843 CSDE1 unr protein. [swissprot;acc:o75534] Measured 5195.48 5741.63 1.10512
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] Ranked 218.521 227.796 1.04244
KRTAP5-8 keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Squared 31100.2 36086.5 1.16033
NUMBL numb-like protein (numb-r). [swissprot;acc:q9y6r0] Rooted 65.0565 69.1533 1.06297
844 no value keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Squared 31100.2 36086.5 1.16033
CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Ranked 178.033 170.82 1.04223
MOBKL3 preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Measured 6276.97 6934.8 1.1048
TULP3 tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Rooted 65.0565 69.1533 1.06297
845 DNAJB11 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] Measured 6276.97 6934.8 1.1048
LSM1 u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Ranked 228.599 219.399 1.04193
STARD5 star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Squared 31100.1 36086.4 1.16033
VPS35 vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Rooted 65.0565 69.1533 1.06297
846 no value methyltransferase like 2. [refseq;acc:nm_018396] Ranked 147.211 153.371 1.04184
HLCS biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Measured 5607.43 6194.98 1.10478
KRTAP4-4 keratin associated protein 4.4. [refseq;acc:nm_032524] Squared 31100.2 36086.5 1.16033
PRKCZ protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Rooted 65.0565 69.1533 1.06297
847 no value alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared 31100.1 36086.4 1.16033
DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Ranked 147.211 153.371 1.04184
NCK2 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Measured 6776.85 7485.55 1.10458
WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] Rooted 51.7527 55.0117 1.06297
848 FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Ranked 147.211 153.371 1.04184
HEATR1 protein bap28. [swissprot;acc:q9h583] Rooted 51.1817 54.4034 1.06295

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/