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.


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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3964 to 4013 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
496 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Measured Subtracted 6167.93 7007.7 839.77
nostrin. [refseq;acc:nm_052946] Divided 4682.87 4093.05 1.1441
pescadillo homolog 1. [swissprot;acc:o00541] Rooted Subtracted 49.2488 54.4603 5.2115
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Ranked Divided 250.938 234.134 1.07177
tubby protein homolog. [swissprot;acc:p50607] Squared 30286.5 36362 1.2006
497 chromodomain y-like protein 2. [refseq;acc:nm_152342] Subtracted 29016.1 34169.2 5153.1
eap30 subunit of ell complex. [refseq;acc:nm_007241] Measured Divided 4682.87 4093.05 1.1441
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Ranked 251.344 234.514 1.07177
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Squared 30286.5 36362 1.2006
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Measured Subtracted 4714.85 5554.38 839.53
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Rooted Divided 55.1759 60.2621 1.09218
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Ranked Subtracted 225.026 209.798 15.228
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Rooted 50.4687 45.2733 5.1954
498 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Measured Divided 4682.87 4093.05 1.1441
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Squared 30286.5 36362 1.2006
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Rooted 55.1759 60.2621 1.09218
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Ranked 220.161 235.95 1.07172
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 237.28 252.492 15.212
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Squared 29012.2 34163.9 5151.7
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Measured 6933.17 7766.54 833.37
499 chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824] Squared 29012.2 34163.9 5151.7
glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] Measured Divided 4682.87 4093.05 1.1441
homeobox protein barh-like 1. [swissprot;acc:q9hbu1] Ranked Subtracted 237.28 252.492 15.212
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 49.7541 54.9425 5.1884
rw1 protein (fragment). [swissprot;acc:q92545] Divided 55.1759 60.2621 1.09218
tbc1 domain family member 5. [swissprot;acc:q92609] Squared 30286.5 36362 1.2006
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Measured Subtracted 6938.22 7770.65 832.43
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Ranked Divided 231.496 248.048 1.0715
500 60s ribosomal protein l7. [swissprot;acc:p18124] Rooted 52.6483 48.2135 1.09198
block of proliferation 1. [swissprot;acc:q14137] Subtracted 49.4884 54.6735 5.1851
gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] Measured Divided 4682.87 4093.05 1.1441
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Subtracted 10733.4 9902.6 830.8
inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] Ranked Divided 224.662 240.673 1.07127
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212
testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7] Squared 29012.4 34164 5151.6
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Divided 30286.5 36362 1.2006
501 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Rooted Subtracted 93.6481 88.4638 5.1843
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Ranked Divided 238.704 255.68 1.07112
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Rooted 50.4253 46.1792 1.09195
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Measured 4682.87 4093.05 1.1441
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Squared Subtracted 29224 34362.1 5138.1
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Measured 10725.6 9896.32 829.28
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Ranked 237.28 252.492 15.212
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Squared Divided 30286.5 36362 1.2006
502 60s ribosomal protein l30. [swissprot;acc:p04645] Rooted 50.4616 46.2257 1.09164
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Measured Subtracted 10719 9891.08 827.92
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Rooted 84.6378 89.8201 5.1823
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Squared Divided 30286.5 36362 1.2006
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Ranked 238.704 255.68 1.07112

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/