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 12814 to 12863 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1602 spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] Measured Divided 5232.14 5605.8 1.07142
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Squared Subtracted 17134.4 19648.7 2514.3
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Rooted 53.2742 51.0444 2.2298
1603 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] Squared Divided 17081.4 18947.6 1.10925
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Ranked Subtracted 228.654 231.933 3.279
fibulin-1 precursor. [swissprot;acc:p23142] Rooted Divided 75.958 78.6278 1.03515
heat shock factor binding protein 1. [swissprot;acc:o75506] Ranked 216.62 213.22 1.01595
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] Measured 5232.14 5605.8 1.07142
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Subtracted 4913.07 5337.95 424.88
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Rooted 65.3797 67.6074 2.2277
suppressor of fused. [refseq;acc:nm_016169] Squared 17134.4 19648.7 2514.3
1604 lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Divided 29262.5 32458.3 1.10921
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] Measured 6176.82 6617.91 1.07141
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Ranked Subtracted 221.934 218.658 3.276
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Rooted Divided 64.0052 66.254 1.03513
phospholipid scramblase 2 (pl scramblase 2) (ca(2+)-dependent phospholipid scramblase 2). [swissprot;acc:q9nry7] Measured Subtracted 6260.43 6685.05 424.62
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Ranked Divided 214.984 211.614 1.01593
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579] Rooted Subtracted 61.6942 63.9187 2.2245
zinc finger protein gli3. [swissprot;acc:p10071] Squared 17134.4 19648.7 2514.3
1605 eyes absent homolog 1. [swissprot;acc:q99502] Rooted 61.9761 64.2003 2.2242
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Ranked Divided 217.322 213.916 1.01592
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Measured 6176.82 6617.91 1.07141
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Squared Subtracted 17134.4 19648.7 2514.3
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Divided 30908.9 34282.7 1.10915
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Rooted 64.0052 66.254 1.03513
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Measured Subtracted 6259.8 6684.31 424.51
zinc finger protein 207. [swissprot;acc:o43670] Ranked 221.934 218.658 3.276
1606 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] Measured Divided 5232.99 5606.53 1.07138
apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Ranked 207.916 204.662 1.0159
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Rooted 64.0052 66.254 1.03513
gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142] Squared Subtracted 17134.4 19648.7 2514.3
heat shock-related 70 kda protein 2 (heat shock 70 kda protein 2). [swissprot;acc:p54652] Divided 30908.9 34282.7 1.10915
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Measured Subtracted 6259.8 6684.3 424.5
sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] Rooted 61.97 64.1935 2.2235
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Ranked 228.477 231.747 3.27
1607 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] Squared Divided 30908.9 34282.7 1.10915
phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645] Rooted 64.0052 66.254 1.03513
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Ranked 214.982 211.622 1.01588
putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] Measured 5232.99 5606.53 1.07138
sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] Rooted Subtracted 61.9702 64.1936 2.2234
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Measured 4379.28 4803.59 424.31
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Ranked 228.484 231.74 3.256
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Squared 17134.4 19648.7 2514.3
1608 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Rooted 61.9701 64.1935 2.2234
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] Ranked 218.789 215.533 3.256
heat shock cognate 71 kda protein. [swissprot;acc:p11142] Squared Divided 30908.9 34282.7 1.10915
kinesin-like protein kif3c. [swissprot;acc:o14782] Subtracted 28486.1 31000.2 2514.1
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Rooted Divided 99.0527 95.6982 1.03505
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] Measured Subtracted 7019.78 7444.06 424.28
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Ranked Divided 208.106 204.867 1.01581

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/