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 [...,...].
Filtered Gene Rank Value Type description Network Comparison Type green network_comparison Interaction Map red
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total
Filtered  : 0
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
description
green
network_comparison
red
126 Measured calcyphosine. [swissprot;acc:q13938] 635.875 1.3457 472.524
Ranked ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 11493.8 1.18216 9722.71
Squared dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] 219.216 1.85456 118.204
Rooted dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 25.9172 1.21538 21.3244
127 Measured lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 64 1.34375 86
Ranked trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 11119.7 1.18152 9411.34
Squared splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 432.882 1.84655 799.337
Rooted putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] 31.257 1.21489 37.9737
128 Measured mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 60.8613 1.33918 81.504
Ranked 60s ribosomal protein l39. [swissprot;acc:p02404] 9794.29 1.18073 11564.4
Squared dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 90.363 1.8456 166.774
Rooted phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] 31.257 1.21489 37.9737
129 Measured protein hspc134 (protein cda04). [swissprot;acc:q9by43] 454.837 1.33341 606.485
Ranked isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 12058.6 1.17945 14222.5
Squared cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 39570.4 1.82158 21723.1
Rooted pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 22.9122 1.21345 27.8028
130 Measured maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 56 1.33333 42
Ranked enigma protein; lim domain protein. [refseq;acc:nm_005451] 17069.5 1.17914 14476.2
Squared cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 38499.2 1.81899 21165.1
Rooted ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 10.4997 1.21286 12.7347
131 Measured serpin b11. [swissprot;acc:q96p15] 56 1.33333 42
Ranked dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 9873.58 1.17887 8375.43
Squared vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] 817.981 1.81308 451.156
Rooted 60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] 16.0484 1.20341 19.3128
132 Measured cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 56 1.33333 42
Ranked rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 22389 1.1754 19048
Squared lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] 0.969467 1.80566 1.75053
Rooted creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] 19.8655 1.20311 23.9003
133 Measured bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] 335 1.32937 252
Ranked alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 8009 1.17537 6814
Squared metaxin 1. [swissprot;acc:q13505] 3429.64 1.79316 6149.89
Rooted tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 22.8323 1.20259 27.4578
134 Measured mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 346.751 1.32862 260.986
Ranked cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 10489.3 1.17404 12314.9
Squared aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] 6483.52 1.79304 11625.2
Rooted dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 12 1.2 10
135 Measured rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] 613.614 1.32736 814.485
Ranked cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 10489.3 1.17404 12314.9
Squared small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] 11769.5 1.79289 21101.4
Rooted spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 51.3517 1.19943 42.8135
136 Measured transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 1150.51 1.3267 1526.38
Ranked cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 10506.8 1.17403 12335.3
Squared sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 1746.18 1.78527 978.105
Rooted daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 20.1222 1.1921 23.9877
137 Measured heat shock factor binding protein 1. [swissprot;acc:o75506] 1233.41 1.3225 1631.18
Ranked cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 10501 1.17403 12328.5
Squared maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 0.742249 1.77778 0.417515
Rooted signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 15.8624 1.19185 18.9056
138 Measured ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 154.804 1.32026 204.382
Ranked likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 10549.4 1.17397 12384.7

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/