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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 description Network Comparison Type Value Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 2901 to 2950 of 9634 in total
Filtered  : 1
Network Comparison Type  : Divided
Value Type  : Measured
Rank
description
Interaction Map
green
red
network_comparison
778 vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] High confidence 6533.23 5874.63 1.11211
779 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 6533.36 5874.76
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Low confidence 8729.16 8379.96 1.04167
780 calcineurin b subunit isoform 1 (protein phosphatase 2b regulatory subunit 1) (protein phosphatase 3 regulatory subunit b alpha isoform 1). [swissprot;acc:p06705] 7631.04 7325.81
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] High confidence 6533.36 5874.76 1.11211
781 secretory pathway component sec31b-1. [refseq;acc:nm_015490]
vav proto-oncogene. [swissprot;acc:p15498] Low confidence 8447.62 8109.84 1.04165
782 putative fork head domain transcription factor afx1 (forkhead box protein o4). [swissprot;acc:p98177] 7852.25 7538.43 1.04163
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] High confidence 6533.33 5874.74 1.11211
783 tweety homolog 1; tweety homolog. [refseq;acc:nm_020659] Low confidence 7852.34 7538.53 1.04163
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] High confidence 6533.37 5874.78 1.1121
784 cytoglobin (histoglobin) (hgb) (stellate cell activation-associated protein). [swissprot;acc:q8wwm9] Low confidence 7852.34 7538.53 1.04163
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] High confidence 6533.36 5874.77 1.1121
785 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 5557.17 4997
hemoglobin gamma-a and gamma-g chains. [swissprot;acc:p02096] Low confidence 7852.24 7538.42 1.04163
786 amyloid beta a4 protein precursor (app) (abpp) (alzheimer's disease amyloid protein) (cerebral vascular amyloid peptide) (cvap) (protease nexin-ii) (pn-ii) (appi) (prea4) [contains: soluble app-alpha (s-app- alpha); soluble app-beta (s-app-beta); c99; beta-amyloid protein 42 (beta-app42); beta-amyloid protein 40 (beta-app40); c83; p3(42); p3(40); gamma-ctf(59) (gamma-secretase c-terminal fragment 59) (amyloid intracellular domain 59) (aid(59)); gamma-ctf(57) (gamma- secretase c-terminal fragment 57) (amyloid intracellular domain 57) (aid(57)); gamma-ctf(50) (gamma-secretase c-terminal fragment 50) (amyloid intracellular domain 50) (aid(50)); c31]. [swissprot;acc:p05067] 7852.27 7538.46
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] High confidence 10347.3 9304.83 1.11204
787 tweety homolog 2. [refseq;acc:nm_032646] Low confidence 7852.28 7538.46 1.04163
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] High confidence 6547.9 5890.49 1.11161
788 hemoglobin zeta chain (hbaz). [swissprot;acc:p02008] Low confidence 7852.24 7538.42 1.04163
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] High confidence 6547.81 5890.41 1.11161
789 alpha 2 globin. [refseq;acc:nm_000517] Low confidence 7852.23 7538.41 1.04163
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] High confidence 6547.99 5890.59 1.1116
790 forkhead box protein o3a (forkhead in rhabdomyosarcoma-like 1) (af6q21 protein). [swissprot;acc:o43524] Low confidence 7852.34 7538.53 1.04163
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] High confidence 6548.28 5890.88 1.1116
791 amyloid-like protein 1 precursor (aplp) (aplp-1) [contains: c30]. [swissprot;acc:p51693] Low confidence 7852.25 7538.43 1.04163
transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] High confidence 4474.3 4025.3 1.11154
792 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 7526.2 6772.75 1.11125
myoglobin. [swissprot;acc:p02144] Low confidence 7852.24 7538.42 1.04163
793 hemoglobin theta-1 chain. [swissprot;acc:p09105] 7852.23 7538.41
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] High confidence 5596.36 5036.92 1.11107
794 amyloid-like protein 2 precursor (amyloid protein homolog) (apph) (cdei-box binding protein) (cdebp). [swissprot;acc:q06481] Low confidence 7852.34 7538.53 1.04163
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] High confidence 7154.55 6441.17 1.11075
795 dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 7154.13 6441.14 1.11069
thyroid receptor interacting protein 12 (trip12). [swissprot;acc:q14669] Low confidence 8147.14 7821.82 1.04159
796 nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 7590.49 6834.54 1.11061
vav-3 protein. [swissprot;acc:q9ukw4] Low confidence 8445.65 8108.45 1.04159
797 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] High confidence 7590.49 6834.54 1.11061
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Low confidence 8731.6 8383.16 1.04156
798 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 8221.03 7893.13 1.04154
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] High confidence 7590.49 6834.54 1.11061
799 transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
zinc finger protein 183-like 1. [refseq;acc:nm_178861] Low confidence 7857 7543.76 1.04152
800 dolichyl-diphosphooligosaccharide--protein glycosyltransferase 67 kda subunit precursor (ec 2.4.1.119) (ribophorin i) (rpn-i). [swissprot;acc:p04843] 8164.84 7839.89 1.04145
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] High confidence 6746.92 6075.55 1.1105
801 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 7169.75 6456.35
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Low confidence 8162.73 7837.99 1.04143
802 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] High confidence 7168.82 6455.66 1.11047
803 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 7167.96 6455.02 1.11045

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/