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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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 [...,...].
Value Type Rank Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 775 to 824 of 12912 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
775 ATP6V1G1 vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] 5874.74 6533.33 1.11211
776 GDAP1L1 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034] 5874.76 6533.36
777 DDX39 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 5874.74 6533.34
778 ATP6V1B1 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] 5874.63 6533.23
779 GDAP1 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36
780 ATP6V1D 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]
781 SEC31B secretory pathway component sec31b-1. [refseq;acc:nm_015490]
782 ATP6V1H 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] 5874.74 6533.33
783 ATP6V1B2 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] 5874.78 6533.37 1.1121
784 ATP6V1E1 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] 5874.77 6533.36
785 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 4997 5557.17
786 PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] 9304.83 10347.3 1.11204
787 ATP6V0A2 vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 5890.49 6547.9 1.11161
788 TCIRG1 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] 5890.41 6547.81
789 ATP6V0A4 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] 5890.59 6547.99 1.1116
790 ATP6V0A1 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] 5890.88 6548.28
791 TBL3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 4025.3 4474.3 1.11154
792 DNALI1 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 6772.75 7526.2 1.11125
793 N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 5036.92 5596.36 1.11107
794 no value dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 6441.17 7154.55 1.11075
795 TOP2B dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 6441.14 7154.13 1.11069
796 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 6834.54 7590.49 1.11061
797 KPNB1 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
798 TBL1X transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]
799 TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
800 NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 6075.55 6746.92 1.1105
801 KPNA3 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 6456.35 7169.75
802 TOE1 target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] 6455.66 7168.82 1.11047
803 KPNA4 importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] 6455.02 7167.96 1.11045
804 NDUFB9 nadh-ubiquinone oxidoreductase b22 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b22) (ci-b22). [swissprot;acc:q9y6m9] 6770.78 7517.97 1.11036
805 no value 60s ribosomal protein l39. [swissprot;acc:p02404] 4708.61 5226.71 1.11003
806 60s ribosomal protein l18a. [swissprot;acc:q02543]
807 RPS19 40s ribosomal protein s19. [swissprot;acc:p39019]
808 RPL31 60s ribosomal protein l31. [swissprot;acc:p12947]
809 WDR3 wd-repeat protein 3. [swissprot;acc:q9unx4] 4039.81 4484.22 1.11001
810 CCDC22 jm1 protein. [refseq;acc:nm_014008] 5794.8 6427.79 1.10923
811 ATP5D atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 6000.07 6655.11 1.10917
812 TOM1 target of myb protein 1. [swissprot;acc:o60784] 5640.79 6255.85 1.10904
813 no value huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] 5641.11 6255.99 1.109
814 TRIO triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] 5641.12
815 MDN1 midasin (midas-containing protein). [swissprot;acc:q9nu22] 4483.08 4971.62 1.10897
816 TOM1L2 target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] 5641.53 6256.17 1.10895
817 ODC1 ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] 6811.2 7547.35 1.10808
818 AASS aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 6807.78 7543.28 1.10804
819 AZIN1 ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] 6805.45 7540.5 1.10801
820 ADC ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] 6805.86 7540.99
821 TRIT1 trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 6257.99 6932.95 1.10786
822 RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] 6311.6 6989.33 1.10738
823 RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] 6311.83 6989.6
824 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 5657.53 6263.02 1.10702

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/