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 [...,...].
description Gene Rank Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 9086 to 9135 of 9634 in total
Value Type  : Measured
Network Comparison Type  : Divided
description
Rank
Interaction Map
Filtered
red
green
network_comparison
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] 2664 Low confidence 1 8152.86 8394.73 1.02967
vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [refseq;acc:nm_013245] 2993 High confidence 0.00001 0.00001 1
4752 Low confidence 7772.88 7873.48 1.01294
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] 1185 7826.1 8111.08 1.03641
1314 High confidence 5401.39 5838.63 1.08095
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] 391 Low confidence 8552.2 9004.53 1.05289
790 High confidence 5890.88 6548.28 1.1116
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] 333 Low confidence 8639.75 9126.51 1.05634
787 High confidence 5890.49 6547.9 1.11161
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] 335 Low confidence 8636.95 9122.21 1.05618
788 High confidence 5890.41 6547.81 1.11161
vacuolar proton-atpase subunit. [sptrembl;acc:q8nhe4] 1953 Low confidence 7680.35 7928.83 1.03235
2821 High confidence 0.00001 0.00001 1
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] 1797 5096.02 5432.63 1.06605
4927 Low confidence 8713.12 8756.73 1.00501
vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1] 2263 7542.03 7777.49 1.03122
2642 High confidence 5935.71 5876.22 1.01012
vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692] 3066 0.00001 0.00001 1
4000 Low confidence 8016.83 8196.09 1.02236
vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765] 2811 High confidence 0.00001 0.00001 1
3996 Low confidence 8016.83 8196.09 1.02236
vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] 90 12768 11571.4 1.10341
vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034] 2261 7994.84 8244.62 1.03124
2840 High confidence 0.00001 0.00001 1
vav proto-oncogene. [swissprot;acc:p15498] 413 6644.99 7707.8 1.15994
781 Low confidence 8109.84 8447.62 1.04165
vav-2 protein. [swissprot;acc:p52735] 421 High confidence 6660.02 7697.78 1.15582
813 Low confidence 8101.08 8434.83 1.0412
vav-3 protein. [swissprot;acc:q9ukw4] 415 High confidence 6647.43 7706.18 1.15927
796 Low confidence 8108.45 8445.65 1.04159
versican core protein precursor (large fibroblast proteoglycan) (chondroitin sulfate proteoglycan core protein 2) (pg-m) (glial hyaluronate-binding protein) (ghap). [swissprot;acc:p13611] 372 0 1298.86 1162.87 1.11694
2522 1 7864.41 8102.27 1.03025
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] 2314 High confidence 6960.99 7273.72 1.04493
2784 Low confidence 8279.23 8520.74 1.02917
very low-density lipoprotein receptor precursor (vldl receptor). [swissprot;acc:p98155] 4618 7846.36 7975.38 1.01644
very-long-chain acyl-coa synthetase (ec 6.2.1.-) (very-long-chain- fatty-acid-coa ligase). [swissprot;acc:o14975] 2312 High confidence 6960.26 7273.01 1.04493
2775 Low confidence 8278.72 8520.49 1.0292
vesicle trafficking protein sec22b. [refseq;acc:nm_004892] 1044 7977.77 8278.9 1.03775
vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106] 1035 8054.13 8358.75 1.03782
3157 High confidence 0.00001 0.00001 1
vesicle-associated membrane protein 1 (vamp-1) (synaptobrevin 1). [swissprot;acc:p23763] 979 6654.42 7296.51 1.09649
1094 Low confidence 8056.88 8356.38 1.03717
vesicle-associated membrane protein 2 (vamp-2) (synaptobrevin 2). [swissprot;acc:p19065] 978 High confidence 6654.42 7296.51 1.09649
1091 Low confidence 8056.93 8356.51 1.03718
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] 983 High confidence 6654.42 7296.51 1.09649
1097 Low confidence 8056.83 8356.23 1.03716
vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0] 2879 7998.65 8227.52 1.02861
3123 High confidence 0.00001 0.00001 1
vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292] 2874 Low confidence 7998.28 8227.33 1.02864
3023 High confidence 0.00001 0.00001 1

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/