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 Network Comparison Type Hugo description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2530 to 2579 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Network Comparison Type
Hugo
description
Interaction Map
red
green
network_comparison
633 Divided TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Low confidence 203.734 197.956 1.02919
Subtracted no value dolichyl-p-man:man(5)glcnac(2)-pp-dolichyl mannosyltransferase (ec 2.4.1.-) (dol-p-man dependent alpha(1-3)-mannosyltransferase) (not56-like protein). [swissprot;acc:q92685] 200.085 194.301 5.784
ABLIM1 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] High confidence 229.072 216.576 12.496
634 Divided no value dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 226.523 213.786 1.05958
TSC22D4 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Low confidence 203.726 197.955 1.02915
Subtracted SYN1 synapsin i (brain protein 4.1). [swissprot;acc:p17600] High confidence 229.072 216.576 12.496
TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Low confidence 203.734 197.956 5.778
635 Divided BBS7 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] 207.763 201.882 1.02913
RPL37 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] High confidence 228.639 242.258 1.05957
Subtracted MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 235.296 247.673 12.377
TSC22D4 tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8] Low confidence 203.726 197.955 5.771
636 Divided RBM19 probable rna-binding protein kiaa0682. [swissprot;acc:q9y4c8] 206.001 200.193 1.02901
SFRS1 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] High confidence 228.639 242.258 1.05957
Subtracted N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Low confidence 204.933 199.164 5.769
VAV1 vav proto-oncogene. [swissprot;acc:p15498] High confidence 212.2 199.849 12.351
637 Divided AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Low confidence 192.166 186.751 1.029
PPAT amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] High confidence 228.639 242.258 1.05957
Subtracted RNF144B ba528a10.3.2 (novel protein similar to kiaa0161, isoform 2) (fragment). [sptrembl;acc:q9bx39] Low confidence 208.62 202.855 5.765
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] High confidence 212.253 199.908 12.345
638 Divided NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Low confidence 203.825 198.081 1.029
SNX17 sorting nexin 17. [swissprot;acc:q15036] High confidence 228.639 242.258 1.05957
Subtracted SURF1 surfeit locus protein 1. [swissprot;acc:q15526] Low confidence 201.211 195.459 5.752
VAV2 vav-2 protein. [swissprot;acc:p52735] High confidence 212.526 200.212 12.314
639 Divided HRB nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] 217.67 230.596 1.05938
N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Low confidence 204.933 199.164 1.02897
Subtracted NOVA1 rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] High confidence 222.554 234.847 12.293
ZFAND5 zinc finger protein 216. [swissprot;acc:o76080] Low confidence 184.361 178.613 5.748
640 Divided no value intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] High confidence 217.67 230.596 1.05938
MEGF6 megf6 (fragment). [sptrembl;acc:o75095] Low confidence 207.235 201.402 1.02896
Subtracted no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] High confidence 244.842 232.577 12.265
ZFAND6 protein associated with prk1. [refseq;acc:nm_019006] Low confidence 184.361 178.613 5.748
641 Divided PRAM1 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] High confidence 217.67 230.596 1.05938
RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 198.493 192.907 1.02896
Subtracted no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] High confidence 244.842 232.577 12.265
NUFIP1 nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Low confidence 203.825 198.081 5.744
642 Divided no value intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] High confidence 217.67 230.596 1.05938
CUL2 cullin homolog 2 (cul-2). [swissprot;acc:q13617] Low confidence 203.883 198.148 1.02894
Subtracted 5.735
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] High confidence 228.944 216.745 12.199
643 Divided HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Low confidence 203.104 197.399 1.0289
HRBL hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] High confidence 217.67 230.596 1.05938
Subtracted MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 218.227 206.078 12.149
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Low confidence 205.897 200.163 5.734
644 Divided C16orf35 cgthba protein (-14 gene protein). [swissprot;acc:q12980] High confidence 217.67 230.596 1.05938
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Low confidence 203.911 198.193 1.02885
Subtracted CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] High confidence 226.497 214.355 12.142
ITGB7 integrin beta-7 precursor. [swissprot;acc:p26010] Low confidence 206.341 200.609 5.732
645 Divided HTATSF1 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] High confidence 217.67 230.596 1.05938
PDIA2 protein disulfide isomerase a2 precursor (ec 5.3.4.1) (pdip). [swissprot;acc:q13087] Low confidence 204.488 198.765 1.02879
Subtracted HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] High confidence 226.497 214.355 12.142

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/