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.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2558 to 2607 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
640 no value intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Divided High confidence 217.67 230.596 1.05938
MEGF6 megf6 (fragment). [sptrembl;acc:o75095] Low confidence 207.235 201.402 1.02896
ZFAND6 protein associated with prk1. [refseq;acc:nm_019006] Subtracted 184.361 178.613 5.748
641 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
PRAM1 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided 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
642 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 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Divided 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
MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 206.078 12.149
ZNF593 zinc finger protein t86. [swissprot;acc:o00488] Low confidence 205.897 200.163 5.734
644 C16orf35 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided High confidence 217.67 230.596 1.05938
CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted 226.497 214.355 12.142
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Divided Low confidence 203.911 198.193 1.02885
ITGB7 integrin beta-7 precursor. [swissprot;acc:p26010] Subtracted 206.341 200.609 5.732
645 HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] High confidence 226.497 214.355 12.142
HTATSF1 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Divided 217.67 230.596 1.05938
ITGB3 integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] Subtracted Low confidence 206.342 200.61 5.732
PDIA2 protein disulfide isomerase a2 precursor (ec 5.3.4.1) (pdip). [swissprot;acc:q13087] Divided 204.488 198.765 1.02879
646 BTF3L1 transcription factor btf3 homolog 1. [swissprot;acc:q13890] 204.634 198.914 1.02876
ITGB2 integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107] Subtracted 206.339 200.608 5.731
SCOC short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Divided High confidence 216.731 229.549 1.05914
SIM1 single-minded homolog 1. [swissprot;acc:p81133] Subtracted 226.497 214.355 12.142
647 ARFGEF1 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6] Divided Low confidence 203.293 197.621 1.0287
DYNLL2 dynein light chain 2. [refseq;acc:nm_080677] High confidence 216.731 229.549 1.05914
HOXA10 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Subtracted 214.257 202.125 12.132
ZEB2 zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Low confidence 205.995 200.27 5.725
648 ALDH3B1 aldehyde dehydrogenase 7 (ec 1.2.1.5). [swissprot;acc:p43353] Divided 210.325 216.359 1.02869
HOXB9 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Subtracted High confidence 214.257 202.132 12.125
MARS methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Divided 218.227 206.078 1.05895
ZEB1 transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Subtracted Low confidence 205.995 200.27 5.725
649 ARFGEF2 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5] Divided 203.283 197.617 1.02867
EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] High confidence 233.725 220.751 1.05877
HOXA9 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 214.257 202.132 12.125
PDIA2 protein disulfide isomerase a2 precursor (ec 5.3.4.1) (pdip). [swissprot;acc:q13087] Low confidence 204.488 198.765 5.723
650 no value u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Divided High confidence 228.986 216.276 1.05877
BTF3L1 transcription factor btf3 homolog 1. [swissprot;acc:q13890] Subtracted Low confidence 204.634 198.914 5.72
HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] High confidence 214.257 202.135 12.122
MARCH6 similar to s. cerevisiae ssm4. [refseq;acc:nm_005885] Divided Low confidence 207.662 201.876 1.02866
651 no value large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379]
BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] High confidence 233.725 220.751 1.05877
GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Subtracted 214.256 202.139 12.117
ITGA6 integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229] Low confidence 206.321 200.601 5.72
652 no value tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Divided High confidence 248.994 235.255 1.0584
FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Subtracted 214.256 202.139 12.117
ITGA7 integrin alpha-7 precursor. [swissprot;acc:q13683] Low confidence 206.32 200.601 5.719

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/