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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Rank description Gene Hugo Value Type Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 651 to 700 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Value Type
green
red
network_comparison
163 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] no value Squared 242989 173408 1.40126
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Measured 18263 23693.7 1.29736
164 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] HOXD4 Squared 242989 173408 1.40126
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] SLC39A6 Ranked 249.187 209.299 1.19058
mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Rooted 65.1534 55.646 1.17086
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] MAGEA9 Measured 18263 23693.7 1.29736
165 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] GAD2 Ranked 249.187 209.299 1.19058
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] HOXB5 Squared 242989 173408 1.40126
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Rooted 65.1478 55.6486 1.1707
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] MAGEA8 Measured 18263 23693.7 1.29736
166 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] NAPG Ranked 249.187 209.299 1.19058
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] HOXA5 Squared 242989 173408 1.40126
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] MXD4 Rooted 65.1458 55.6495 1.17064
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] MAGEC1 Measured 18263 23693.7 1.29736
167 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] GAD1 Ranked 249.187 209.299 1.19058
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] no value Squared 242989 173408 1.40126
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] RAB24 Rooted 65.1448 55.65 1.17062
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] MAGEA4 Measured 18263 23693.7 1.29736
168 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] no value Ranked 98.0548 82.5916 1.18722
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Measured 18263 23693.7 1.29736
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Squared 242989 173408 1.40126
small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Rooted 65.8949 56.3709 1.16895
169 apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 Ranked 98.0548 82.5916 1.18722
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 Rooted 53.7761 62.762 1.1671
melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 Measured 18263 23693.7 1.29736
symplekin. [swissprot;acc:q92797] SYMPK Squared 88668.8 124118 1.39979
170 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 Rooted 45.9227 53.4993 1.16499
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 Squared 69286.7 96730.5 1.39609
melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Measured 18263 23693.7 1.29736
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 Ranked 192.715 227.199 1.17894
171 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS Squared 69211.2 96602.7 1.39577
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 Rooted 71.7355 61.6639 1.16333
melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Measured 18263 23693.7 1.29736
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 Ranked 192.823 227.202 1.17829
172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL 205.556 174.667 1.17685
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T Squared 87259.3 121579 1.39331
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 Rooted 65.9889 56.7592 1.16261
trophinin. [swissprot;acc:q12816] TRO Measured 18263 23693.7 1.29736
173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Rooted 168.796 145.551 1.1597
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] BCAR3 Measured 5940.64 4579.34 1.29727
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] SEPT4 Squared 115061 82624.3 1.39258
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Ranked 193.056 227.032 1.17599
174 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] DGCR14 286 335 1.17133
mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Measured 5774.03 4455.95 1.2958
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 Rooted 168.796 145.551 1.1597
sedlin. [swissprot;acc:o14582] ZNF547 Squared 157033 112820 1.39189
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 Ranked 234.187 199.949 1.17123
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] MXI1 Measured 5773.77 4456.67 1.29553
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] PANK2 Rooted 168.796 145.551 1.1597
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] no value Squared 157033 112820 1.39189

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/