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 Gene Value Type Hugo description Network Comparison Type Interaction Map Filtered red green 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
Value Type
Hugo
description
red
green
network_comparison
163 Squared no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 173408 242989 1.40126
Rooted EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] 52.7702 61.8915 1.17285
164 Measured MAGEA9 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 23693.7 18263 1.29736
Ranked SLC39A6 liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 209.299 249.187 1.19058
Squared HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 173408 242989 1.40126
Rooted MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] 55.646 65.1534 1.17086
165 Measured MAGEA8 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 23693.7 18263 1.29736
Ranked GAD2 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329] 209.299 249.187 1.19058
Squared HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 173408 242989 1.40126
Rooted MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 55.6486 65.1478 1.1707
166 Measured MAGEC1 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 23693.7 18263 1.29736
Ranked NAPG gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 209.299 249.187 1.19058
Squared HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 173408 242989 1.40126
Rooted MXD4 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 55.6495 65.1458 1.17064
167 Measured MAGEA4 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 23693.7 18263 1.29736
Ranked GAD1 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 209.299 249.187 1.19058
Squared no value homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 173408 242989 1.40126
Rooted RAB24 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 55.65 65.1448 1.17062
168 Measured no value melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] 23693.7 18263 1.29736
Ranked gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 82.5916 98.0548 1.18722
Squared HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 173408 242989 1.40126
Rooted SNRPD3 small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] 56.3709 65.8949 1.16895
169 Measured MAGEA10 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] 23693.7 18263 1.29736
Ranked ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 82.5916 98.0548 1.18722
Squared SYMPK symplekin. [swissprot;acc:q92797] 124118 88668.8 1.39979
Rooted COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 62.762 53.7761 1.1671
170 Measured MAGEB4 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] 23693.7 18263 1.29736
Ranked TIA1 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 192.715 1.17894
Squared CTPS2 cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 96730.5 69286.7 1.39609
Rooted B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 53.4993 45.9227 1.16499
171 Measured MAGED2 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] 23693.7 18263 1.29736
Ranked TIAL1 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 227.202 192.823 1.17829
Squared CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 96602.7 69211.2 1.39577
Rooted LASS2 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 61.6639 71.7355 1.16333
172 Measured TRO trophinin. [swissprot;acc:q12816] 23693.7 18263 1.29736
Ranked TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 1.17685
Squared CSTF2T likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] 121579 87259.3 1.39331
Rooted SF3B1 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 56.7592 65.9889 1.16261
173 Measured BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 4579.34 5940.64 1.29727
Ranked SNRPD1 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 227.032 193.056 1.17599
Squared SEPT4 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] 82624.3 115061 1.39258
Rooted MRPS17 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] 145.551 168.796 1.1597
174 Measured MXD1 mad protein (max dimerizer). [swissprot;acc:q05195] 4455.95 5774.03 1.2958
Ranked DGCR14 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 335 286 1.17133
Squared ZNF547 sedlin. [swissprot;acc:o14582] 112820 157033 1.39189
Rooted PANK1 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] 145.551 168.796 1.1597
175 Measured MXI1 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 4456.67 5773.77 1.29553
Ranked COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 199.949 234.187 1.17123
Squared no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] 112820 157033 1.39189
Rooted PANK2 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] 145.551 168.796 1.1597

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/