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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2758 to 2807 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
green
network_comparison
345 SH3GL1 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Divided Squared 35793 44595.3 1.24592
SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Subtracted Rooted 57.9068 64.8562 6.9494
SORBS3 vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Squared 29160.4 35570.2 6409.8
346 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Measured 4068.78 5082.18 1013.4
CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Divided Squared 34018.3 42373 1.24559
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Rooted 61.4282 68.0107 1.10716
RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 241.612 265.119 1.09729
SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 14229.2 16780.7 1.17931
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Subtracted Rooted 57.9819 64.9302 6.9483
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Ranked 231.492 211.136 20.356
VAV1 vav proto-oncogene. [swissprot;acc:p15498] Squared 31223.8 37614.3 6390.5
347 no value transcription factor btf3 homolog 3. [swissprot;acc:q13892] 34268.1 40650.4 6382.3
AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Divided Ranked 242.14 265.697 1.09729
CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Subtracted Measured 4068.82 5082.21 1013.39
KLF5 krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Rooted 57.9819 64.9302 6.9483
PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Divided Measured 4991.02 5885.09 1.17914
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Subtracted Ranked 231.481 211.131 20.35
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Divided Squared 16573.6 20637.8 1.24522
TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted 66.4284 60.0004 1.10713
348 no value adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked 242.14 265.696 1.09728
CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Subtracted Measured 4068.91 5082.27 1013.36
DVL1 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted 59.0296 65.951 6.9214
GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Divided Squared 42566.2 52985.3 1.24477
NOC3L ad24 protein. [refseq;acc:nm_022451] Rooted 49.2558 54.5235 1.10695
SF3B2 splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Measured 4991.02 5885.09 1.17914
SLC15A2 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] Subtracted Ranked 185.969 165.623 20.346
VAV3 vav-3 protein. [swissprot;acc:q9ukw4] Squared 31248.8 37623.4 6374.6
349 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 34219.8 40585.4 6365.6
CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 255.112 234.804 20.308
DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Divided Measured 4714.85 5554.38 1.17806
DVL2 segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Subtracted Rooted 59.029 65.9421 6.9131
LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 56.0061 61.9704 1.10649
MED22 surfeit locus protein 5. [swissprot;acc:q15528] Ranked 242.14 265.696 1.09728
SH3GL2 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Squared 35533.9 44227 1.24464
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Subtracted Measured 3349.9 4362.61 1012.71
350 no value tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Ranked 233.376 253.539 20.163
ARMET armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Divided Squared 35508.7 44191.4 1.24452
CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Subtracted Measured 4074.83 5086.49 1011.66
DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Rooted 59.026 65.8955 6.8695
ETFA electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Squared 31583 37925.6 6342.6
NAV2 neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Divided Rooted 61.3383 67.8668 1.10643
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Ranked 242.14 265.696 1.09728
ZNF547 sedlin. [swissprot;acc:o14582] Measured 17396.9 20483.9 1.17745
351 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
ADI1 sipl protein. [refseq;acc:nm_018269] Subtracted Squared 30155.1 36495 6339.9
ANKS1B e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Divided Rooted 61.3352 67.8618 1.10641
GTF2H1 tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780] Subtracted Ranked 233.376 253.539 20.163
HDC histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Divided Squared 35508.6 44191.3 1.24452
NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Subtracted Measured 7878.27 8879.08 1000.81
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Divided Ranked 242.14 265.696 1.09728

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/