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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Hugo Rank measured Gene description expected final
Results: HTML CSV LaTeX Showing element 2608 to 2657 of 3206 in total
Hugo
Rank
measured
description
expected
final
SEC61A1 1954 1.32564 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 1 (SEC61 ALPHA- 1). [SWISSPROT;Acc:P38378] 5.73234 0.231256346
SEC61A2 1957 1.30722 PROTEIN TRANSPORT PROTEIN SEC61 ALPHA SUBUNIT ISOFORM 2 (SEC61 ALPHA- 2). [SWISSPROT;Acc:Q9Y2R3] 5.6527 0.23125586
SEC61G 2031 0.114962 PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT. [SWISSPROT;Acc:P38384] 0.499271 0.230259719
SEPHS1 102 0.0620748 "SELENIDE,WATER DIKINASE 1 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 1) (SELENIUM DONOR PROTEIN 1). [SWISSPROT;Acc:P49903]" 0.166067 0.37379371
SEPHS2 103 0.0447647 "SELENIDE,WATER DIKINASE 2 (EC 2.7.9.3) (SELENOPHOSPHATE SYNTHETASE 2) (SELENIUM DONOR PROTEIN 2). [SWISSPROT;Acc:Q99611]" 0.119758 0.373792983
SEPSECS 1047 0.293391 SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN. [RefSeq;Acc:NM_153825] 1.16068 0.252775097
SEPT1 2963 0.0798252 SEPTIN 1 (LARP) (SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR- 24). [SWISSPROT;Acc:Q8WYJ6] 0.547429 0.145818362
SEPT10 3022 0.106813 SEPTIN 10 ISOFORM 1. [RefSeq;Acc:NM_144710] 0.88182 0.121127895
SEPT11 3007 0.136179 1.08705 0.125273906
SEPT4 2989 0.16041 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] 1.17491 0.136529607
SEPT6 3008 0.116797 SEPTIN 6. [SWISSPROT;Acc:Q14141] 0.952641 0.122603373
SEPT7 3009 0.09144 SEPTIN 7 (CDC10 PROTEIN HOMOLOG). [SWISSPROT;Acc:Q16181] 0.749104 0.122065828
SEPT8 3023 0.118014 SEPTIN-LIKE PROTEIN KIAA0202 (FRAGMENT). [SWISSPROT;Acc:Q92599] 0.986632 0.119612986
SERBP1 1311 0.0417836 0.170042 0.245725174
SERINC1 2417 0.0257797 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] 0.118068 0.218346207
SERINC2 2414 0.0249219 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] 0.114139 0.218346928
SERINC3 2415 0.0298377 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] 0.136653 0.218346469
SERPINB1 2319 0.0244744 LEUKOCYTE ELASTASE INHIBITOR (LEI) (MONOCYTE/NEUTROPHIL ELASTASE INHIBITOR) (M/NEI) (EI). [SWISSPROT;Acc:P30740] 0.110346 0.221796893
SERPINB10 2322 0.0196713 BOMAPIN (PROTEASE INHIBITOR 10) (SERPIN B10). [SWISSPROT;Acc:P48595] 0.088691 0.221795898
SERPINB12 1577 0.0598165 SERPIN B12. [SWISSPROT;Acc:Q96P63] 0.248312 0.240892506
SERPINB4 1580 0.0820308 SQUAMOUS CELL CARCINOMA ANTIGEN 1 (SCCA-1) (PROTEIN T4-A). [SWISSPROT;Acc:P29508] 0.340529 0.240892259
SERPINB6 2327 0.0199527 PLACENTAL THROMBIN INHIBITOR (CYTOPLASMIC ANTIPROTEINASE) (CAP) (PROTEASE INHIBITOR 6) (PI-6). [SWISSPROT;Acc:P35237] 0.0899599 0.221795489
SERPINB7 1581 0.056548 MEGSIN (TP55) (SERPIN B7). [SWISSPROT;Acc:O75635] 0.234744 0.240892206
SERPINB8 2328 0.0198854 PLASMINOGEN ACTIVATOR INHIBITOR-2 PRECURSOR (PAI-2) (PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR) (MONOCYTE ARG-SERPIN) (UROKINASE INHIBITOR). [SWISSPROT;Acc:P05120] 0.0896565 0.221795408
SERPINB9 2321 0.0200935 CYTOPLASMIC ANTIPROTEINASE 3 (CAP3) (CAP-3) (PROTEASE INHIBITOR 9) (SERPIN B9). [SWISSPROT;Acc:P50453] 0.0905944 0.22179627
SERPINC1 1585 0.0555356 ANTITHROMBIN-III PRECURSOR (ATIII) (PRO0309). [SWISSPROT;Acc:P01008] 0.230542 0.240891464
SESN1 622 0.699473 SESTRIN 1 (P53-REGULATED PROTEIN PA26). [SWISSPROT;Acc:Q9Y6P5] 2.60745 0.268259411
SESN2 628 0.553815 SESTRIN 2 (HI95). [SWISSPROT;Acc:P58004] 2.06448 0.268258835
SESN3 635 0.578823 SESTRIN 3. [SWISSPROT;Acc:P58005] 2.15771 0.268258014
SETD3 2436 0.0346049 0.159272 0.2172692
SETMAR 3014 0.379831 SET DOMAIN AND MARINER TRANSPOSASE FUSION GENE. [RefSeq;Acc:NM_006515] 3.11762 0.121833642
SF3A1 339 0.894103 SPLICING FACTOR 3 SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 114) (SAP 114) (SF3A120). [SWISSPROT;Acc:Q15459] 3.13898 0.284838706
SF3A2 298 0.374541 SPLICING FACTOR 3A SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 62) (SAP 62) (SF3A66). [SWISSPROT;Acc:Q15428] 1.24681 0.300399419
SF3A3 340 0.0420473 SPLICING FACTOR 3A SUBUNIT 3 (SPLICEOSOME ASSOCIATED PROTEIN 61) (SAP 61) (SF3A60). [SWISSPROT;Acc:Q12874] 0.147618 0.28483857
SF3B1 225 0.764466 SPLICING FACTOR 3B SUBUNIT 1 (SPLICEOSOME ASSOCIATED PROTEIN 155) (SAP 155) (SF3B155) (PRE-MRNA SPLICING FACTOR SF3B 155 KDA SUBUNIT). [SWISSPROT;Acc:O75533] 2.41141 0.317020333
SF3B2 275 0.557721 SPLICING FACTOR 3B SUBUNIT 2 (SPLICEOSOME ASSOCIATED PROTEIN 145) (SAP 145) (SF3B150) (PRE-MRNA SPLICING FACTOR SF3B 145 KDA SUBUNIT). [SWISSPROT;Acc:Q13435] 1.82999 0.304767239
SF3B4 363 0.0893365 SPLICING FACTOR 3B SUBUNIT 4 (SPLICEOSOME ASSOCIATED PROTEIN 49) (SAP 49) (SF3B50) (PRE-MRNA SPLICING FACTOR SF3B 49 KDA SUBUNIT). [SWISSPROT;Acc:Q15427] 0.318821 0.280208957
SF4 2944 0.0588972 SPLICING FACTOR 4 ISOFORM B; RNA-BINDING PROTEIN. [RefSeq;Acc:NM_021164] 0.382047 0.154162184
SFPQ 1672 0.263446 "SPLICING FACTOR, PROLINE-AND GLUTAMINE-RICH (POLYPYRIMIDINE TRACT- BINDING PROTEIN-ASSOCIATED SPLICING FACTOR) (PTB-ASSOCIATED SPLICING FACTOR) (PSF) (DNA-BINDING P52/P100 COMPLEX, 100 KDA SUBUNIT). [SWISSPROT;Acc:P23246]" 1.10501 0.238410512
SFRS1 1685 0.0238444 "SPLICING FACTOR, ARGININE/SERINE-RICH 1 (PRE-MRNA SPLICING FACTOR SF2, P33 SUBUNIT) (ALTERNATIVE SPLICING FACTOR ASF-1). [SWISSPROT;Acc:Q07955]" 0.100146 0.238096379
SFRS10 412 0.368948 ARGININE/SERINE-RICH SPLICING FACTOR 10 (TRANSFORMER-2-BETA) (HTRA2- BETA) (TRANSFORMER 2 PROTEIN HOMOLOG) (SILICA-INDUCED PROTEIN 41) (RA301). [SWISSPROT;Acc:Q15815] 1.32916 0.277579825
SFRS11 901 0.148259 SPLICING FACTOR ARGININE/SERINE-RICH 11 (ARGININE-RICH 54 KDA NUCLEAR PROTEIN) (P54). [SWISSPROT;Acc:Q05519] 0.571608 0.259371807
SFRS18 848 0.479679 SR RICH PROTEIN. [RefSeq;Acc:NM_032870] 1.84052 0.260621455
SFRS3 638 0.280063 "SPLICING FACTOR, ARGININE/SERINE-RICH 3 (PRE-MRNA SPLICING FACTOR SRP20) (X16 PROTEIN). [SWISSPROT;Acc:P23152]" 1.04414 0.26822361
SFRS8 1121 0.155587 "SPLICING FACTOR, ARGININE/SERINE-RICH 8 (SUPPRESSOR OF WHITE APRICOT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q12872]" 0.620608 0.250700926
SFT2D3 673 0.105333 0.394979 0.266680001
SGCD 1878 0.0630725 DELTA-SARCOGLYCAN (SG-DELTA) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q92629] 0.270962 0.232772492
SGCG 1877 0.0566858 GAMMA-SARCOGLYCAN (GAMMA-SG) (35 KDA DYSTROPHIN-ASSOCIATED GLYCOPROTEIN) (35DAG). [SWISSPROT;Acc:Q13326] 0.243524 0.232772951
SGCZ 1876 0.0628075 SARCOGLYCAN ZETA; ZETA-SARCOGLYCAN. [RefSeq;Acc:NM_139167] 0.269823 0.232772966
SGPL1 2114 0.0601623 SPHINGOSINE-1-PHOSPHATE LYASE 1; SPHINGOSINE-1-PHOSPHATE LYASE. [RefSeq;Acc:NM_003901] 0.263668 0.228174447

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/