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

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/